• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of prosciprotein sciencecshl presssubscriptionsetoc alertsthe protein societyjournal home
Protein Sci. Sep 1998; 7(9): 1884–1897.
PMCID: PMC2144175

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design.

Abstract

Identification and size characterization of surface pockets and occluded cavities are initial steps in protein structure-based ligand design. A new program, CAST, for automatically locating and measuring protein pockets and cavities, is based on precise computational geometry methods, including alpha shape and discrete flow theory. CAST identifies and measures pockets and pocket mouth openings, as well as cavities. The program specifies the atoms lining pockets, pocket openings, and buried cavities; the volume and area of pockets and cavities; and the area and circumference of mouth openings. CAST analysis of over 100 proteins has been carried out; proteins examined include a set of 51 monomeric enzyme-ligand structures, several elastase-inhibitor complexes, the FK506 binding protein, 30 HIV-1 protease-inhibitor complexes, and a number of small and large protein inhibitors. Medium-sized globular proteins typically have 10-20 pockets/cavities. Most often, binding sites are pockets with 1-2 mouth openings; much less frequently they are cavities. Ligand binding pockets vary widely in size, most within the range 10(2)-10(3)A3. Statistical analysis reveals that the number of pockets and cavities is correlated with protein size, but there is no correlation between the size of the protein and the size of binding sites. Most frequently, the largest pocket/cavity is the active site, but there are a number of instructive exceptions. Ligand volume and binding site volume are somewhat correlated when binding site volume is < or =700 A3, but the ligand seldom occupies the entire site. Auxiliary pockets near the active site have been suggested as additional binding surface for designed ligands (Mattos C et al., 1994, Nat Struct Biol 1:55-58). Analysis of elastase-inhibitor complexes suggests that CAST can identify ancillary pockets suitable for recruitment in ligand design strategies. Analysis of the FK506 binding protein, and of compounds developed in SAR by NMR (Shuker SB et al., 1996, Science 274:1531-1534), indicates that CAST pocket computation may provide a priori identification of target proteins for linked-fragment design. CAST analysis of 30 HIV-1 protease-inhibitor complexes shows that the flexible active site pocket can vary over a range of 853-1,566 A3, and that there are two pockets near or adjoining the active site that may be recruited for ligand design.

