Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites

A Supramolecular Nanosheet Assembled from Carpyridines and Water

The use of water as a solvent to facilitate supramolecular self-assembly and polymerization is well-documented; however, it is rare that water acts as a monomer that undergoes polymerization. We report the formation of nanosheets composed of water and a saddle-shaped porphyrinoid macrocycle, carpyridine, which allows for linearly stacked, eclipsed columns within formed 2D structures. Self-assembling carpyridine monomers from solutions with different extents of wetness permit the formation of nanosheets that appear identical by microscopy. Structural analysis through electron diffraction reveals fundamental changes in the local organization. Under dry conditions, carpyridine stacks are formed through π-π interactions between curved surfaces, whereas in solutions containing greater quantities of water, a hydrogen-bonded water-to-carpyridine-core network is propagated throughout perfectly linear columns. The observed wet phase can be interconverted to a dry one through vapor annealing, indicating an accessible energy surface of polymorphism.

Study of Protein Hydration Water with the V4S Structural Index: Focus on Binding Site Description

V4S, a new structural indicator for water specially designed to be suitable for hydration and nanoconfined contexts, has been recently introduced and preliminarily applied for water in contact with self-assembled monolayers and graphene-like systems. This index enabled an accurate detection of defective high local density water molecules (called HDA-like given their structural resemblance with the high-density amorphous ice, HDA). In the present work, we shall apply this new metric to characterize protein hydration water with particular interest in protein binding sites. As a first result, we shall find that protein hydration water has a higher concentration of HDA-like molecular arrangements compared to the bulk. Significantly, we shall show that the concentration of HDA-like molecules sharply decreases beyond the first hydration layer. Finally, we shall also reveal a highly nonuniform spatial distribution of the V4S values for the first hydration shell on the protein surface, where the higher hydrophobicity inherent to the ligand binding site will be evident from an enrichment in HDA-like molecules as compared to the population exhibited by the global protein surface.

The Importance of Structural Water in HDAC8 for Correct Binding Pose Applied for Drug Design of Anticancer Molecules

AIMS

Validating the docking procedure and maintaining the structural water molecules at HDAC8 catalytic site.

BACKGROUND

Molecular docking simulations play a significant role in Computer-Aided Drug Design, contributing to the development of new molecules. To ensure the reliability of these simulations, a validation process called "self-docking or re-docking" is employed, focusing on the binding mode of a ligand co-crystallized with the protein of interest.

OBJECTIVE

In this study, several molecular docking studies were conducted using five X-ray structures of HDAC8-ligand complexes from the PDB.

METHODS

Ligands initially complexed with HDAC8 were removed and re-docked onto the free protein, revealing a poor reproduction of the expected binding mode. In response to this, we observed that most HDAC8-ligand complexes contained one to two water molecules in the catalytic site, which were crucial for maintaining the cocrystallized ligand.

RESULTS

These water molecules enhance the binding mode of the co-crystallized ligand by stabilizing the proteinligand complex through hydrogen bond interactions between ligand and water molecules. Notably, these interactions are lost if water molecules are removed, as is often done in classical docking methodologies. Considering this, molecular docking simulations were repeated, both with and without one or two conserved water molecules near Zn+2 in the catalytic cavity. Simulations indicated that replicating the native binding pose of co-crystallized ligands on free HDAC8 without these water molecules was challenging, showing greater coordinate displacements (RMSD) compared to those including conserved water molecules from crystals.

CONCLUSION

The study highlighted the importance of conserved water molecules within the active site, as their presence significantly influenced the successful reproduction of the ligands' native binding modes. The results suggest an optimal molecular docking procedure for validating methods suitable for filtering new HDAC8 inhibitors for future experimental assays.

Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities

Macromolecular recognition and ligand binding are at the core of biological function and drug discovery efforts. Water molecules play a significant role in mediating the protein-ligand interaction, acting as more than just the surrounding medium by affecting the thermodynamics and thus the outcome of the binding process. As individual water contributions are impossible to measure experimentally, a range of computational methods have emerged to identify hydration sites in protein pockets and characterize their energetic contributions for drug discovery applications. Even though several methods model solvation effects explicitly, they focus on determining the stability of specific water sites independently and neglect solvation correlation effects upon replacement of clusters of water molecules, which typically happens in hit-to-lead optimization. In this work, we rigorously determine the conjoint effects of replacing all combinations of water molecules in protein binding pockets through the use of the RE-EDS multistate free-energy method, which combines Hamiltonian replica exchange (RE) and enveloping distribution sampling (EDS). Applications on the small bovine pancreatic trypsin inhibitor and four proteins of the bromodomain family illustrate the extent of solvation correlation effects on water thermodynamics, with the favorability of replacement of the water sites by pharmacophore probes highly dependent on the composition of the water network and the pocket environment. Given the ubiquity of water networks in biologically relevant protein targets, we believe our approach can be helpful for computer-aided drug discovery by providing a pocket-specific and a priori systematic consideration of solvation effects on ligand binding and selectivity.

Structural and functional role of invariant water molecules in matrix metalloproteinases: a data-mining approach

Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases known to degrade extracellular matrix (ECM). Being involved in many biological and physiological processes of tissue remodeling, MMPs play a crucial role in many pathological conditions such as arthritis, cancer, cardiovascular diseases, etc. Typically, MMPs possess a propeptide, a zinc-containing catalytic domain, a hinge region and a hemopexin domain. Based on their structural domain organization and substrates, MMPs are classified into six different classes, viz. collagenases, stromelysins, gelatinases, matrilysins, membrane-type and other MMPs. As per previous studies, a set of invariant water (IW) molecules of MMP-1 (a collagenase) play a significant role in stabilizing their catalytic domain. However, a functional role of IW molecule in other classes of MMPs has not been reported yet. Thus, in this study, IW molecules of MMPs from different classes were located and their plausible role(s) have been assigned. The results suggest that IW molecules anchor the structurally and functionally essential metal ions present in the vicinity of the active site of MMPs. Further, they (in)directly interlink different structural features and bridge the active site metal ions of MMPs. This study provides the key IW molecules that are structurally and functionally relevant to MMPs and hence, in turn, might facilitate the development of potent generalized inhibitor(s) against different classes of MMPs. Communicated by Ramaswamy H. Sarma.

A Core-Shell Approach for Systematically Coarsening Nanoparticle-Membrane Interactions: Application to Silver Nanoparticles

The continuous release of engineered nanomaterial (ENM) into the environment may bring about health concerns following human exposure. One important source of ENMs are silver nanoparticles (NPs) that are extensively used as anti-bacterial additives. The introduction of ENMs into the human body can occur via ingestion, skin uptake or the respiratory system. Therefore, evaluating how NPs translocate over bio-membranes is essential in assessing their primary toxicity. Unfortunately, data regarding membrane-NP interaction is still scarce, as is theoretical and in silico insight into what governs adhesion and translocation for the most relevant NPs and membranes. Coarse-grained (CG) molecular descriptions have the potential to alleviate this situation, but are hampered by the absence of a direct link to NP materials and membrane adhesion mechanisms. Here, we interrogate the relationship between the most common NP representation at the CG level and the adhesion characteristics of a model lung membrane. We find that this representation for silver NPs is non-transferable, meaning that a proper CG representation for one size is not suited for other sizes. We also identify two basic types of primary adhesion-(partial) NPs wrapping by the membrane and NP insertion into the membrane-that closely relate to the overall NP hydrophobicity and significantly differ in terms of lipid coatings. The proven non-transferability of the standard CG representation with size forms an inspiration for introducing a core-shell model even for bare NPs that are uniform in composition. Using existing all-atom molecular dynamics (MD) data as a reference, we show that this extension does allow us to reproduce size-dependent NP adhesion properties and lipid responses to NP binding at the CG level. The subsequent CGMD evaluation for 10 nm Ag NPs provides new insight into membrane binding for relevant NP sizes and into the role of water in trapping NPs into defected mixed monolayer-bilayer states. This development will be instrumental for simulating NP-membrane adhesion towards more experimentally relevant length and time scales for particular NP materials.

