Skip to main content
NIHPA Author Manuscripts logoLink to NIHPA Author Manuscripts
. Author manuscript; available in PMC: 2015 Jul 15.
Published in final edited form as: Bioorg Med Chem Lett. 2014 May 9;24(14):3164–3167. doi: 10.1016/j.bmcl.2014.04.114

Protein-Ligand Interactions: Probing the Energetics of a Putative Cation-π Interaction

James M Myslinski 1, John H Clements 1, Stephen F Martin 1,*
PMCID: PMC4077163  NIHMSID: NIHMS593752  PMID: 24856058

Abstract

In order to probe the energetics associated with a putative cation-π interaction, thermodynamic parameters are determined for complex formation between the Grb2 SH2 domain and tripeptide derivatives of RCO–pTyr–Ac6c–Asn wherein the R group is varied to include different alkyl, cycloalkyl, and aryl groups. Although an indole ring is reputed to have the strongest interaction with a guanidinium ion ion, binding free energies, ΔG°, for derivatives of RCO–pTyr–Ac6c–Asn bearing cyclohexyl and phenyl groups were slightly more favorable than their indolyl analog. Crystallographic analysis of two complexes reveals that test ligands bind in similar poses with the notable exception of the relative orientation and proximity of the phenyl and indolyl rings relative to an arginine residue of the domain. These spatial orientations are consistent with those observed in other cation-π interactions, but there is no net energetic benefit to such an interaction in this biological system. Accordingly, although cation-π interactions are well documented as important noncovalent forces in molecular recognition, the energetics of such interactions may be mitigated by other nonbonded interactions and solvation effects in protein-ligand associations.


One of the most difficult problems in contemporary molecular recognition involving protein-ligand interactions is understanding how and why changes in the structures of small molecules affect relative thermodynamic binding parameters.1 From a historical perspective, experimental and computational studies for associations of proteins and small molecules typically reported Kis, IC50s, and binding free energies, ΔG, but since the advent of isothermal titration calorimetry (ITC), binding enthalpies, ΔH, and entropies, ΔS, are more commonly determined.2,3 As these data have become available, paradigms to increase ligand potency by modifying ligand structure to enhance binding enthalpies and/or entropies are beginning to emerge.4 However, applications of such strategies do not necessarily result in increased affinities because of enthalpy/entropy compensation, which may be virtually balancing,5 and because there is often no correlation between ΔG° and either ΔH° or −TΔS°. Moreover, it is becoming increasingly apparent that some common strategies used to enhance protein binding entropies of small molecules are not uniformly reliable. For example, we discovered that ligand preorganization does not necessarily lead to enhanced protein binding entropies, even when flexible and constrained ligands bind in similar conformations.79 Although the hydrophobic effect is generally viewed as having a favorable impact on binding entropy,10 we and others have found that increasing the nonpolar surface area of a ligand can eventuate in more favorable protein binding enthalpies and less favorable binding entropies.3,11 Determining the origin(s) of such enthalpy driven hydrophobic interactions is the subject of a number of theoretical studies.12

In ongoing studies directed toward correlating structure and energetics in protein-ligand interactions, we recently became interested in explicitly elucidating the energetics associated with cation-π interactions.1318 Such interactions are important structural features in protein folding and protein-ligand interactions and involve a non-covalent interaction between the monopole of a cationic amino group on the side chain of a Lys or Arg residue, and the negatively charged portion of the quadrupole of the aryl group of a Tyr or Trp residue. Although the involvement of such interactions in model systems has been widely studied, there are relatively few investigations directed toward quantifying the detailed energetic contributions of cation-π interactions in protein-ligand associations. For example, Diederich has shown that cation-π interactions contribute about 2.8 kcal mol−1 to binding free energy for complexation of ligands to the aromatic box of factor Xa, but binding enthalpies and entropies were not reported.16a,b On the other hand, Marshall and coworkers have found that such interactions can be mitigated by competing, adjacent salt-bridges.18

