메뉴 건너뛰기




Volumn 9, Issue 10, 2013, Pages

A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; CHEMICAL ANALYSIS; LIGANDS; MOLECULES; SCAFFOLDS; SCAFFOLDS (BIOLOGY);

EID: 84887265599     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003302     Document Type: Article
Times cited : (107)

References (57)
  • 1
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S, (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28: 27-30.
    • (2000) Nucleic Acids Research , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 4
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • Liang J, Edelsbrunner H, Woodward C, (1998) Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science 7: 1884-1897.
    • (1998) Protein Science , vol.7 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 7
    • 59849106371 scopus 로고    scopus 로고
    • Protein promiscuity and its implications for biotechnology
    • Nobeli I, Favia AD, Thornton JM, (2009) Protein promiscuity and its implications for biotechnology. Nature Biotechnology 27: 157-167.
    • (2009) Nature Biotechnology , vol.27 , pp. 157-167
    • Nobeli, I.1    Favia, A.D.2    Thornton, J.M.3
  • 10
    • 0027122748 scopus 로고
    • Proteins - 1000 families for the molecular biologist
    • Chothia C, (1992) Proteins- 1000 families for the molecular biologist. Nature 357: 543-544.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 11
    • 84878737382 scopus 로고    scopus 로고
    • Interplay of physics and evolution in the likely origin of protein biochemical function
    • Skolnick J, Gao M, (2013) Interplay of physics and evolution in the likely origin of protein biochemical function. Proc Natl Acad Sci U S A 110: 9344-9349.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 9344-9349
    • Skolnick, J.1    Gao, M.2
  • 13
    • 33846108633 scopus 로고    scopus 로고
    • BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
    • Liu TQ, Lin YM, Wen X, Jorissen RN, Gilson MK, (2007) BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Research 35: D198-D201.
    • (2007) Nucleic Acids Research , vol.35
    • Liu, T.Q.1    Lin, Y.M.2    Wen, X.3    Jorissen, R.N.4    Gilson, M.K.5
  • 14
    • 0017272554 scopus 로고
    • Enzyme recruitment in evolution of new function
    • Jensen RA, (1976) Enzyme recruitment in evolution of new function. Annual review of microbiology 30: 409-425.
    • (1976) Annual Review of Microbiology , vol.30 , pp. 409-425
    • Jensen, R.A.1
  • 15
    • 77956925998 scopus 로고    scopus 로고
    • Messy biology and the origins of evolutionary innovations
    • Tawfik DS, (2010) Messy biology and the origins of evolutionary innovations. Nat Chem Biol 6: 692-696.
    • (2010) Nat Chem Biol , vol.6 , pp. 692-696
    • Tawfik, D.S.1
  • 17
    • 79953100964 scopus 로고    scopus 로고
    • Structure-based systems biology for analyzing off-target binding
    • Xie L, Xie L, Bourne PE, (2011) Structure-based systems biology for analyzing off-target binding. Current Opinion in Structural Biology 21: 189-199.
    • (2011) Current Opinion in Structural Biology , vol.21 , pp. 189-199
    • Xie, L.1    Xie, L.2    Bourne, P.E.3
  • 18
    • 29444457054 scopus 로고    scopus 로고
    • Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships
    • Gold ND, Jackson RM, (2006) Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships. Journal of Molecular Biology 355: 1112-1124.
    • (2006) Journal of Molecular Biology , vol.355 , pp. 1112-1124
    • Gold, N.D.1    Jackson, R.M.2
  • 19
    • 44949110143 scopus 로고    scopus 로고
    • Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions
    • Minai R, Matsuo Y, Onuki H, Hirota H, (2008) Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions. Proteins-Structure Function and Bioinformatics 72: 367-381.
    • (2008) Proteins-Structure Function and Bioinformatics , vol.72 , pp. 367-381
    • Minai, R.1    Matsuo, Y.2    Onuki, H.3    Hirota, H.4
  • 20
    • 84860838201 scopus 로고    scopus 로고
    • Structure-based computational analysis of protein binding sites for function and druggability prediction
    • Nisius B, Sha F, Gohlke H, (2012) Structure-based computational analysis of protein binding sites for function and druggability prediction. Journal of Biotechnology 159: 123-134.
    • (2012) Journal of Biotechnology , vol.159 , pp. 123-134
    • Nisius, B.1    Sha, F.2    Gohlke, H.3
  • 21
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • Schmitt S, Kuhn D, Klebe G, (2002) A new method to detect related function among proteins independent of sequence and fold homology. Journal of Molecular Biology 323: 387-406.