The druggable genome: Twenty years later

The concept of the druggable genome has been with us for 20 years. During this time, researchers have developed several methods and resources to help assess a target's druggability. In parallel, evidence for target-disease associations has been collated at scale by Open Targets. More recently, the Protein Data Bank in Europe (PDBe) have built a knowledge base matching per-residue annotations with available protein structure. While each resource is useful in isolation, we believe there is enormous potential in bringing all relevant data into a single knowledge graph, from gene-level to protein residue. Automation is vital for the processing and assessment of all available structures. We have developed scalable, automated workflows that provide hotspot-based druggability assessments for all available structures across large numbers of targets. Ultimately, we will run our method at a proteome scale, an ambition made more realistic by the arrival of AlphaFold 2. Bringing together annotations from the residue up to the gene level and building connections within the graph to represent pathways or protein-protein interactions will create complexity that mirrors the biological systems they represent. Such complexity is difficult for the human mind to utilise effectively, particularly at scale. We believe that graph-based AI methods will be able to expertly navigate such a knowledge graph, selecting the targets of the future.

Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization

Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying "magic bullets" amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand-target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural-energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.

Tumor-Promoting ATAD2 and Its Preclinical Challenges

ATAD2 has received extensive attention in recent years as one prospective oncogene with tumor-promoting features in many malignancies. ATAD2 is a highly conserved bromodomain family protein that exerts its biological functions by mainly AAA ATPase and bromodomain. ATAD2 acts as an epigenetic decoder and transcription factor or co-activator, which is engaged in cellular activities, such as transcriptional regulation, DNA replication, and protein modification. ATAD2 has been reported to be highly expressed in a variety of human malignancies, including gastrointestinal malignancies, reproductive malignancies, urological malignancies, lung cancer, and other types of malignancies. ATAD2 is involved in the activation of multiple oncogenic signaling pathways and is closely associated with tumorigenesis, progression, chemoresistance, and poor prognosis, but the oncogenic mechanisms vary in different cancer types. Moreover, the direct targeting of ATAD2’s bromodomain may be a very challenging task. In this review, we summarized the role of ATAD2 in various types of malignancies and pointed out the pharmacological direction.

Coordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain

The ATPase Family, AAA domain-containing protein 2 (ATAD2) bromodomain (BRD) has a canonical bromodomain structure consisting of four α-helices. ATAD2 functions as a co-activator of the androgen and estrogen receptors as well as the MYC and E2F transcription factors. ATAD2 also functions during DNA replication, recognizing newly synthesized histones. In addition, ATAD2 is shown to be up-regulated in multiple forms of cancer including breast, lung, gastric, endometrial, renal, and prostate. Furthermore, up-regulation of ATAD2 is strongly correlated with poor prognosis in many types of cancer, making the ATAD2 bromodomain an innovative target for cancer therapeutics. In this study, we describe the recognition of histone acetyllysine modifications by the ATAD2 bromodomain. Residue-specific information on the complex formed between the histone tail and the ATAD2 bromodomain, obtained through nuclear magnetic resonance spectroscopy (NMR) and X-ray crystallography, illustrates key residues lining the binding pocket, which are involved in coordination of di-acetylated histone tails. Analytical ultracentrifugation, NMR relaxation data, and isothermal titration calorimetry further confirm the monomeric state of the functionally active ATAD2 bromodomain in complex with di-acetylated histone ligands. Overall, we describe histone tail recognition by ATAD2 BRD and illustrate that one acetyllysine group is primarily engaged by the conserved asparagine (N1064), the "RVF" shelf residues, and the flexible ZA loop. Coordination of a second acetyllysine group also occurs within the same binding pocket but is essentially governed by unique hydrophobic and electrostatic interactions making the di-acetyllysine histone coordination more specific than previously presumed.

