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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
1dp2LPBThiosulfate sulfurtransferase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1dp2LPBThiosulfate sulfurtransferase/1.000
4uz6SCRPalmitoleoyl-protein carboxylesterase NOTUM/0.504
1rvvINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.503
2gevCOKPantothenate kinase2.7.1.330.502
5aglH4BNitric oxide synthase, brain1.14.13.390.500
4fvzH4BNitric oxide synthase, brain1.14.13.390.497
1pt8ACOFormyl-CoA:oxalate CoA-transferase/0.496
3af1GDPPantothenate kinase2.7.1.330.491
3jtaH4BNitric oxide synthase, brain1.14.13.390.491
2zs9ADPPantothenate kinase2.7.1.330.489
2zsaADPPantothenate kinase2.7.1.330.488
3inrGDUUDP-galactopyranose mutase5.4.99.90.486
2mjiKTRFatty acid-binding protein, intestinal/0.484
3q9aH4BNitric oxide synthase, brain1.14.13.390.483
1fmjRTLRetinol dehydratase/0.480
3px3T3QdTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase2.1.1.2350.479
4kq1U5PGlycogen [starch] synthase/0.479
3dr7GPDGDP-perosamine synthase/0.478
3jt4H4BNitric oxide synthase, brain1.14.13.390.478
1hb3SCVIsopenicillin N synthase1.21.3.10.476
2zs8ADPPantothenate kinase2.7.1.330.476
3frkTQPQdtB/0.476
3zoiM2WIsopenicillin N synthase1.21.3.10.475
5agkH4BNitric oxide synthase, brain1.14.13.390.475
2y60M8FIsopenicillin N synthase1.21.3.10.474
3jt6H4BNitric oxide synthase, brain1.14.13.390.474
2geuCOKPantothenate kinase2.7.1.330.473
3q7fED2Uncharacterized protein/0.473
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.473
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.473
3hgoFMN12-oxophytodienoate reductase 31.3.1.420.471
4lez1SYCyclic GMP-AMP synthase/0.471
2gesCOKPantothenate kinase2.7.1.330.469
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.469
4k88HFGBifunctional glutamate/proline--tRNA ligase6.1.1.150.469
1pt5ACOFormyl-CoA:oxalate CoA-transferase/0.468
1qiqACCIsopenicillin N synthase1.21.3.10.468
4esoNAPPutative oxidoreductase/0.468
3c8aARG_ARG_GLY_LEU_NH2Botulinum neurotoxin type A3.4.24.690.467
1qjfACSIsopenicillin N synthase1.21.3.10.466
3zkyWT4Isopenicillin N synthase1.21.3.10.466
3af3GCPPantothenate kinase2.7.1.330.465
3jt3H4BNitric oxide synthase, brain1.14.13.390.465
1eyyNAPNADP-dependent fatty aldehyde dehydrogenase1.2.1.40.464
4gtv7TRGeranylgeranyl transferase type-2 subunit beta2.5.1.600.464
2bu9HFVIsopenicillin N synthase1.21.3.10.463
2xeiARKGlutamate carboxypeptidase 23.4.17.210.463
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.463
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.463
1k9sFM1Purine nucleoside phosphorylase DeoD-type/0.462
2vbdV10Isopenicillin N synthase1.21.3.10.462
2vcmM11Isopenicillin N synthase1.21.3.10.462
3mz9BHNNickel-binding periplasmic protein/0.462
4dya0MFNucleoprotein/0.462
4k5eH4BNitric oxide synthase, brain1.14.13.390.462
3h4vNAPPteridine reductase 11.5.1.330.461
3pfhT3QdTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase2.1.1.2350.461
5brpPNGGlycoside Hydrolase Family 13/0.461
2g6j7APNitric oxide synthase, brain1.14.13.390.460
2wgs1AZGlutamine synthetase6.3.1.20.460
3sopGDPNeuronal-specific septin-3/0.460
1blzACVIsopenicillin N synthase1.21.3.10.459
1sa5BMVProtein farnesyltransferase subunit beta2.5.1.580.459
1zisINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.459
2po3T4K4-dehydrase/0.459
