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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
4lcw1VYMajor histocompatibility complex class I-related gene protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
4lcw1VYMajor histocompatibility complex class I-related gene protein/1.000
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.510
2iviACWIsopenicillin N synthase1.21.3.10.505
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.505
1hb1OCVIsopenicillin N synthase1.21.3.10.504
1hb3SCVIsopenicillin N synthase1.21.3.10.503
4l4v1VYMajor histocompatibility complex class I-related gene protein/0.503
1x1cSAHC-20 methyltransferase/0.502
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.499
1qiqACCIsopenicillin N synthase1.21.3.10.495
1obnASVIsopenicillin N synthase1.21.3.10.494
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.493
1bk0ACVIsopenicillin N synthase1.21.3.10.491
1oc1ASVIsopenicillin N synthase1.21.3.10.491
3zkyWT4Isopenicillin N synthase1.21.3.10.491
4bb3KKAIsopenicillin N synthase1.21.3.10.486
3wqmB29Diterpene synthase3.1.7.80.485
2xejOKDGlutamate carboxypeptidase 23.4.17.210.484
4to1DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.484
5dp2NAPCurF/0.484
4ybnFADFlavin-nucleotide-binding protein/0.482
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.481
2vbpVB1Isopenicillin N synthase1.21.3.10.481
3s5wFADL-ornithine N(5)-monooxygenase/0.479
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.479
4mqt2CUMuscarinic acetylcholine receptor M2/0.479
2xegCI9Glutamate carboxypeptidase 23.4.17.210.478
2jb4A14Isopenicillin N synthase1.21.3.10.477
2zsdCOAPantothenate kinase2.7.1.330.477
4nv1TYDFormyl transferase/0.477
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.476
3zkuHCVIsopenicillin N synthase1.21.3.10.476
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.476
1wkgPOI[LysW]-aminoadipate semialdehyde transaminase/0.475
3irhDTPHD domain protein/0.475
4eqrCOACoenzyme A disulfide reductase/0.475
1blzACVIsopenicillin N synthase1.21.3.10.473
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.473
2oatPFMOrnithine aminotransferase, mitochondrial2.6.1.130.472
2wo7ASVIsopenicillin N synthase1.21.3.10.472
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.472
4to4DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.472
2vbdV10Isopenicillin N synthase1.21.3.10.471
2y60M8FIsopenicillin N synthase1.21.3.10.471
4qg1DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.471
4wbdADPPutative cysteine ligase BshC/0.471
1jdzFMBPurine nucleoside phosphorylase/0.470
1qjfACSIsopenicillin N synthase1.21.3.10.470
2y6fM9FIsopenicillin N synthase1.21.3.10.470
4bfxZVXPantothenate kinase2.7.1.330.468
1qs2NADVip2Ac/0.466
2b8jADNClass B acid phosphatase3.1.3.20.466
3hmvHBTcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.466
4rxpDTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.466
5cxv0HKMuscarinic acetylcholine receptor M1/0.466
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.465
1yhjR6CPyridoxal kinase2.7.1.350.465
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.465
5d6lCAUBeta-2 adrenergic receptor/0.465
1dgbNDPCatalase1.11.1.60.464
1k4gAIQQueuine tRNA-ribosyltransferase2.4.2.290.464
2iu8UD1UDP-3-O-acylglucosamine N-acyltransferase2.3.10.464
3zoiM2WIsopenicillin N synthase1.21.3.10.464
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.464
2gesCOKPantothenate kinase2.7.1.330.463
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.463
1w06W05Isopenicillin N synthase1.21.3.10.462
3uayADNPurine nucleoside phosphorylase DeoD-type/0.462
4b65NDPL-ornithine N(5)-monooxygenase/0.462
2ycxP32Beta-1 adrenergic receptor/0.462
3mhpFADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.461
4uugPXGBranched-chain amino acid aminotransferase, putative/0.461
4j7hTRHPCZA361.3/0.460
4rxrDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.460
1pr4MTPPurine nucleoside phosphorylase DeoD-type/0.459
1ry0PG2Aldo-keto reductase family 1 member C3/0.459
2xeiARKGlutamate carboxypeptidase 23.4.17.210.459
3ufl508Beta-secretase 13.4.23.460.459
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.459
3ziaADPATP synthase subunit beta, mitochondrial3.6.3.140.459
4nwiCTN7-methylguanosine phosphate-specific 5'-nucleotidase/0.459
4xwtU5PRibonuclease J/0.459
1isgAGSADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 23.2.2.60.458
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.458
4j0v1H7Beta-secretase 13.4.23.460.458
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.457
2getCOKPantothenate kinase2.7.1.330.457
2zevIPEGeranylgeranyl pyrophosphate synthase/0.457
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.457
5d5aCAUBeta-2 adrenergic receptor/0.457
1cnfFADNitrate reductase [NADH]1.7.1.10.456
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.456
2iko7IGRenin3.4.23.150.456
3b7dCNIGlutamate receptor 2/0.456
5a4vQUEGlutathione S-transferase F22.5.1.180.456
2g8yNADHydroxycarboxylate dehydrogenase B/0.455
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.455
2ylrNAPPhenylacetone monooxygenase1.14.13.920.455
3e4aQIXInsulin-degrading enzyme3.4.24.560.455
3pm1ETHTH-type transcriptional regulator QacR/0.455
3rsv3RSBeta-secretase 13.4.23.460.455
4dbs0HVAldo-keto reductase family 1 member C3/0.455
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
2b82ADNClass B acid phosphatase3.1.3.20.454
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.454
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.454
2xuqTZ4Acetylcholinesterase3.1.1.70.454
3g4kROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.454
4isuIKMGlutamate receptor 2/0.454
2g1a5HGClass B acid phosphatase3.1.3.20.453
2in6839Wee1-like protein kinase2.7.10.20.453
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.453
2xysSY9Soluble acetylcholine receptor/0.453
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.453
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.453
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.453
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.453
4yfy0FXVioF/0.453
2rh1CAUBeta-2 adrenergic receptor/0.453
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.452
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.452
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.452
3ewkFADSensory box histidine kinase/response regulator/0.452
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.452
4kfqKFQGlutamate receptor ionotropic, NMDA 1/0.452
4nbjD3YD-tyrosyl-tRNA(Tyr) deacylase/0.452
4to3DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.452
1vfsDCSAlanine racemase/0.451
1z5uCMPClass B acid phosphatase/0.451
2xupTZ5Acetylcholinesterase3.1.1.70.451
3q9bB3NAcetylpolyamine amidohydrolase/0.451
3qgf46FGenome polyprotein2.7.7.480.451
3w78CBDFMN-dependent NADH-azoreductase/0.451
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.451
4drhRAPSerine/threonine-protein kinase mTOR2.7.11.10.451
4drhRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.451
4ey6GNTAcetylcholinesterase3.1.1.70.451
4u140HKMuscarinic acetylcholine receptor M3/0.451
1d3dBZTProthrombin3.4.21.50.450
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.450
1ypeUIPProthrombin3.4.21.50.450
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2aouCQAHistamine N-methyltransferase2.1.1.80.450
3rtnRTNBeta-secretase 13.4.23.460.450
3ska053Genome polyprotein2.7.7.480.450
4b1e6T6Beta-secretase 13.4.23.460.450
3d4sTIMBeta-2 adrenergic receptor/0.450
1c7oPPGHemolysin/0.449
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.449
1x1bSAHC-20 methyltransferase/0.449
3bi6396Wee1-like protein kinase2.7.10.20.449
3cr0809Wee1-like protein kinase2.7.10.20.449
3cv9VDXVitamin D3 dihydroxylase/0.449
3fktSIIBeta-secretase 13.4.23.460.449
3ihgVAKAklavinone 12-hydroxylase RdmE/0.449
4c2z646Glycylpeptide N-tetradecanoyltransferase 1/0.449
4fam0SZAldo-keto reductase family 1 member C3/0.449
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.448
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
2ipiAKYAclacinomycin-N/aclacinomycin-A oxidase/0.448
2q153MRBeta-secretase 13.4.23.460.448
3pkaY02Methionine aminopeptidase 2/0.448
3rviRVIBeta-secretase 13.4.23.460.448
4bftZVTPantothenate kinase2.7.1.330.448
4hhz15SPoly [ADP-ribose] polymerase 12.4.2.300.448
4qfzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.448
5f54TMPSingle-stranded-DNA-specific exonuclease/0.448
1yqzCOACoenzyme A disulfide reductase/0.447
2gpjFADSiderophore-interacting protein/0.447
2ok8FADFerredoxin--NADP reductase, apicoplast/0.447
3zhvTDWMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.447
4dkbDUNDeoxyuridine triphosphatase, putative/0.447