A Fragmenting Protocol with Explicit Hydration for Calculation of Binding Enthalpies of Target-Ligand Complexes at a Quantum Mechanical Level

Optimization of the enthalpy component of binding thermodynamics of drug candidates is a successful pathway of rational molecular design. However, the large size and missing hydration structure of target-ligand complexes often hinder such optimizations with quantum mechanical (QM) methods. At the same time, QM calculations are often necessitated for proper handling of electronic effects. To overcome the above problems, and help the QM design of new drugs, a protocol is introduced for atomic level determination of hydration structure and extraction of structures of target-ligand complex interfaces. The protocol is a combination of a previously published program MobyWat, an engine for assigning explicit water positions, and Fragmenter, a new tool for optimal fragmentation of protein targets. The protocol fostered a series of fast calculations of ligand binding enthalpies at the semi-empirical QM level. Ligands of diverse chemistry ranging from small aromatic compounds up to a large peptide helix of a molecular weight of 3000 targeting a leukemia protein were selected for systematic investigations. Comparison of various combinations of implicit and explicit water models demonstrated that the presence of accurately predicted explicit water molecules in the complex interface considerably improved the agreement with experimental results. A single scaling factor was derived for conversion of QM reaction heats into binding enthalpy values. The factor links molecular structure with binding thermodynamics via QM calculations. The new protocol and scaling factor will help automated optimization of binding enthalpy in future molecular design projects.

Large-Scale Study of Hydration Environments through Hydration Sites

Hydration sites are locations of interest to water and they can be used to classify the behavior of water around chemical motifs commonly found on the surface of proteins. Inhomogeneous fluid solvation theory (IFST) is a method for calculating hydration free-energy changes from molecular dynamics (MD) trajectories. In this paper, hydration sites are identified from MD simulations of 380 diverse protein structures. The hydration free energies of the hydration sites are calculated using IFST and distributions of these free-energy changes are analyzed. The results show that for some hydration sites near features conventionally regarded as attractive to water, such as hydrogen bond donors, the water molecules are actually relatively weakly bound and are easily displaced. We also construct plots of the spatial density of hydration sites with high, medium, and low hydration free-energy changes which represent weakly and strongly bound hydration sites. It is found that these plots show consistent features around common polar amino acids for all of the proteins studied.

Prediction of GABARAP interaction with the GABA type A receptor

We have performed docking simulations on GABARAP interacting with the GABA type A receptor using SwarmDock. We have also used a novel method to study hydration sites on the surface of these two proteins; this method identifies regions around proteins where desolvation is relatively easy, and these are possible locations where proteins can bind each other. There is a high degree of consistency between the predictions of these two methods. Moreover, we have also identified binding sites on GABARAP for other proteins, and listed possible binding sites for as yet unknown proteins on both GABARAP and the GABA type A receptor intracellular domain.

Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field

In this study, the differences of binding patterns between two type HIV (HIV-1 and HIV-2) protease and two inhibitors (darunavir and amprenavir) are analyzed and compared using the newly developed interaction entropy (IE) method for the entropy change calculation combined with the polarized force field. The functional role of protonation states in the two HIV-2 complexes is investigated and our study finds that the protonated OD1 atom of Asp25' in B chain is the optimal choice. Those calculated binding free energies obtained from the polarized force field combined with IE method are significantly consistent with the experimental observed. The bridging water W301 is favorable to the binding of HIV-1 complexes; however, it is unfavorable to the HIV-2 complexes in current study. The volume of pocket, B-factor of Cα atoms and the distance of flap tip in HIV-2 complexes are smaller than that of HIV-1 consistently. These changes may cause localized rearrangement of residues lining their surface and finally result in the different binding mode for the two types HIV. Predicated hot-spot residues (Ala28/Ala28', Ile50/Ile50', and Ile84/Ile84') are nearly same in the four systems. However, the contribution to the free energy of Asp30 residue is more favorable in HIV-1 system than in HIV-2 system. Current study, to some extent, reveals the origin for the decrease in binding affinity of inhibitors against HIV-2 compared with HIV-1 and will provides theoretical guidance for future design of potent dual inhibitors targeting two type HIV protease.

Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo

Conserved water molecules are of interest in drug design, as displacement of such waters can lead to higher affinity ligands and in some cases, contribute towards selectivity. Bromodomains, small protein domains involved in the epigenetic regulation of gene transcription, display a network of four conserved water molecules in their binding pockets and have recently been the focus of intense medicinal chemistry efforts. Understanding why certain bromodomains have displaceable water molecules and others do not is extremely challenging, and it remains unclear which water molecules in a given bromodomain can be targeted for displacement. Here we estimate the stability of the conserved water molecules in 35 bromodomains via binding free energy calculations using all-atom grand canonical Monte Carlo simulations. Encouraging quantitative agreement to the available experimental evidence is found. We thus discuss the expected ease of water displacement in different bromodomains and the implications for ligand selectivity.

Quantitative metrics for drug-target ligandability

Ligandability is a prerequisite for druggability and is a much easier concept to understand, model and predict because it does not depend on the complex pharmacodynamic and pharmacokinetic mechanisms in the human body. In this review, we consider a metric for quantifying ligandability from experimental data. We discuss ligandability in terms of the balance between effort and reward. The metric is evaluated for a standard set of well-studied drug targets - some traditionally considered to be ligandable and some regarded as difficult. We suggest that this metric should be used to systematically improve computational predictions of ligandability, which can then be applied to novel drug targets to predict their tractability.

Benchmark Study Based on 2P2IDB to Gain Insights into the Discovery of Small-Molecule PPI Inhibitors

Protein-protein interactions (PPIs) have been regarded as novel and highly promising drug targets in drug discovery. Numerous new experimental techniques and computational approaches have been developed to assist the design of PPI modulators during the past two decades. However, identification and optimization of small-molecule inhibitors targeting PPIs is still a particularly challenging task due to the "undruggable" profiles of PPI interfaces. Nowadays, in silico screening, especially docking-based virtual screening, has emerged as an effective method to complement experimental high-throughput screening in identifying novel and potent small-molecule PPI inhibitors. Here, on the basis of the 2P2I_DB database, we explored the structural features of the known small-molecule PPI inhibitors and analyzed the characteristics of the PPI binding pockets. More importantly, we evaluated the sampling power and screening power of six popular docking programs for PPI targets. Our results indicate that the chlorinated conjugate group and amidelike linkage are two types of privileged fragments of PPI inhibitors; the average druggability of the binding sites of the PPI targets in 2P2IDB is slightly worse than that of traditional ones; both academic and commercial docking programs exhibit an acceptable accuracy on pose prediction for PPI inhibitors, but their screening powers for identifying PPI inhibitors are still not satisfactory. It is expected that our work can provide valuable guidance on the construction of PPI-focused library, the determination of druggable PPI binding pocket, and the selection of docking program for the screening of small-molecule PPI inhibitors.

The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force

Classical density functional theory (DFT) can be used to relate the thermodynamic properties of solutions to the indirect solvent mediated part of the solute-solvent potential of mean force (PMF). Standard, but powerful numerical methods can be used to estimate the solute-solvent PMF from which the indirect part can be extracted. In this work we show how knowledge of the direct and indirect parts of the solute-solvent PMF for water at the interface of a protein receptor can be used to gain insights about how to design tighter binding ligands. As we show, the indirect part of the solute-solvent PMF is equal to the sum of the 1-body (energy + entropy) terms in the inhomogeneous solvation theory (IST) expansion of the solvation free energy. To illustrate the effect of displacing interfacial water molecules with particular direct/indirect PMF signatures on the binding of ligands, we carry out simulations of protein binding with several pairs of congeneric ligands. We show that interfacial water locations that contribute favorably or unfavorably at the 1-body level (energy + entropy) to the solvation free energy of the solute can be targeted as part of the ligand design process. Water locations where the indirect PMF is larger in magnitude provide better targets for displacement when adding a functional group to a ligand core.

Mechanistic insights into peptide and ligand binding of the ATAD2-bromodomain via atomistic simulations disclosing a role of induced fit and conformational selection

Atomistic simulations of the ATAD2-bromodomain disclose a role of induced fit and conformational selection upon ligand and peptide binding.

