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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4lcw1VYMajor histocompatibility complex class I-related gene protein

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4lcw1VYMajor histocompatibility complex class I-related gene protein/1.000
3e6eDCSAlanine racemase/0.510
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.499
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.496
1hb1OCVIsopenicillin N synthase1.21.3.10.489
2iviACWIsopenicillin N synthase1.21.3.10.486
4l4v1VYMajor histocompatibility complex class I-related gene protein/0.484
5dp2NAPCurF/0.484
3wqmB29Diterpene synthase3.1.7.80.483
1obnASVIsopenicillin N synthase1.21.3.10.479
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.479
3x2fNAIAdenosylhomocysteinase/0.479
3zkyWT4Isopenicillin N synthase1.21.3.10.479
1hb3SCVIsopenicillin N synthase1.21.3.10.477
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.476
2xegCI9Glutamate carboxypeptidase 23.4.17.210.476
1bk0ACVIsopenicillin N synthase1.21.3.10.475
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.475
1oc1ASVIsopenicillin N synthase1.21.3.10.475
2vbpVB1Isopenicillin N synthase1.21.3.10.475
3ntrNADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.475
2wp9CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.473
2wp9CBESuccinate dehydrogenase cytochrome b556 subunit/0.473
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.473
4to1DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.473
4bfuZVUPantothenate kinase2.7.1.330.471
1qiqACCIsopenicillin N synthase1.21.3.10.470
1z6tADPApoptotic protease-activating factor 1/0.470
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.470
3zkuHCVIsopenicillin N synthase1.21.3.10.470
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.470
2wo7ASVIsopenicillin N synthase1.21.3.10.469
4isuIKMGlutamate receptor 2/0.469
4bb3KKAIsopenicillin N synthase1.21.3.10.468
4wbdADPPutative cysteine ligase BshC/0.468
5jqhCAUBeta-2 adrenergic receptor/0.468
2xejOKDGlutamate carboxypeptidase 23.4.17.210.467
4eqrCOACoenzyme A disulfide reductase/0.467
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.467
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.466
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.466
2b8jADNClass B acid phosphatase3.1.3.20.466
5cxv0HKMuscarinic acetylcholine receptor M1/0.466
3br3ETHTH-type transcriptional regulator QacR/0.465
3bw4FMNPutative 2-nitropropane dioxygenase/0.465
4b68NAPL-ornithine N(5)-monooxygenase/0.465
1jdzFMBPurine nucleoside phosphorylase/0.464
1k4gAIQQueuine tRNA-ribosyltransferase2.4.2.290.464
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.464
2iu8UD1UDP-3-O-acylglucosamine N-acyltransferase2.3.10.464
4q7f3D1Uncharacterized protein/0.464
1qjfACSIsopenicillin N synthase1.21.3.10.463
2zsdCOAPantothenate kinase2.7.1.330.463
3caqNDP3-oxo-5-beta-steroid 4-dehydrogenase/0.463
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.463
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.463
1qs2NADVip2Ac/0.462
1xf0ASDAldo-keto reductase family 1 member C3/0.462
2ejzSAHDiphthine synthase/0.462
2gesCOKPantothenate kinase2.7.1.330.462
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.462
2zs9ADPPantothenate kinase2.7.1.330.462
4to4DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.462
1s7gNADNAD-dependent protein deacylase 2/0.461
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.461
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.461
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.461
4qg1DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.461
1blzACVIsopenicillin N synthase1.21.3.10.460
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.460
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.460
3af1GDPPantothenate kinase2.7.1.330.460
4mprTPPBenzoylformate decarboxylase4.1.1.70.460
3hmvHBTcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.459
3s5wFADL-ornithine N(5)-monooxygenase/0.459
4bfxZVXPantothenate kinase2.7.1.330.459
4j7hTRHPCZA361.3/0.459
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.459
1isgAGSADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 23.2.2.60.458
1pr4MTPPurine nucleoside phosphorylase DeoD-type/0.458
2xeiARKGlutamate carboxypeptidase 23.4.17.210.458
3mhpFADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.458
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.457
2gbyBRNHTH-type transcriptional regulator QacR/0.457
2y60M8FIsopenicillin N synthase1.21.3.10.457
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.457
1cnfFADNitrate reductase [NADH]1.7.1.10.456
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.456
2y6fM9FIsopenicillin N synthase1.21.3.10.456
3exfTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.456
3exfTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.456
4rxpDTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.456
4rxrDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.456
5a0yCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.456
5a0yCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.456
2vbdV10Isopenicillin N synthase1.21.3.10.455
3rviRVIBeta-secretase 13.4.23.460.455
2oatPFMOrnithine aminotransferase, mitochondrial2.6.1.130.454
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.454
4bfwZVWPantothenate kinase2.7.1.330.454
4br0AU1Ectonucleoside triphosphate diphosphohydrolase 2/0.454
1pj6FOLDimethylglycine oxidase1.5.3.100.453
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.453
2ylrNAPPhenylacetone monooxygenase1.14.13.920.453
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.453
4dkbDUNDeoxyuridine triphosphatase, putative/0.453
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.453
4uthFMNXenobiotic reductase/0.453
2getCOKPantothenate kinase2.7.1.330.452
2in6839Wee1-like protein kinase2.7.10.20.452
3ewkFADSensory box histidine kinase/response regulator/0.452
3r43ID8Aldo-keto reductase family 1 member C3/0.452
3uayADNPurine nucleoside phosphorylase DeoD-type/0.452
3vrbFTNSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.452
3vrbFTNCytochrome b-large subunit/0.452
5a4vQUEGlutathione S-transferase F22.5.1.180.452
2iko7IGRenin3.4.23.150.451
2jb4A14Isopenicillin N synthase1.21.3.10.451
2tplHPPTyrosine phenol-lyase4.1.99.20.451
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.451
2xupTZ5Acetylcholinesterase3.1.1.70.451
3e23SAMUncharacterized protein/0.451
3qgf46FGenome polyprotein2.7.7.480.451
3ufl508Beta-secretase 13.4.23.460.451
3zoiM2WIsopenicillin N synthase1.21.3.10.451
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.451
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.450
1rxjBNIStreptavidin/0.450
1ygkRRCPyridoxal kinase2.7.1.350.450
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2hzqSTRApolipoprotein D/0.450
4j0v1H7Beta-secretase 13.4.23.460.450
4jeyPLPAcetylornithine/succinyldiaminopimelate aminotransferase2.6.1.110.450
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.450
1d3dBZTProthrombin3.4.21.50.449
2qjpANJCytochrome b/0.449
3rsv3RSBeta-secretase 13.4.23.460.449
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.449
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.449
4dbs0HVAldo-keto reductase family 1 member C3/0.449
4g2wNI0cGMP-specific 3',5'-cyclic phosphodiesterase/0.449
2ipiAKYAclacinomycin-N/aclacinomycin-A oxidase/0.448
3cr0809Wee1-like protein kinase2.7.10.20.448
3pkaY02Methionine aminopeptidase 2/0.448
4acuQN7Beta-secretase 13.4.23.460.448
4bfvZVVPantothenate kinase2.7.1.330.448
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.447
2b82ADNClass B acid phosphatase3.1.3.20.447
2g1a5HGClass B acid phosphatase3.1.3.20.447
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.447
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.447
2ntjP1HEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
2ok8FADFerredoxin--NADP reductase, apicoplast/0.447
3bi6396Wee1-like protein kinase2.7.10.20.447
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3rtnRTNBeta-secretase 13.4.23.460.447
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.447
4bftZVTPantothenate kinase2.7.1.330.447
4fpy0V8Sialidase B3.2.1.180.447
