Journal of Computer-Aided Molecular Design

, Volume 25, Issue 1, pp 1–12 | Cite as

Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes

  • Alpeshkumar K. Malde
  • Alan E. Mark


Despite its central role in structure based drug design the determination of the binding mode (position, orientation and conformation in addition to protonation and tautomeric states) of small heteromolecular ligands in protein:ligand complexes based on medium resolution X-ray diffraction data is highly challenging. In this perspective we demonstrate how a combination of molecular dynamics simulations and free energy (FE) calculations can be used to correct and identify thermodynamically stable binding modes of ligands in X-ray crystal complexes. The consequences of inappropriate ligand structure, force field and the absence of electrostatics during X-ray refinement are highlighted. The implications of such uncertainties and errors for the validation of virtual screening and fragment-based drug design based on high throughput X-ray crystallography are discussed with possible solutions and guidelines.


X-ray crystallography Ligand design Molecular dynamics simulations Free energy calculations Binding mode 



Aminoacyl-tRNA synthetases


Automated Topology Builder


Cyclin Depdendent Kinase


Crystallography and NMR System




Free Energy




Glycogen Phosphorylase b


Human Immunodeficiency Virus-1










Molecular Dynamics


Molecular Mechanics


N-terminal editing domain of Pyrococcus abyssi threonyl-tRNA synthetase


Protein Data Bank


Phosphodiesterase 4B


Phenylethanolamine N-methyltransferase


Quantum Mechanics








Tet repressor protein



The computational resources provided by NCI National Facility through projects m72 and n63 are greatly acknowledged.

Supplementary material

10822_2010_9397_MOESM1_ESM.doc (67 kb)
Supplementary material 1 (DOC 67 kb)