We previously identified the SH2 domain of the growth receptor binding protein 2 (Grb2), a cytosolic adapter protein that participates in the Ras signal transduction pathway,19 as an excellent model system for studying molecular recognition in a biological system.8,11c In the context of cation-π interactions, Furet and coworkers discovered that the affinity of 3 (IC50 = 65 nM) for the Grb2 SH2 domain was about two orders of magnitude greater than for the related tripeptides 1 and 2, which were approximately equipotent.20 Based upon modeling studies, they attributed the enhanced potency to favorable stacking, or a cation-π interaction, between the electron-rich aniline ring at the N-terminus of 3 and the Arg67 residue of the Grb2 SH2 domain. In a subsequent study, Nioche and coworkers found that the related phosphotyrosine derivatives 4–6 bound with approximately equal affinity (IC50 of 6 = 13 nM) to the Grb2 SH2 domain.21 An X-ray study revealed that the aromatic ring of the m-amino-Cbz group of 6 in its complex with the domain aligned in a parallel, but not completely stacked, orientation relative to the plane of the Arg67 residue.

graphic file with name nihms593752f3.jpg

In order to probe the role and detailed energetics associated with the putative cation-π interactions between the Grb2 SH2 domain and tripeptide ligands related to 3 and 6, the phosphotyrosine analogs 7–12 were prepared, and the thermodynamic binding parameters (Ka, ΔG°, ΔH°, ΔS°) for their associations with the Grb2 SH2 domain were determined by isothermal titration calorimetry (ITC) (Table 1). The selection of the Ac6c replacement for the pTyr+1 residue was predicated upon the requirement that we wanted a series of high affinity compounds, and the known compound 922 (IC50 = 1 nM) was about 65-fold more potent than 3 and comparable in potency to 4–6. Compounds 7–9 were prepared for comparison with compounds 1–3 and 4–6 of the prior art. The indole analog 10 was selected because the indole side-chain of Trp is the aromatic group most commonly involved in energetically significant cation-π interactions in proteins.14c Compound 11 would enable a comparison with the carbamate 8 and the cyclohexane analog 12 would be a control for 11.

Table 1.

Thermodynamic data for complexes of 712 and the Grb2 SH2 domain.[a,b]

Ligand R Ka
(× 106 M−1)
ΔG°
(kcal mol−1)
ΔH°
(kcal mol−1)
−TΔS°
(kcal mol−1)
7 Me 7.0 ± 1.2 −9.3 ± 0.1 −8.5 ± 0.4 −0.8 ± 0.4
8 graphic file with name nihms593752t1.jpg 6.5 ± 0.1 −9.3 ± 0.1 −9.3 ± 0.3 0.0 ± 0.1
9 graphic file with name nihms593752t2.jpg 8.8 ± 0.9 −9.5 ± 0.1 −9.1 ± 0.5 −0.4 ± 0.3
10 graphic file with name nihms593752t3.jpg 11.4 ± 0.3 −9.6 ± 0.1 −10.0 ± 0.3 +0.4 ± 0.1
11 graphic file with name nihms593752t4.jpg 23.4 ± 0.9 −10.1 ± 0.1 −9.5 ± 0.5 −0.6 ± 0.1
12 graphic file with name nihms593752t5.jpg 28.8 ± 1.3 −10.2 ± 0.1 −10.0 ± 0.5 −0.2 ± 0.1
[a]

ITC experiments were conducted at 25 °C in HEPES (50 mM) with NaCl (150 mM) at pH 7.45 ± 0.05 as previously reported.8b

[b]

Three or more experiments were performed for each ligand, and the averages are reported following normalization of the n values for each experiment by adjusting ligand concentration (See Supporting Information). Errors in the thermodynamic values were determined by the method of Krishnamurthy.2a

graphic file with name nihms593752f4.jpg

Examination of the ITC data in Table 1 reveals that 7–9 bind to the Grb2 SH2 domain with approximately equal affinity, an observation consistent with the findings of Nioche21 but not Furet.20 The chain linking the carbonyl and phenyl groups of 8 has an oxygen atom, whereas there are only carbon atoms in the linking chain of 11. This variation in atom types may result in subtle conformational or desolvation effects that account for the slightly more favorable binding free energy of 11, the origin of which appears to be entropic. Furthermore, in contrast to what we expected based upon a putative cation-π interaction, the phenyl and cyclohexyl derivatives 11 and 12, respectively, were about two-fold more potent than the corresponding indolyl compound 10. Given the narrow range of ΔG° values for 10–12 and experimental error, interpreting the importance of the minor differences in corresponding ΔH° and −TΔS° values is problematic. However, given the close similarities in the thermodynamic parameters for 10–12, a cation-π interaction does not appear to contribute significantly to relative binding energetics.