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.447
4i6gFADCryptochrome-2/0.447
4jt81NRNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.447
5ah5LSSLeucine--tRNA ligase/0.447
1b2lNDCAlcohol dehydrogenase1.1.1.10.446
1synF89Thymidylate synthase/0.446
1w06W05Isopenicillin N synthase1.21.3.10.446
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.446
2bu9HFVIsopenicillin N synthase1.21.3.10.446
4b1e6T6Beta-secretase 13.4.23.460.446
4b65NDPL-ornithine N(5)-monooxygenase/0.446
4blcNDPCatalase1.11.1.60.446
4d2dALA_ALA_ALADi-or tripeptide:H+ symporter/0.446
4dz5NAPAldo-keto reductase family 1 member C3/0.446
4eqsCOACoenzyme A disulfide reductase/0.446
4ey6GNTAcetylcholinesterase3.1.1.70.446
4nbjD3YD-tyrosyl-tRNA(Tyr) deacylase/0.446
1q84TZ4Acetylcholinesterase3.1.1.70.445
1u08PLPMethionine aminotransferase/0.445
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
2futH1SHeparin and heparin-sulfate lyase/0.445
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
2w6zL21Biotin carboxylase6.3.4.140.445
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.445
3qdzPRO_ALA_PRO_ARGProthrombin3.4.21.50.445
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.445
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.445
5cmx0G6Prothrombin3.4.21.50.445
1dghNDPCatalase1.11.1.60.444
1lqaNDPProtein tas/0.444
1uwhBAXSerine/threonine-protein kinase B-raf2.7.11.10.444
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
2g1r3IGRenin3.4.23.150.444
2pdj393Aldose reductase1.1.1.210.444
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.444
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3fhxPLPPyridoxal kinase2.7.1.350.444
3fktSIIBeta-secretase 13.4.23.460.444
3nx2FERFerulic acid decarboxylase/0.444
1dduCB3Thymidylate synthase/0.443
1uhhCZPAequorin-2/0.443
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
2qe2452Polyprotein/0.443
2y01Y00Beta-1 adrenergic receptor/0.443
2zseACPPantothenate kinase2.7.1.330.443
3e4aQIXInsulin-degrading enzyme3.4.24.560.443
3qgi33FGenome polyprotein2.7.7.480.443
4htx19FcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.443
4z87GDPInosine-5'-monophosphate dehydrogenase/0.443
1f3eDPZQueuine tRNA-ribosyltransferase2.4.2.290.442
1vfsDCSAlanine racemase/0.442
1ypeUIPProthrombin3.4.21.50.442
2zs8ADPPantothenate kinase2.7.1.330.442
3c6n2S8Protein TRANSPORT INHIBITOR RESPONSE 1/0.442
3gc4AAQQueuine tRNA-ribosyltransferase2.4.2.290.442
4lh71X8DNA ligase/0.442
4xt8TMQPossible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc/0.442
1dduDDUThymidylate synthase/0.441
1ry0PG2Aldo-keto reductase family 1 member C3/0.441
1votHUPAcetylcholinesterase3.1.1.70.441
1yqzCOACoenzyme A disulfide reductase/0.441
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.441
2pb1NFGGlucan 1,3-beta-glucosidase/0.441
2vqqTFGHistone deacetylase 43.5.1.980.441
2x86ADPADP-L-glycero-D-manno-heptose-6-epimerase/0.441
2zevIPEGeranylgeranyl pyrophosphate synthase/0.441
3b7dCNIGlutamate receptor 2/0.441
3b9oFMNAlkane monoxygenase/0.441
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.441
3gfbNADL-threonine 3-dehydrogenase/0.441
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.441
4j7gTRHPCZA361.3/0.441
4l091URTankyrase-22.4.2.300.441
4to2DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.441
4yx6FMNOmega-3 polyunsaturated fatty acid synthase subunit PfaD/0.441
8catNDPCatalase1.11.1.60.441
5d5aCAUBeta-2 adrenergic receptor/0.441
1ychFMNNitric oxide reductase10.440
2a5c8DAAvidin/0.440
2w6cBM4Acetylcholinesterase3.1.1.70.440
2zevB71Geranylgeranyl pyrophosphate synthase/0.440
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.440
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.440
3dz2A8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.440
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3opmLUIDipeptidyl peptidase 4/0.440
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.440
3w78CBDFMN-dependent NADH-azoreductase/0.440
4cthRDFNeprilysin/0.440
4e32DWNMethyltransferase/0.440
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.440
3pblETQD(3) dopamine receptor/0.440