4htx19FcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.447
4to2DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.447
1q9mROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
1synF89Thymidylate synthase/0.446
1tllFMNNitric oxide synthase, brain1.14.13.390.446
1yplRA8Prothrombin3.4.21.50.446
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.446
3fsjD7KBenzoylformate decarboxylase4.1.1.70.446
3r7mSUZAldo-keto reductase family 1 member C3/0.446
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.445
1q84TZ4Acetylcholinesterase3.1.1.70.445
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
2futH1SHeparin and heparin-sulfate lyase/0.445
3br3ETHTH-type transcriptional regulator QacR/0.445
3c49KU8Poly [ADP-ribose] polymerase 32.4.2.300.445
4eqsCOACoenzyme A disulfide reductase/0.445
4rxsTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.445
8catNDPCatalase1.11.1.60.445
1dduCB3Thymidylate synthase/0.444
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.444
1kyyINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.444
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
1rpwDIDHTH-type transcriptional regulator QacR/0.444
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.444
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.444
2pdj393Aldose reductase1.1.1.210.444
2pj4414Carboxypeptidase B/0.444
2w6cBM4Acetylcholinesterase3.1.1.70.444
2x86ADPADP-L-glycero-D-manno-heptose-6-epimerase/0.444
4e2yJHZMethyltransferase/0.444
4e32DWNMethyltransferase/0.444
4frjDWBBeta-secretase 13.4.23.460.444
4jt81NRNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.444
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.444
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.443
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.443
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.443
1uhhCZPAequorin-2/0.443
1ychFMNNitric oxide reductase10.443
2gv8NDPThiol-specific monooxygenase1.14.130.443
3arvSAUChitinase A/0.443
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3gc4AAQQueuine tRNA-ribosyltransferase2.4.2.290.443
3uyk0CXProbable NDP-rhamnosyltransferase/0.443
4b5nFMNNAD(P)H:flavin oxidoreductase Sye4/0.443
4bfvZVVPantothenate kinase2.7.1.330.443
4bfwZVWPantothenate kinase2.7.1.330.443
4e2zJHZMethyltransferase/0.443
4j7gTRHPCZA361.3/0.443
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.443
4ttjFMCPurine nucleoside phosphorylase DeoD-type/0.443
5a4wQCTGlutathione S-transferase F22.5.1.180.443
5d4vYGPUncharacterized protein MJ0489/0.443
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.442
3af0GDPPantothenate kinase2.7.1.330.442
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.442
4da6GA2Purine nucleoside phosphorylase DeoD-type2.4.2.10.442
4xt8TMQPossible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc/0.442
1d3pBT3Prothrombin3.4.21.50.441
1ut6A8NAcetylcholinesterase3.1.1.70.441
1ygjRMCPyridoxal kinase2.7.1.350.441
1z71L17Prothrombin3.4.21.50.441
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.441
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
2pb1NFGGlucan 1,3-beta-glucosidase/0.441
2zevB71Geranylgeranyl pyrophosphate synthase/0.441
3fhxPLPPyridoxal kinase2.7.1.350.441
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.441
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.441
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.441
4h3j10WBeta-secretase 13.4.23.460.441
4l091URTankyrase-22.4.2.300.441
5dozNDPJamJ/0.441
5d5bCAUBeta-2 adrenergic receptor/0.441
1gaqFADFerredoxin/0.440
1kyvRBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
1s1rNAPAldo-keto reductase family 1 member C3/0.440
2a5c8DAAvidin/0.440
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.440
3dz2A8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.440
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
3opmLUIDipeptidyl peptidase 4/0.440
3zpqXF5Beta-1 adrenergic receptor/0.440
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4ax9N5NProthrombin3.4.21.50.440
4b66FADL-ornithine N(5)-monooxygenase/0.440
4cthRDFNeprilysin/0.440
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.440
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.440
4dya0MFNucleoprotein/0.440
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4u163C0Muscarinic acetylcholine receptor M3/0.440