Although we sought to analyze the structures of the complexes of 8–12 with the Grb2 SH2 domain, suitable crystals were only obtained for complexes of 8 and 10. These structures were solved at resolutions of 1.6 and 1.8 Å, respectively, by molecular replacement using the structure of the domain in complex with the parent molecule 7 (PDB code: 3S8O).23 Alignment of the backbone atoms belonging to the domain in the complexes of 8 and 10 yields root mean square deviations (RMSDs) for all backbone atoms of <0.2 Å (Figure 1). Although there are obvious differences in the spatial orientations of the pTyr–1 side-chains in the bound forms of 8 and 10, there is little variation in the positions of equivalent atoms of 8 and 10, which superimpose with a RMSD < 0.2 Å, which is less than the coordinate error that is associated with the molecular models,24 following alignment of the domains.

Figure 1.

Figure 1

Complexes of the Grb2 SH2 domain with 8 and 10. Oxygen, nitrogen, and phosphorous atoms are colored red, blue, and orange, respectively. Carbon atoms belonging to the complex with 8 and 10 are colored magenta and cyan, respectively. (a) Alignment of backbone atoms belonging to the domains in the complexes, showing the domains (ribbons) and the bound ligands (sticks). (b) The bound ligands (sticks) only. Dashed black line represents the internal hydrogen bond between the pTyr carbonyl oxygen atoms and the amide nitrogen atoms of the pTyr+3 sites.

In their respective complexes, both 8 and 10 make 14 direct and five water-mediated polar contacts to the domain.25 The cyclohexane ring at the pTyr+1 position in each complex makes a total of 15 van der Waals (vdW) contacts with the domain.26 The favorable nonbonded interactions between the Grb2 SH2 domain and the atoms common to both 8 and 10 are thus virtually identical to one another. However, because the phenyl group of 8 is positioned closer to Arg67 of the domain than the indolyl moiety of 10, 8 makes 23 vdW contacts with the pTyr–1 subsite, whereas 10 makes only five such contacts. However, this large difference in the number of vdW contacts is not reflected in any significant differences in the thermodynamic binding parameters (Table 1).

Cation-π interactions involving arginine side chains in proteins tend to adopt a so-called parallel electron donor-acceptor geometry rather than an oblique or T-shaped geometry.14c,15 Examination of the structure of the complex of 8 with the domain reveals that the phenyl ring in the Cbz group indeed adopts such a parallel geometry relative to the guanidinium ion of Arg67 (Figure 2a), and the carbon atoms of the phenyl ring are 3.4–3.8 Å removed from the central carbon atom of guanidinium group. On the other hand, the distance between the carbon atoms in the benzenoid ring of the indole ring and the nearest nitrogen atom of the guanidinium group in the complex of 10 range from 3.5–4.5 Å, and the planes of the guanidinium moiety of Arg67 and the indole ring at the pTyr–1 site of 10 are oblique (Figure 2b). Although this is not the preferred relative orientation in protein structures, it is not possible to confidently correlate variations of energetics with interplane angle, because there are strong cation-π interactions having oblique geometries.14c

Figure 2.

Figure 2

Interactions between the pTyr–1 and pTyr moieties of the bound ligands (sticks) in the complexes of 8 (a) and 10 (b) and Arg67 of the Grb2 SH2 domain (lines); interactions between Nη atoms of Arg67 and the phosphate and pTyr–1 C=O groups not shown (see text).

Comparing the results of these studies with those of Furet20 and Nioche21 clearly shows that energetic effects associated with varying the pTyr–1 side chain of Grb2 SH2 binding ligands depend upon the nature of the pTyr+1 residue. X-Ray crystallographic studies of 8 and 10 reveal that the relative orientations of the guanidine moiety of Arg67 and the aromatic groups in the side chains of 8 and 10 are consistent with what is expected for a cation-π interaction, although the geometry in the complex of 10 is not ideal. If one assumes that the binding poses for 8, 11, and 12 are similar, any net contribution of a cation-π interaction to the binding free energies in this system are negligible. Indeed, the observation that both phenyl and cyclohexyl group replacements of an indole ring give ligands of comparable potency indicates that other factors are at play. Solvation effects may be a play, but interactions of other functional groups on the ligand with Arg67 may be more significant. For example, Marshall has suggested that energetics associated with adjacent salt-bridges may dominate cation-π interactions.18 Accordingly, the salt-bridge between Arg67 and the phosphate groups of 8 and 10, which have interaction distances of 2.8 Å (Figure 2), may mitigate the energetic effects of any cation-π interaction. There are hydrogen bonding interactions, which range from 2.8–3.3 Å, between the pTyr–1 carbonyl oxygen atoms and the two Nη atoms of the Arg67 side chains in these complexes. Thus, although cation-π interactions are well documented as important noncovalent forces in molecular recognition, the energetics of such interactions may be mitigated by other nonbonded interactions and solvation effects in protein-ligand associations.

