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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
1by5GLY_GLY_GLY_AHO_AHO_AHO_FEFerrichrome-iron receptor

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1by5GLY_GLY_GLY_AHO_AHO_AHO_FEFerrichrome-iron receptor/1.000
2j3qTFLAcetylcholinesterase3.1.1.70.528
2wzySQXSoluble acetylcholine receptor/0.505
1odcA8BAcetylcholinesterase3.1.1.70.502
1zgbA1EAcetylcholinesterase3.1.1.70.500
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.500
2gyuHI6Acetylcholinesterase3.1.1.70.498
1qtiGNTAcetylcholinesterase3.1.1.70.495
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.490
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.490
2cekN8TAcetylcholinesterase3.1.1.70.488
2xuoTZ4Acetylcholinesterase3.1.1.70.488
4b7zQ4QAcetylcholinesterase3.1.1.70.488
1w6rGNTAcetylcholinesterase3.1.1.70.485
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.485
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.483
2w6cBM4Acetylcholinesterase3.1.1.70.482
3mj4URMUDP-galactopyranose mutase/0.481
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.481
2gv8NDPThiol-specific monooxygenase1.14.130.480
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.480
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.480
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.479
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.478
2aot2PMHistamine N-methyltransferase2.1.1.80.478
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.478
4arbC57Acetylcholinesterase3.1.1.70.478
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.476
3zv7NHGAcetylcholinesterase3.1.1.70.476
4j4nD44Peptidylprolyl isomerase/0.475
1x1aSAMC-20 methyltransferase/0.474
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.474
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.474
1eveE20Acetylcholinesterase3.1.1.70.473
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.473
2ha6SCKAcetylcholinesterase3.1.1.70.473
2xytTC9Soluble acetylcholine receptor/0.471
3q9bB3NAcetylpolyamine amidohydrolase/0.471
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.471
1h22E10Acetylcholinesterase3.1.1.70.470
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.469
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.469
3aezGDPPantothenate kinase2.7.1.330.468
3v0p4GWHisto-blood group ABO system transferase/0.468
2ga2A19Methionine aminopeptidase 2/0.467
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
3pqbVGPPutative oxidoreductase/0.467
4to1DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.467
1u65CP0Acetylcholinesterase3.1.1.70.466
2xupTZ5Acetylcholinesterase3.1.1.70.466
3c3xNAPEugenol synthase 11.1.1.3180.466
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.466
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.466
4qfyDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.465
1enoNADEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.464
1w4lGL8Acetylcholinesterase3.1.1.70.464
2ea2F77Methionine aminopeptidase 2/0.464
2whqHI6Acetylcholinesterase3.1.1.70.464
3wqmB29Diterpene synthase3.1.7.80.464
4araC56Acetylcholinesterase3.1.1.70.464
4mlp2CXCryptochrome-2/0.464
4psbGA3Cytokinin-specific binding protein/0.464
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
3gf4UPGUDP-galactopyranose mutase5.4.99.90.463
3v2uATPProtein GAL3/0.463
1icqOPD12-oxophytodienoate reductase 11.3.1.420.462
1kw0H4BPhenylalanine-4-hydroxylase1.14.16.10.462
4a83DXCMajor pollen allergen Bet v 1-A/0.462
1nj6A5AProline--tRNA ligase/0.461
1yw8A75Methionine aminopeptidase 2/0.460
2xuhTZ4Acetylcholinesterase3.1.1.70.460
3frkTQPQdtB/0.460
4bzbDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.460
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.459
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.459
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.459
3zhuTD8Multifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.458
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.457
2xnvVU3Soluble acetylcholine receptor/0.457
2xuiTZ5Acetylcholinesterase3.1.1.70.457
3h3qH13Collagen type IV alpha-3-binding protein/0.457
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.457
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.456
1q84TZ4Acetylcholinesterase3.1.1.70.456
2ggbU17Methionine aminopeptidase/0.456
3fuhBESLeukotriene A-4 hydrolase3.3.2.60.456
5d5aCAUBeta-2 adrenergic receptor/0.456
5jqhCAUBeta-2 adrenergic receptor/0.456
2ckmAA7Acetylcholinesterase3.1.1.70.455
3apwDP0Alpha-1-acid glycoprotein 2/0.455
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.455
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.455
4lutDCSAlanine racemase/0.455
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.454
1r5gAO1Methionine aminopeptidase 2/0.454
1szgFNSCytochrome b2, mitochondrial1.1.2.30.454
2qimZEAClass 10 plant pathogenesis-related protein/0.454
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
5c1gGDUHisto-blood group ABO system transferase/0.454
2q94A04Methionine aminopeptidase/0.453
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