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.459
3fufBESLeukotriene A-4 hydrolase3.3.2.60.459
3rykTYDdTDP-4-dehydrorhamnose 3,5-epimerase/0.459
4uthFMNXenobiotic reductase/0.458
1evjNADGlucose--fructose oxidoreductase1.1.99.280.457
1mmvH4BNitric oxide synthase, brain1.14.13.390.456
1tojHCIAspartate aminotransferase2.6.1.10.456
2lbvEB4Extracellular fatty acid-binding protein/0.456
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.456
1e64FADFerredoxin--NADP reductase1.18.1.20.455
2bxoOPBSerum albumin/0.455
4j7gTRHPCZA361.3/0.455
1hb1OCVIsopenicillin N synthase1.21.3.10.454
1yw8A75Methionine aminopeptidase 2/0.454
3buzTADIota toxin component Ia/0.454
3nksACJProtoporphyrinogen oxidase1.3.3.40.454
3pz43PZProtein farnesyltransferase subunit beta2.5.1.580.454
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.454
4m2bUPGUDP-glucose pyrophosphorylase/0.454
5cc9DDFDihydrofolate reductase1.5.1.30.454
1u1gBBBUridine phosphorylase2.4.2.30.453
2apcUDMAlpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase2.4.1.1010.453
4fm80UQBeta-secretase 13.4.23.460.453
5c3rHMUThymine dioxygenase/0.453
1pnqNDPNAD(P) transhydrogenase subunit beta1.6.1.20.452
2cjeDUNDUTPase/0.452
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.452
2ix5CAAAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.452
2vbpVB1Isopenicillin N synthase1.21.3.10.452
2zsbADPPantothenate kinase2.7.1.330.452
3dr4G4MGDP-perosamine synthase/0.452
3v0o4GWHisto-blood group ABO system transferase/0.452
3wthIM4Acetylcholine-binding protein/0.452
1lrkUD1UDP-glucose 4-epimerase5.1.3.20.451
1zvlH4BNitric oxide synthase, brain1.14.13.390.451
1zzrH4BNitric oxide synthase, brain1.14.13.390.451
2h8xFMNXenA/0.451
2jb4A14Isopenicillin N synthase1.21.3.10.451
4d6qPD2Lysine-specific demethylase 4D1.14.110.451
2ehuNAD1-pyrroline-5-carboxylate dehydrogenase/0.450
2wwjY28Lysine-specific demethylase 4A/0.450
3jq3ADPLombricine kinase/0.450
4wx2F6FTryptophan synthase alpha chain/0.450
4wx2F6FTryptophan synthase beta chain4.2.1.200.450
1nhkCMPNucleoside diphosphate kinase2.7.4.60.449
2getCOKPantothenate kinase2.7.1.330.449
2uxoTACHTH-type transcriptional regulator TtgR/0.449
3l5lFMNXenobiotic reductase/0.449
3n19FNRXenobiotic reductase/0.449
3p8iFMNPentaerythritol tetranitrate reductase/0.449
1tw2ERTCarminomycin 4-O-methyltransferase DnrK2.1.1.2920.448
4a3uFMNNADH:flavin oxidoreductase/NADH oxidase/0.448
4h6pFMNChromate reductase/0.448
4tyqAP5Adenylate kinase/0.448
1om5H4BNitric oxide synthase, brain1.14.13.390.447
1xr2C2F5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase2.1.1.140.447
1yunATPProbable nicotinate-nucleotide adenylyltransferase2.7.7.180.447
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.447
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.447
2zsdCOAPantothenate kinase2.7.1.330.447
3l05SN0N-acetylornithine carbamoyltransferase2.1.3.90.447
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.447
4gi40EXQueuine tRNA-ribosyltransferase2.4.2.290.447
4h6kFMNNADPH dehydrogenase 11.6.99.10.447
4kfqKFQGlutamate receptor ionotropic, NMDA 1/0.447
1obnASVIsopenicillin N synthase1.21.3.10.446
2jl1NAPTriphenylmethane reductase/0.446
3af0GDPPantothenate kinase2.7.1.330.446
3n14FMNXenobiotic reductase/0.446
3n5wXFJNitric oxide synthase, brain1.14.13.390.446
3otwCOAPhosphopantetheine adenylyltransferase/0.446
3tycXHPDihydropteroate synthase/0.446