    • (2002) Journal of Molecular Biology , vol.323 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 22
    • 49649083383 scopus 로고    scopus 로고
    • Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
    • Najmanovich R, Kurbatova N, Thornton J, (2008) Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites. Bioinformatics 24: I105-I111.
    • (2008) Bioinformatics , vol.24
    • Najmanovich, R.1    Kurbatova, N.2    Thornton, J.3
  • 23
    • 44449139387 scopus 로고    scopus 로고
    • Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
    • Xie L, Bourne PE, (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proceedings of the National Academy of Sciences of the United States of America 105: 5441-5446.
    • (2008) Proceedings of the National Academy of Sciences of the United States of America , vol.105 , pp. 5441-5446
    • Xie, L.1    Bourne, P.E.2
  • 25
    • 19544389524 scopus 로고    scopus 로고
    • Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
    • Morris RJ, Najmanovich RJ, Kahraman A, Thornton JM, (2005) Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics 21: 2347-2355.
    • (2005) Bioinformatics , vol.21 , pp. 2347-2355
    • Morris, R.J.1    Najmanovich, R.J.2    Kahraman, A.3    Thornton, J.M.4
  • 26
    • 77953587057 scopus 로고    scopus 로고
    • Real-time ligand binding pocket database search using local surface descriptors
    • Chikhi R, Sael L, Kihara D, (2010) Real-time ligand binding pocket database search using local surface descriptors. Proteins-Structure Function and Bioinformatics 78: 2007-2028.
    • (2010) Proteins-Structure Function and Bioinformatics , vol.78 , pp. 2007-2028
    • Chikhi, R.1    Sael, L.2    Kihara, D.3
  • 27
    • 75749155406 scopus 로고    scopus 로고
    • Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein-Ligand Binding Sites
    • Weill N, Rognan D, (2010) Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein-Ligand Binding Sites. Journal of Chemical Information and Modeling 50: 123-135.
    • (2010) Journal of Chemical Information and Modeling , vol.50 , pp. 123-135
    • Weill, N.1    Rognan, D.2
  • 28
    • 84874754249 scopus 로고    scopus 로고
    • APoc: large-scale identification of similar protein pockets
    • Gao M, Skolnick J, (2013) APoc: large-scale identification of similar protein pockets. Bioinformatics 29: 597-604.
    • (2013) Bioinformatics , vol.29 , pp. 597-604
    • Gao, M.1    Skolnick, J.2
  • 29
    • 67650912101 scopus 로고    scopus 로고
    • FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling
    • Brylinski M, Skolnick J, (2009) FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling. PLoS Computational Biology 5: e1000405.
    • (2009) PLoS Computational Biology , vol.5
    • Brylinski, M.1    Skolnick, J.2
  • 31
    • 33746318035 scopus 로고    scopus 로고
    • Trans-activation of the DNA-damage signalling protein kinase Chk2 by T-loop exchange
    • Oliver AW, Paul A, Boxall KJ, Barrie SE, Aherne GW, et al. (2006) Trans-activation of the DNA-damage signalling protein kinase Chk2 by T-loop exchange. EMBO J 25: 3179-3190.
    • (2006) EMBO J , vol.25 , pp. 3179-3190
    • Oliver, A.W.1    Paul, A.2    Boxall, K.J.3    Barrie, S.E.4    Aherne, G.W.5
  • 32
    • 0742324523 scopus 로고    scopus 로고
    • Crystal structure of a cAMP-dependent protein kinase mutant at 1.26A: new insights into the catalytic mechanism
    • Yang J, Ten Eyck LF, Xuong NH, Taylor SS, (2004) Crystal structure of a cAMP-dependent protein kinase mutant at 1.26A: new insights into the catalytic mechanism. J Mol Biol 336: 473-487.
    • (2004) J Mol Biol , vol.336 , pp. 473-487
    • Yang, J.1    Ten Eyck, L.F.2    Xuong, N.H.3    Taylor, S.S.4
  • 33
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Zhang Y, Skolnick J, (2004) Scoring function for automated assessment of protein structure template quality. Proteins-Structure Function and Bioinformatics 57: 702-710.
    • (2004) Proteins-Structure Function and Bioinformatics , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 34
    • 77953097386 scopus 로고    scopus 로고
    • Inositol 1,3,4,5,6-pentakisphosphate 2-kinase is a distant IPK member with a singular inositide binding site for axial 2-OH recognition
    • Gonzalez B, Banos-Sanz JI, Villate M, Brearley CA, Sanz-Aparicio J, (2010) Inositol 1,3,4,5,6-pentakisphosphate 2-kinase is a distant IPK member with a singular inositide binding site for axial 2-OH recognition. Proc Natl Acad Sci U S A 107: 9608-9613.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 9608-9613
    • Gonzalez, B.1    Banos-Sanz, J.I.2    Villate, M.3    Brearley, C.A.4    Sanz-Aparicio, J.5
  • 35
    • 0029787639 scopus 로고    scopus 로고
    • A pseudo-michaelis quaternary complex in the reverse reaction of a ligase: structure of Escherichia coli B glutathione synthetase complexed with ADP, glutathione, and sulfate at 2.0 A resolution
    • Hara T, Kato H, Katsube Y, Oda J, (1996) A pseudo-michaelis quaternary complex in the reverse reaction of a ligase: structure of Escherichia coli B glutathione synthetase complexed with ADP, glutathione, and sulfate at 2.0 A resolution. Biochemistry 35: 11967-11974.