ATAD2 in cancer: a pharmacologically challenging but tractable target

INTRODUCTION

ATAD2 protein is an emerging oncogene that has strongly been linked to the etiology of multiple advanced human cancers. Therapeutically, despite the fact that genetic suppression/knockdown studies have validated it as a compelling drug target for future therapeutic development, recent druggability assessment data suggest that direct targeting of ATAD2's bromodomain (BRD) may be a very challenging task. ATAD2's BRD has been predicted as a 'difficult to drug' or 'least druggable' target due to the concern that its binding pocket, and the areas around it, seem to be unfeasible for ligand binding. Areas covered: In this review, after shedding light on the multifaceted roles of ATAD2 in normal physiology as well as in cancer-etiology, we discuss technical challenges rendered by ATAD2's BRD active site and the recent drug discovery efforts to find small molecule inhibitors against it. Expert opinion: The identification of a novel low-nanomolar semi-permeable chemical probe against ATAD2's BRD by recent drug discovery campaign has demonstrated it to be a pharmacologically tractable target. Nevertheless, the development of high quality bioavailable inhibitors against ATAD2 is still a pending task. Moreover, ATAD2 may also potentially be utilized as a promising target for future development of RNAi-based therapy to treat cancers.

Relationship between Solvation Thermodynamics from IST and DFT Perspectives

Inhomogeneous solvation theory (IST) and classical density functional theory (DFT) each provide a framework for relating distribution functions of solutions to their thermodynamic properties. As reviewed in this work, both IST and DFT can be formulated in a way that use two "end point" simulations, one of the pure solvent and the other of the solution, to determine the solute chemical potential and other thermodynamic properties of the solution and of subvolumes in regions local to the solute containing hydrating waters. In contrast to IST, where expressions for the excess energy and entropy of solution are the object of analysis, in the DFT end point formulation of the problem, the solute-solvent potential of mean force (PMF) plays a central role. The indirect part of the PMF corresponds to the lowest order (1-body) truncation of the IST expression. Because the PMF is a free energy function, powerful numerical methods can be used to estimate it. We show that the DFT expressions for the solute excess chemical potential can be written in a form which is local, involving integrals only over regions proximate to the solute. The DFT end point route to estimating solvation free energies provides an alternative path to that of IST for analyzing solvation effects on molecular recognition and conformational changes in solution, which can lead to new insights. In order to illustrate the kind of information that is contained in the solute-solvent PMF, we have carried out simulations of β-cyclodextrin in water. This solute is a well studied "host" molecule to which "guest" molecules bind; host-guest systems serve as models for molecular recognition. We illustrate the range of values the direct and indirect parts of the solute-solvent PMF can have as a water molecule is brought to the interface of β-cyclodextrin from the bulk; we discuss the "competition" between these two terms, and the role it plays in molecular recognition.

Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory

Molecular dynamics simulations have been analyzed with the Grid Cell Theory (GCT) method to spatially resolve the binding enthalpies and entropies of water molecules at the interface of 17 structurally diverse proteins. Correlations between computed energetics and structural descriptors have been sought to facilitate the development of simple models of protein hydration. Little correlation was found between GCT-computed binding enthalpies and continuum electrostatics calculations. A simple count of contacts with functional groups in charged amino acids correlates well with enhanced water stabilization, but the stability of water near hydrophobic and polar residues depends markedly on its coordination environment. The positions of X-ray-resolved water molecules correlate with computed high-density hydration sites, but many unresolved waters are significantly stabilized at the protein surfaces. A defining characteristic of ligand-binding pockets compared to nonbinding pockets was a greater solvent-accessible volume, but average water thermodynamic properties were not distinctive from other interfacial regions. Interfacial water molecules are frequently stabilized by enthalpy and destabilized entropy with respect to bulk, but counter-examples occasionally occur. Overall detailed inspection of the local coordinating environment appears necessary to gauge the thermodynamic stability of water in protein structures.