Supplementary Material

01

Acknowledgment

We thank the National Institutes of Health (GM 84965), the National Science Foundation (CHE 0750329), the Robert A. Welch Foundation (F-652), and the Norman Hackerman Advanced Research Program for their generous support of this research.

Footnotes

Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Supporting Information Available. Methods and materials for ITC and X-ray crystallographic experiments, X-ray diffraction statistics, electron density difference maps, contact diagrams, and plots of thermodynamic data are available free of charge via the Internet at http://pubs.acs.org.

REFERENCES

  • 1.For some reviews and lead references, see: Gohlke H, Klebe G. Angew. Chem. Int. Ed. 2002;41:2644. doi: 10.1002/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O. Hunter CA. Angew. Chem. Int. Ed. 2004;43:5310. doi: 10.1002/anie.200301739. Homans SW. Topics Curr. Chem. 2007;272:51. Bissantz C, Kuhn B, Stahl M. J. Med. Chem. 2010;53:5061. doi: 10.1021/jm100112j. Mobley DL, Dill KA. Structure. 2009;17:489. doi: 10.1016/j.str.2009.02.010. Martin SF, Clements JH. Annu. Rev. Biochem. 2013;82:267. doi: 10.1146/annurev-biochem-060410-105819.
  • 2.For some representative examples, see: Krishnamurthy VM, Bohall BR, Semetey V, Whitesides GM. J. Am. Chem. Soc. 2006;128:5802. doi: 10.1021/ja060070r. Steuber H, Heine A, Klebe G. J. Mol. Biol. 2007;368:618. doi: 10.1016/j.jmb.2006.12.004. Baum B, Mohamed M, Zayed M, Gerlach C, Heine A, Hangauer D, Klebe G. J. Mol. Biol. 2009;390:56. doi: 10.1016/j.jmb.2009.04.051. Kawasaki Y, Chufan EE, Lafont V, Hidaka K, Kiso Y, Amzel LM, Freire E. Chem. Biol. Drug Des. 2010;75:143. doi: 10.1111/j.1747-0285.2009.00921.x. Baum B, Muley L, Smolinski M, Heine A, Hangauer D, Klebe G. J. Mol. Biol. 2010;397:1042. doi: 10.1016/j.jmb.2010.02.007. Mecinović J, Snyder PW, Mirica KA, Bai S, Mack ET, Kwant RL, Moustakas DT, Héroux A, Whitesides GM. J. Am. Chem. Soc. 2011;133:14017. doi: 10.1021/ja2045293. Brandt T, Holzmann N, Muley L, Khayat M, Wegscheid-Gerlach C, Baum B, Heine A, Hangauer D, Klebe G. J. Mol. Biol. 2011;405:1170. doi: 10.1016/j.jmb.2010.11.038.
  • 3.For review of thermodynamic data in protein-ligand interactions, see: Olsson TSG, Williams MA, Pitt WR, Ladbury JE. J. Mol. Biol. 2008;384:1002. doi: 10.1016/j.jmb.2008.09.073.
  • 4.(a) Freire E. Chem. Biol. Drug Des. 2009;74:468. doi: 10.1111/j.1747-0285.2009.00880.x. [DOI] [PMC free article] [PubMed] [Google Scholar]; (b) Ladbury JE, Klebe G, Freire E. Nat. Rev. Drug Discovery. 2010;9:23. doi: 10.1038/nrd3054. [DOI] [PubMed] [Google Scholar]; (c) Fernández A, Fraser C, Scott LR. Trends in Biotech. 2012;30:1. doi: 10.1016/j.tibtech.2011.07.003. [DOI] [PubMed] [Google Scholar]