    • (1996) Biochemistry , vol.35 , pp. 11967-11974
    • Hara, T.1    Kato, H.2    Katsube, Y.3    Oda, J.4
  • 36
    • 37849005665 scopus 로고    scopus 로고
    • Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii
    • Zhang Y, White RH, Ealick SE, (2008) Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii. Biochemistry 47: 205-217.
    • (2008) Biochemistry , vol.47 , pp. 205-217
    • Zhang, Y.1    White, R.H.2    Ealick, S.E.3
  • 37
    • 2342434852 scopus 로고    scopus 로고
    • Conformational changes in the reaction of pyridoxal kinase
    • Li MH, Kwok F, Chang WR, Liu SQ, Lo SC, et al. (2004) Conformational changes in the reaction of pyridoxal kinase. J Biol Chem 279: 17459-17465.
    • (2004) J Biol Chem , vol.279 , pp. 17459-17465
    • Li, M.H.1    Kwok, F.2    Chang, W.R.3    Liu, S.Q.4    Lo, S.C.5
  • 38
    • 33846106811 scopus 로고    scopus 로고
    • Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 A
    • Gruswitz F, O'Connell J 3rd, Stroud RM, (2007) Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 A. Proc Natl Acad Sci U S A 104: 42-47.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 42-47
    • Gruswitz, F.1    O'Connell III, J.2    Stroud, R.M.3
  • 39
    • 77951689893 scopus 로고    scopus 로고
    • Analysis of imatinib and sorafenib binding to p38alpha compared with c-Abl and b-Raf provides structural insights for understanding the selectivity of inhibitors targeting the DFG-out form of protein kinases
    • Namboodiri HV, Bukhtiyarova M, Ramcharan J, Karpusas M, Lee Y, et al. (2010) Analysis of imatinib and sorafenib binding to p38alpha compared with c-Abl and b-Raf provides structural insights for understanding the selectivity of inhibitors targeting the DFG-out form of protein kinases. Biochemistry 49: 3611-3618.
    • (2010) Biochemistry , vol.49 , pp. 3611-3618
    • Namboodiri, H.V.1    Bukhtiyarova, M.2    Ramcharan, J.3    Karpusas, M.4    Lee, Y.5
  • 40
    • 67649995940 scopus 로고    scopus 로고
    • Development of a fluorescent-tagged kinase assay system for the detection and characterization of allosteric kinase inhibitors
    • Simard JR, Getlik M, Grutter C, Pawar V, Wulfert S, et al. (2009) Development of a fluorescent-tagged kinase assay system for the detection and characterization of allosteric kinase inhibitors. J Am Chem Soc 131: 13286-13296.
    • (2009) J Am Chem Soc , vol.131 , pp. 13286-13296
    • Simard, J.R.1    Getlik, M.2    Grutter, C.3    Pawar, V.4    Wulfert, S.5
  • 41
    • 0030461132 scopus 로고    scopus 로고
    • Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents
    • Kurumbail RG, Stevens AM, Gierse JK, McDonald JJ, Stegeman RA, et al. (1996) Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents. Nature 384: 644-648.
    • (1996) Nature , vol.384 , pp. 644-648
    • Kurumbail, R.G.1    Stevens, A.M.2    Gierse, J.K.3    McDonald, J.J.4    Stegeman, R.A.5
  • 42
    • 78149284251 scopus 로고    scopus 로고
    • The novel benzopyran class of selective cyclooxygenase-2 inhibitors. Part 2: the second clinical candidate having a shorter and favorable human half-life
    • Wang JL, Limburg D, Graneto MJ, Springer J, Hamper JR, et al. (2010) The novel benzopyran class of selective cyclooxygenase-2 inhibitors. Part 2: the second clinical candidate having a shorter and favorable human half-life. Bioorg Med Chem Lett 20: 7159-7163.