Full Text

The Full Text of this article is available as a PDF (8.4M).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Delaney JS. Finding and filling protein cavities using cellular logic operations. J Mol Graph. 1992 Sep;10(3):174–163. [PubMed]
  • DesJarlais RL, Sheridan RP, Seibel GL, Dixon JS, Kuntz ID, Venkataraghavan R. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J Med Chem. 1988 Apr;31(4):722–729. [PubMed]
  • Finney JL. Volume occupation, environment and accessibility in proteins. The problem of the protein surface. J Mol Biol. 1975 Aug 25;96(4):721–732. [PubMed]
  • Gellatly BJ, Finney JL. Calculation of protein volumes: an alternative to the Voronoi procedure. J Mol Biol. 1982 Oct 25;161(2):305–322. [PubMed]
  • Gerstein M, Tsai J, Levitt M. The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J Mol Biol. 1995 Jun 23;249(5):955–966. [PubMed]
  • Hubbard SJ, Gross KH, Argos P. Intramolecular cavities in globular proteins. Protein Eng. 1994 May;7(5):613–626. [PubMed]
  • Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996 Feb;14(1):33–28. [PubMed]
  • Kim S, Liang J, Barry BA. Chemical complementation identifies a proton acceptor for redox-active tyrosine D in photosystem II. Proc Natl Acad Sci U S A. 1997 Dec 23;94(26):14406–14411. [PMC free article] [PubMed]
  • Kleywegt GJ, Jones TA. Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr D Biol Crystallogr. 1994 Mar 1;50(Pt 2):178–185. [PubMed]
  • Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J Mol Biol. 1982 Oct 25;161(2):269–288. [PubMed]
  • Laskowski RA. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph. 1995 Oct;13(5):323–308. [PubMed]
  • Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971 Feb 14;55(3):379–400. [PubMed]
  • Levitt DG, Banaszak LJ. POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph. 1992 Dec;10(4):229–234. [PubMed]
  • Liang J, McGee MP. Hydration structure of antithrombin conformers and water transfer during reactive loop insertion. Biophys J. 1998 Aug;75(2):573–582. [PMC free article] [PubMed]
  • Liang J, Subramaniam S. Computation of molecular electrostatics with boundary element methods. Biophys J. 1997 Oct;73(4):1830–1841. [PMC free article] [PubMed]
  • Lin SL, Nussinov R, Fischer D, Wolfson HJ. Molecular surface representations by sparse critical points. Proteins. 1994 Jan;18(1):94–101. [PubMed]
  • Mattos C, Giammona DA, Petsko GA, Ringe D. Structural analysis of the active site of porcine pancreatic elastase based on the X-ray crystal structures of complexes with trifluoroacetyl-dipeptide-anilide inhibitors. Biochemistry. 1995 Mar 14;34(10):3193–3203. [PubMed]
  • Mattos C, Rasmussen B, Ding X, Petsko GA, Ringe D. Analogous inhibitors of elastase do not always bind analogously. Nat Struct Biol. 1994 Jan;1(1):55–58. [PubMed]
  • Mattos C, Ringe D. Locating and characterizing binding sites on proteins. Nat Biotechnol. 1996 May;14(5):595–599. [PubMed]
  • McGee MP, Teuschler H, Liang J. Effective electrostatic charge of coagulation factor X in solution and on phospholipid membranes: implications for activation mechanisms and structure-function relationships of the Gla domain. Biochem J. 1998 Feb 15;330(Pt 1):533–539. [PMC free article] [PubMed]
  • Munson PJ, Singh RK. Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. Protein Sci. 1997 Jul;6(7):1467–1481. [PMC free article] [PubMed]
  • Navia MA, Fitzgerald PM, McKeever BM, Leu CT, Heimbach JC, Herber WK, Sigal IS, Darke PL, Springer JP. Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1. Nature. 1989 Feb 16;337(6208):615–620. [PubMed]
  • Rashin AA, Iofin M, Honig B. Internal cavities and buried waters in globular proteins. Biochemistry. 1986 Jun 17;25(12):3619–3625. [PubMed]
  • Richards FM. Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng. 1977;6:151–176. [PubMed]
  • Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci. 1995 Sep;20(9):374–374. [PubMed]
  • Singh RK, Tropsha A, Vaisman II. Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues. J Comput Biol. 1996 Summer;3(2):213–221. [PubMed]
  • Smart OS, Goodfellow JM, Wallace BA. The pore dimensions of gramicidin A. Biophys J. 1993 Dec;65(6):2455–2460. [PMC free article] [PubMed]
  • Shuker SB, Hajduk PJ, Meadows RP, Fesik SW. Discovering high-affinity ligands for proteins: SAR by NMR. Science. 1996 Nov 29;274(5292):1531–1534. [PubMed]
  • Van Duyne GD, Standaert RF, Karplus PA, Schreiber SL, Clardy J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J Mol Biol. 1993 Jan 5;229(1):105–124. [PubMed]
  • Vondrasek J, Wlodawer A. Database of HIV proteinase structures. Trends Biochem Sci. 1997 May;22(5):183–183. [PubMed]
  • Voorintholt R, Kosters MT, Vegter G, Vriend G, Hol WG. A very fast program for visualizing protein surfaces, channels and cavities. J Mol Graph. 1989 Dec;7(4):243–245. [PubMed]
  • Williams MA, Goodfellow JM, Thornton JM. Buried waters and internal cavities in monomeric proteins. Protein Sci. 1994 Aug;3(8):1224–1235. [PMC free article] [PubMed]
  • Wlodawer A, Erickson JW. Structure-based inhibitors of HIV-1 protease. Annu Rev Biochem. 1993;62:543–585. [PubMed]
  • Wlodawer A, Miller M, Jaskólski M, Sathyanarayana BK, Baldwin E, Weber IT, Selk LM, Clawson L, Schneider J, Kent SB. Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science. 1989 Aug 11;245(4918):616–621. [PubMed]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...