  • 5.(a) Dunitz JD. Chem. Biol. 1995;2:709. doi: 10.1016/1074-5521(95)90097-7. [DOI] [PubMed] [Google Scholar]; (b) Lafont V, Armstrong AA, Ohtaka H, Kiso Y, Amzel LM, Freire E. Chem. Biol. Drug. Des. 2007;69:413. doi: 10.1111/j.1747-0285.2007.00519.x. [DOI] [PubMed] [Google Scholar]; (c) Olsson TSG, Ladbury JE, Pitt WR, Williams MA. Protein Sci. 2011;20:1607. doi: 10.1002/pro.692. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Reynolds CH, Holloway MK. ACS Med. Chem. Lett. 2011;2:433. doi: 10.1021/ml200010k. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Davidson JP, Lubman O, Rose T, Waksman G, Martin SF. J. Am. Chem. Soc. 2002;124:205. doi: 10.1021/ja011746f. [DOI] [PubMed] [Google Scholar]
  • 8.(a) Benfield AP, Teresk MG, Plake HR, DeLorbe JE, Millspaugh LE, Martin SF. Angew. Chem. Int. Ed. 2006;45:6830. doi: 10.1002/anie.200600844. [DOI] [PubMed] [Google Scholar]; (b) DeLorbe JE, Clements JH, Teresk MG, Benfield AP, Plake HR, Millspaugh LE, Martin SF. J. Am. Chem. Soc. 2009;131:16758. doi: 10.1021/ja904698q. [DOI] [PubMed] [Google Scholar]; (c) DeLorbe JE, Clements JH, Whiddon BB, Martin SF. ACS Med. Chem. Lett. 2010;1:448. doi: 10.1021/ml100142y. [DOI] [PMC free article] [PubMed] [Google Scholar]; (d) Shi Y, Zhu CZ, Martin SF, Ren P. J. Phys. Chem. B. 2012;116:1716. doi: 10.1021/jp210265d. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.See also: Udugamasooriya DG, Spaller MR. Biopolymers. 2008;8:653. doi: 10.1002/bip.20983.
  • 10.(a) Kyte J. Biophys. Chem. 2003;100:193. doi: 10.1016/s0301-4622(02)00281-8. [DOI] [PubMed] [Google Scholar]; (b) Dill KA, Truskett TM, Vlachy V, Hribar-Lee B. Ann. Rev. Biophys. Biomol. Struct. 2005;34:173. doi: 10.1146/annurev.biophys.34.040204.144517. [DOI] [PubMed] [Google Scholar]; (c) Chandler D. Nature. 2005;437:640. doi: 10.1038/nature04162. [DOI] [PubMed] [Google Scholar]
  • 11.For some leading references, see: Malham R, Johnstone S, Bingham RJ, Barratt E, Phillips SEV, Laughton CA, Homans SW. J. Am. Chem. Soc. 2005;127:17061. doi: 10.1021/ja055454g. Snyder PW, Mecinović J, Moustakas DT, Thomas SW, III, Harder M, Mack ET, Lockett MR, Héroux A, Sherman W, Whitesides GM. Proc. Natl. Acad. Sci. USA. 2011;108:17889. doi: 10.1073/pnas.1114107108. Myslinski JM, DeLorbe JE, Clements JH, Martin SF. J. Am. Chem. Soc. 2011;133:18518. doi: 10.1021/ja2068752.
  • 12.For example, see: Carey C, Cheng Y-K, Rossky P. Chem. Phys. 2000;258:415. Homans SW. Drug Discovery Today. 2007;12:534. doi: 10.1016/j.drudis.2007.05.004. Setny P, Baron R, McCammon JA. J. Chem. Theory, Comput. 2010;6:2866. doi: 10.1021/ct1003077. Wang L, Berne BJ, Friesner RA. Proc. Nat. Acad. Sci. USA. 2011;108:1326. doi: 10.1073/pnas.1016793108.
  • 13.For reviews, see: Ma JC, Dougherty DA. Chem. Rev. 1997;97:1303. doi: 10.1021/cr9603744. Meyer EA, Castellano RK, Diederich F. Angew. Chem. Int. Ed. 2003;42:1210. doi: 10.1002/anie.200390319. Schneider H-J. Angew. Chem. Int. Ed. 2009;48:3924. doi: 10.1002/anie.200802947. Salonen LM, Ellermann M, Diederich F. Angew. Chem. Int. Ed. 2011;50:4808. doi: 10.1002/anie.201007560. Dougherty DA. Acc. Chem. Res. 2013;46:885. doi: 10.1021/ar300265y.