    • (2010) Bioorg Med Chem Lett , vol.20 , pp. 7159-7163
    • Wang, J.L.1    Limburg, D.2    Graneto, M.J.3    Springer, J.4    Hamper, J.R.5
  • 43
    • 79960189764 scopus 로고    scopus 로고
    • Structure-based design of a new series of D-glutamic acid based inhibitors of bacterial UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD)
    • Tomasic T, Zidar N, Sink R, Kovac A, Blanot D, et al. (2011) Structure-based design of a new series of D-glutamic acid based inhibitors of bacterial UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD). J Med Chem 54: 4600-4610.
    • (2011) J Med Chem , vol.54 , pp. 4600-4610
    • Tomasic, T.1    Zidar, N.2    Sink, R.3    Kovac, A.4    Blanot, D.5
  • 44
    • 57349132464 scopus 로고    scopus 로고
    • Novel naphthalene-N-sulfonyl-D-glutamic acid derivatives as inhibitors of MurD, a key peptidoglycan biosynthesis enzyme
    • Humljan J, Kotnik M, Contreras-Martel C, Blanot D, Urleb U, et al. (2008) Novel naphthalene-N-sulfonyl-D-glutamic acid derivatives as inhibitors of MurD, a key peptidoglycan biosynthesis enzyme. J Med Chem 51: 7486-7494.
    • (2008) J Med Chem , vol.51 , pp. 7486-7494
    • Humljan, J.1    Kotnik, M.2    Contreras-Martel, C.3    Blanot, D.4    Urleb, U.5
  • 45
    • 0043168030 scopus 로고    scopus 로고
    • Coactivator binding promotes the specific interaction between ligand and the pregnane X receptor
    • Watkins RE, Davis-Searles PR, Lambert MH, Redinbo MR, (2003) Coactivator binding promotes the specific interaction between ligand and the pregnane X receptor. J Mol Biol 331: 815-828.
    • (2003) J Mol Biol , vol.331 , pp. 815-828
    • Watkins, R.E.1    Davis-Searles, P.R.2    Lambert, M.H.3    Redinbo, M.R.4
  • 46
    • 0037501542 scopus 로고    scopus 로고
    • 2.1 A crystal structure of human PXR in complex with the St. John's wort compound hyperforin
    • Watkins RE, Maglich JM, Moore LB, Wisely GB, Noble SM, et al. (2003) 2.1 A crystal structure of human PXR in complex with the St. John's wort compound hyperforin. Biochemistry 42: 1430-1438.
    • (2003) Biochemistry , vol.42 , pp. 1430-1438
    • Watkins, R.E.1    Maglich, J.M.2    Moore, L.B.3    Wisely, G.B.4    Noble, S.M.5
  • 49
    • 35848947748 scopus 로고    scopus 로고
    • Why metabolic enzymes are essential or nonessential for growth of Escherichia coli k12 on glucose
    • Kim J, Copley SD, (2007) Why metabolic enzymes are essential or nonessential for growth of Escherichia coli k12 on glucose. Biochemistry 46: 12501-12511.
    • (2007) Biochemistry , vol.46 , pp. 12501-12511
    • Kim, J.1    Copley, S.D.2
  • 53
    • 84893482610 scopus 로고
    • Solution for best rotation to relate two sets of vectors
    • Kabsch W, (1976) Solution for best rotation to relate two sets of vectors. Acta Crystallographica Section A 32: 922-923.
    • (1976) Acta Crystallographica Section A , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 54
    • 9644260215 scopus 로고
    • The shortest augumenting path method for solving assignment problems - Motivation and computational experience
    • In: Monma CL, editor. Basel: Baltzer
    • Derigs U (1985) The shortest augumenting path method for solving assignment problems- Motivation and computational experience. In: Monma CL, editor. Algorithms and software for optimization. Basel: Baltzer. pp. 57-102.
    • (1985) Algorithms and software for optimization , pp. 57-102
    • Derigs, U.1
  • 55
    • 57849165513 scopus 로고    scopus 로고
    • Combinatorial Bounds via Measure and Conquer: Bounding Minimal Dominating Sets and Applications
    • Fomin FV, Grandoni F, Pyatkin AV, Stepanov AA, (2008) Combinatorial Bounds via Measure and Conquer: Bounding Minimal Dominating Sets and Applications. Acm Transactions on Algorithms 5: 9.
    • (2008) Acm Transactions on Algorithms , vol.5 , pp. 9
    • Fomin, F.V.1    Grandoni, F.2    Pyatkin, A.V.3    Stepanov, A.A.4
  • 57
    • 80054911951 scopus 로고    scopus 로고
    • LigPlot+: multiple ligand-protein interaction diagrams for drug discovery
    • Laskowski RA, Swindells MB, (2011) LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model 51: 2778-2786.
    • (2011) J Chem Inf Model , vol.51 , pp. 2778-2786
    • Laskowski, R.A.1    Swindells, M.B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.