1gpnHUBAcetylcholinesterase3.1.1.70.452
1t7o152Carnitine O-acetyltransferase2.3.1.70.452
1yw7A41Methionine aminopeptidase 2/0.452
1yw9A84Methionine aminopeptidase 2/0.452
2iko7IGRenin3.4.23.150.452
2npfMOUElongation factor 2/0.452
2q92B23Methionine aminopeptidase/0.452
2xi4AFTAcetylcholinesterase3.1.1.70.452
3d27W29Methionine aminopeptidase/0.452
4j7hTRHPCZA361.3/0.452
4xo7NAPAldo-keto reductase family 1 member C2/0.452
1ejeFMNProtein MTH_152/0.451
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.451
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
2evcFC3Methionine aminopeptidase/0.451
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.451
2ikuLIYRenin3.4.23.150.451
2q93B21Methionine aminopeptidase/0.451
3af0GDPPantothenate kinase2.7.1.330.451
3hl0NADMaleylacetate reductase/0.451
3zhvTDWMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.451
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.451
4flkY10Methionine aminopeptidase 1/0.451
4m0f1YKAcetylcholinesterase3.1.1.70.451
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.450
3hdyGDUUDP-galactopyranose mutase/0.450
3pkeY10Methionine aminopeptidase 2/0.450
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.450
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.450
4fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.450
4fapARDSerine/threonine-protein kinase mTOR2.7.11.10.450
1obnASVIsopenicillin N synthase1.21.3.10.449
1z71L17Prothrombin3.4.21.50.449
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.449
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.449
4qfzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.449
1gj4132Prothrombin3.4.21.50.448
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.448
2aouCQAHistamine N-methyltransferase2.1.1.80.448
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4jiq1L5GTN Reductase/0.448
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.448
1dx6GNTAcetylcholinesterase3.1.1.70.447
1e66HUXAcetylcholinesterase3.1.1.70.447
1gveNAPAflatoxin B1 aldehyde reductase member 310.447
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.447
2evmFC2Methionine aminopeptidase/0.447
2xugTZ4Acetylcholinesterase3.1.1.70.447
4lcnGNGCytidine and deoxycytidylate deaminase zinc-binding region/0.447
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.446
1ja1FMNNADPH--cytochrome P450 reductase/0.446
1votHUPAcetylcholinesterase3.1.1.70.446
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.446
3ivcFG4Pantothenate synthetase6.3.2.10.446
4iah1DXAlr2278 protein/0.446
4n1gCEIObelin/0.446
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.445
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.445
1w76GNTAcetylcholinesterase3.1.1.70.445
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.445
2gywOBIAcetylcholinesterase3.1.1.70.445
3af1GDPPantothenate kinase2.7.1.330.445
3cavCI23-oxo-5-beta-steroid 4-dehydrogenase/0.445
4kxjP34Nucleoprotein/0.445
1q83TZ5Acetylcholinesterase3.1.1.70.444
1vftDCSAlanine racemase/0.444
1x1bSAHC-20 methyltransferase/0.444
2xlpFADPutative flavin-containing monooxygenase/0.444
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.444
3eq6BCOAcyl-coenzyme A synthetase ACSM2A, mitochondrial6.2.1.20.444
4dc0NDPPutative ketoacyl reductase1.3.10.444
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.444
2x92X92Angiotensin-converting enzyme3.4.15.10.443
3bl7DD1m7GpppX diphosphatase3.6.1.590.443
3c1oNAPEugenol synthase/0.443
3ei8PL5LL-diaminopimelate aminotransferase, chloroplastic/0.443
3h3t16HCollagen type IV alpha-3-binding protein/0.443
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.443
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3uzxAOM3-oxo-5-beta-steroid 4-dehydrogenase/0.443
4tnyDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.443
4gbrCAUBeta-2 adrenergic receptor/0.443
1r58AO5Methionine aminopeptidase 2/0.442
1s4pGDPGlycolipid 2-alpha-mannosyltransferase/0.442
2b3dFADModulator of drug activity B/0.442
2zs8ADPPantothenate kinase2.7.1.330.442
4a8v2ANMajor pollen allergen Bet v 1-J/0.442
4bfuZVUPantothenate kinase2.7.1.330.442
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.442
1gj5130Prothrombin3.4.21.50.441
1xr2C2F5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase2.1.1.140.441
2bf4FADNADPH--cytochrome P450 reductase/0.441
2jj2ANPATP synthase subunit beta, mitochondrial3.6.3.140.441
2pncCLUPrimary amine oxidase, liver isozyme/0.441
3h7rNAPAldo-keto reductase family 4 member C8/0.441
1a9cGTPGTP cyclohydrolase 13.5.4.160.440
2g247IGRenin3.4.23.150.440
2jf0HBPAcetylcholinesterase3.1.1.70.440
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.440
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.440
2xuqTZ4Acetylcholinesterase3.1.1.70.440
3bxoUPPdTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose/0.440
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.440
3mjrAC2Deoxycytidine kinase2.7.1.740.440
3mztTFXBeta-2-microglobulin/0.440
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.440
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.440