  • 14.(a) Dougherty DA. Science. 1996;271:163. doi: 10.1126/science.271.5246.163. [DOI] [PubMed] [Google Scholar]; (b) Ma JC, Dougherty DA. Chem. Rev. 1997;97:1303. doi: 10.1021/cr9603744. [DOI] [PubMed] [Google Scholar]; (b) Zhong W, Gallivan JP, Zhang Y, Li L, Lester HA, Dougherty DA. Proc. Natl. Acad. Sci. U.S.A. 1998;95:12088. doi: 10.1073/pnas.95.21.12088. [DOI] [PMC free article] [PubMed] [Google Scholar]; (c) Gallivan JP, Dougherty DA. Proc. Natl. Acad. Sci. U. S. A. 1999;96:9459. doi: 10.1073/pnas.96.17.9459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Crowley PB, Golovin A. Proteins: Struct. Funct. Bioinf. 2005;59:231–239. doi: 10.1002/prot.20417. [DOI] [PubMed] [Google Scholar]
  • 16.(a) Tatko CD, Waters ML. J. Am. Chem. Soc. 2004;126:2028. doi: 10.1021/ja038258n. [DOI] [PubMed] [Google Scholar]; (b) Hughes RM, Wiggins KR, Khorasanizadeh S, Waters ML . Proc. Natl. Acad. Sci. USA. 2007;104:11184. doi: 10.1073/pnas.0610850104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.(a) Schärer K, Morgenthaler M, Paulini R, Obst-Sander U, Banner DW, Schlatter D, Benz J, Stihle M, Diederich F. Angew. Chem. Int. Ed. 2005;44:4400. doi: 10.1002/anie.200500883. [DOI] [PubMed] [Google Scholar]; (b) Salonen LM, Holland MC, Kaib PSJ, Haap W, Benz J, Mary J-L, Kuster O, Schweizer WB, Banner DW, Diederich F. Chem. Eur. J. 2012;18:213. doi: 10.1002/chem.201102571. [DOI] [PubMed] [Google Scholar]
  • 18.Anderson MA, Ogbay B, Arimoto R, Sha W, Kisselev OG, Cistola DP, Marshall GR. J. Am. Chem. Soc. 2006;128:7531. doi: 10.1021/ja058513z. [DOI] [PubMed] [Google Scholar]
  • 19.For a review of SH2 domains, see: Bradshaw JM, Waksman G. Adv. Protein Chem. 2002;61:161. doi: 10.1016/s0065-3233(02)61005-8.
  • 20. Furet P, Gay B, Garcia-Echeverria C, Rahuel J, Fretz H, Schoepfer J, Caravatti G. J. Med. Chem. 1997;40:3551. doi: 10.1021/jm9702185. See also: Rahuel J, Garcia-Echeverria C, Furet P, Strauss A, Caravatti G, Fretz H, Schoepfer J, Gay B. J. Mol. Biol. 1998;279:1013. doi: 10.1006/jmbi.1998.1790.
  • 21.Nioche P, Liu W-Q, Broutin I, Charbonnier F, Latreille M-T, Vidal M, Roques B, Garbay C, Ducruix A. J. Mol. Biol. 2002;315:1167. doi: 10.1006/jmbi.2001.5299. [DOI] [PubMed] [Google Scholar]
  • 22.Garcia-Echeverria C, Furet P, Gay B, Fretz H, Rahuel J, Schoepfer J, Caravatti G. J. Med. Chem. 1998;41:1741. doi: 10.1021/jm970856n. [DOI] [PubMed] [Google Scholar]
  • 23.Accession numbers in the RCSB Protein Data Bank for complexes of the Grb2 SH2 domain with compounds 8 and 10 are 4P9V and 4P9Z, respectively.
  • 24.Luzzati V. Acta. Cryst. 1952;5:802. [Google Scholar]
  • 25.Non-hydrogen donor-acceptor distances for direct and single water-mediated hydrogen bonding contacts between protein and ligand are within the range 2.5–3.5 Å.
  • 26.A vdW contact is defined by an interatomic distance in the range of 3.4–4.2 Å between a carbon atom of the bound ligand and a carbon, nitrogen, or oxygen atom in the domain.

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

01

RESOURCES