  1. 1.
    Kleywegt GJ, Henrick K, Dodson EJ, van Aalten DMF (2003) Structure 11:1051CrossRefGoogle Scholar
  2. 2.
    Davis AM, Teague SJ, Kleywegt GJ (2003) Angew Chemie-Int Ed 42:2718CrossRefGoogle Scholar
  3. 3.
    Davis AM, St-Gallay SA, Kleywegt GJ (2008) Drug Discov Today 13:831CrossRefGoogle Scholar
  4. 4.
    Kleywegt GJ (2007) Acta Crystallogr D Biol Crystallogr 63:94CrossRefGoogle Scholar
  5. 5.
    Engh RA, Huber R (1991) Acta Crystallogr A 47:392CrossRefGoogle Scholar
  6. 6.
    Yu N, Li X, Cui GL, Hayik SA, Merz KM (2006) Protein Sci 15:2773CrossRefGoogle Scholar
  7. 7.
    Wlodek S, Skillman AG, Nicholls A (2006) Acta Crystallogr D Biol Crystallogr 62:741CrossRefGoogle Scholar
  8. 8.
    Xu RX, Rocque WJ, Lambert MH, Vanderwall DE, Luther MA, Nolte RT (2004) J Mol Biol 337:355CrossRefGoogle Scholar
  9. 9.
    Chrysina ED, Oikonomakos NG, Zographos SE, Kosmopoulou MN, Bischler N, Leonidas DD, Kovacs L, Docsa T, Gergely P, Somsak L (2003) Biocatal Biotransformation 21:233CrossRefGoogle Scholar
  10. 10.
    Watson KA, Chrysina ED, Tsitsanou KE, Zographos SE, Archontis G, Fleet GWJ, Oikonomakos NG (2005) Proteins 61:966CrossRefGoogle Scholar
  11. 11.
    Kurumbail RG, Stevens AM, Gierse JK, McDonald JJ, Stegeman RA, Pak JY, Gildehaus D, Miyashiro JM, Penning TD, Seibert K, Isakson PC, Stallings WC (1996) Nature 384:644CrossRefGoogle Scholar
  12. 12.
    Villa A, Zangi R, Pieffet G, Mark AE (2003) J Comput Aided Mol Des 17:673CrossRefGoogle Scholar
  13. 13.
    Swain AL, Miller MM, Green J, Rich DH, Schneider J, Kent SBH, Wlodawer A (1990) Proc Natl Acad Sci USA 87:8805CrossRefGoogle Scholar
  14. 14.
    Ferguson DM, Radmer RJ, Kollman PA (1991) J Med Chem 34:2654CrossRefGoogle Scholar
  15. 15.
    Tropsha A, Hermans J (1992) Protein Eng 5:29CrossRefGoogle Scholar
  16. 16.
    Malde AK, Mark AE (2009) J Am Chem Soc 131:3848CrossRefGoogle Scholar
  17. 17.
    Hussain T, Kruparani SP, Pal B, Dock-Bregeon AC, Dwivedi S, Shekar MR, Sureshbabu K, Sankaranarayanan R (2006) EMBO J 25:4152CrossRefGoogle Scholar
  18. 18.
    Drinkwater N, Gee CL, Puri M, Criscione KR, McLeish MJ, Grunewald GL, Martin JL (2009) Biochem J 422:463CrossRefGoogle Scholar
  19. 19.
    Gee CL, Drinkwater N, Tyndall JDA, Grunewald GL, Wu Q, McLeish MJ, Martin JL (2007) J Med Chem 50:4845CrossRefGoogle Scholar
  20. 20.
    Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, Snoeyink J, Richardson JS, Richardson DC (2007) Nucleic Acids Res 35:W375CrossRefGoogle Scholar
  21. 21.
    Furet P, Meyer T, Strauss A, Raccuglia S, Rondeau JM (2002) Bioorg Med Chem Lett 12:221CrossRefGoogle Scholar
  22. 22.
    Donnini S, Villa A, Groenhof G, Mark AE, Wierenga RK, Juffer AH (2009) Proteins 76:138CrossRefGoogle Scholar
  23. 23.
    Aleksandrov A, Proft J, Hinrichs W, Simonson T (2007) Chembiochem 8:675CrossRefGoogle Scholar
  24. 24.
    McDonald IK, Thornton JM (1995) Protein Eng 8:217CrossRefGoogle Scholar
  25. 25.
    Weichenberger CX, Sippl MJ (2006) Structure 14:967CrossRefGoogle Scholar
  26. 26.
    Word JM, Lovell SC, Richardson JS, Richardson DC (1999) J Mol Biol 285:1735CrossRefGoogle Scholar
  27. 27.
    Watson KA, Mitchell EP, Johnson LN, Son JC, Bichard CJF, Orchard MG, Fleet GWJ, Oikonomakos NG, Leonidas DD, Kontou M, Papageorgioui A (1994) Biochemistry 33:5745CrossRefGoogle Scholar
  28. 28.
    Kleywegt GJ, Harris MR (2007) Acta Crystallogr D Biol Crystallogr 63:935CrossRefGoogle Scholar
  29. 29.
    Martin JL, Begun J, McLeish MJ, Caine JM, Grunewald GL (2001) Structure 9:977CrossRefGoogle Scholar
  30. 30.
    Petrov V, Petrova V, Girichev GV, Oberhammer H, Giricheva NI, Ivanov S (2006) J Org Chem 71:2952CrossRefGoogle Scholar
  31. 31.
    Perola E, Walters WP, Charifson PS (2004) Proteins 56:235CrossRefGoogle Scholar
  32. 32.
    Nilsson K, Lecerof D, Sigfridsson E, Ryde U (2003) Acta Crystallogr D Biol Crystallogr 59:274CrossRefGoogle Scholar
  33. 33.
    Schuttelkopf AW, van Aalten DMF (2004) Acta Crystallogr D Biol Crystallogr 60:1355CrossRefGoogle Scholar
  34. 34.
    Kleywegt GJ, Jones TA (1998) Acta Crystallogr D Biol Crystallogr D54:1119CrossRefGoogle Scholar
  35. 35.
    Wang JM, Wang W, Kollman PA, Case DA (2006) J Mol Graph Model 25:247CrossRefGoogle Scholar
  36. 36.
    Miller BT, Singh RP, Klauda JB, Hodoscek M, Brooks BR, Woodcock HL (2008) J Chem Inf Model 48:1920CrossRefGoogle Scholar
  37. 37.
    Li X, He X, Wang B, Merz K (2009) J Am Chem Soc 131:7742CrossRefGoogle Scholar
  38. 38.
    Fenn TD, Schnieders MJ, Brunger AT, Pande VS (2010) Acta Cryst 98:2984Google Scholar
  39. 39.
    Martin YC (2009) J Comput Aided Mol Des 23:693CrossRefGoogle Scholar
  40. 40.
    Cui GL, Li X, Merz KM (2007) Biochemistry 46:1303CrossRefGoogle Scholar
  41. 41.
    Böhm H-J (1994) J Comput Aided Mol Des 8:243CrossRefGoogle Scholar
  42. 42.
    Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) J Comput Aided Mol Des 11:425CrossRefGoogle Scholar
  43. 43.
    Wang R, Lai L, Wang S (2002) J Comput Aided Mol Des 16:11CrossRefGoogle Scholar
  44. 44.
    Raub S, Steffen A, Kämper A, Marian CM (2008) J Chem Inf Model 48:1492CrossRefGoogle Scholar
  45. 45.
    Raha K, Merz KM (2005) J Med Chem 48:4558CrossRefGoogle Scholar
  46. 46.
    van Gunsteren WF, Dolenc J, Mark AE (2008) Curr Opin Struct Biol 18:149Google Scholar
  47. 47.
    Yusuf D, Davis AM, Kleywegt GJ, Schmitt S (2008) J Chem Inf Model 48:1411CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.School of Chemistry and Molecular BiosciencesUniversity of QueenslandSt. LuciaAustralia
  2. 2.Institute for Molecular BioscienceUniversity of QueenslandSt. LuciaAustralia

Personalised recommendations