4cx4H4BNitric oxide synthase, brain1.14.13.390.446
4e2yJHZMethyltransferase/0.446
4e2zJHZMethyltransferase/0.446
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.446
1e0jANPDNA primase/helicase2.7.70.445
1icpFMN12-oxophytodienoate reductase 11.3.1.420.445
1orrCDPCDP-paratose 2-epimerase/0.445
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.445
1qomH4BNitric oxide synthase, inducible1.14.13.390.445
2c92TP66,7-dimethyl-8-ribityllumazine synthase2.5.1.780.445
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.445
3kroIPEGeranyl diphosphate synthase large subunit/0.445
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.445
4lv5ADPRhoptry protein 5B/0.445
4rnvFMNNADPH dehydrogenase 11.6.99.10.445
1el4CTZObelin/0.444
1gtiGTBGlutathione S-transferase P 12.5.1.180.444
2eixFADNADH-cytochrome b5 reductase/0.444
2imkGTXAGAP009194-PA/0.444
3g4kROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
3qpg3QPAspartate aminotransferase2.6.1.10.444
3rtnRTNBeta-secretase 13.4.23.460.444
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.444
4qx5CMPcGMP-dependent protein kinase 12.7.11.120.444
5choFADFlavin reductase/0.444
1ahgTYR_PLPAspartate aminotransferase2.6.1.10.443
1esmCOAPantothenate kinase2.7.1.330.443
1icqFMN12-oxophytodienoate reductase 11.3.1.420.443
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.443
2r59PH0Leukotriene A-4 hydrolase3.3.2.60.443
3aezGDPPantothenate kinase2.7.1.330.443
3ftxBESLeukotriene A-4 hydrolase3.3.2.60.443
3l67FMNXenobiotic reductase/0.443
3zrrPXGSerine-pyruvate aminotransferase (AgxT)/0.443
4d1oH4BNitric oxide synthase, endothelial1.14.13.390.443
4tnpDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.443
4zm3PLPAminotransferase/0.443
1akcPPEAspartate aminotransferase, mitochondrial2.6.1.10.442
1h6aNDPGlucose--fructose oxidoreductase1.1.99.280.442
1n0sFLUBilin-binding protein/0.442
1x8lOXRRetinol dehydratase/0.442
2c9bPUG6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
2ixkTDOdTDP-4-dehydrorhamnose 3,5-epimerase5.1.3.130.442
2o6hINI6,7-dimethyl-8-ribityllumazine synthase 12.5.1.780.442
3fx6BPXCarboxypeptidase A13.4.17.10.442
3hggCHDCmeR/0.442
3pz23PZGeranylgeranyl transferase type-2 subunit beta2.5.1.600.442
4k97ATPCyclic GMP-AMP synthase/0.442
1amoFMNNADPH--cytochrome P450 reductase/0.441
1lb9DNQGlutamate receptor 2/0.441
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
2poqISDTrans-1,2-dihydrobenzene-1,2-diol dehydrogenase1.3.1.200.441
2rqfJH3Hemolymph juvenile hormone binding protein/0.441
3fr5I4AFatty acid-binding protein, adipocyte/0.441
3n66XFNNitric oxide synthase, brain1.14.13.390.441
3to3ATPPetrobactin biosynthesis protein AsbB/0.441
3zlmANPAdenosine monophosphate-protein transferase NmFic2.7.7.n10.441
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.441
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.440
1y56FMNUncharacterized protein/0.440
1y56FMN382aa long hypothetical sarcosine oxidase/0.440
2iviACWIsopenicillin N synthase1.21.3.10.440
2lfoGCHFatty acid-binding protein, liver/0.440
2y05RALProstaglandin reductase 1/0.440
3af4GCPPantothenate kinase2.7.1.330.440
3e30ED4Protein farnesyltransferase subunit beta2.5.1.580.440
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.440
4d2cALA_PHEDi-or tripeptide:H+ symporter/0.440
4hn1TYDdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.440
4jyzATPGlutamine--tRNA ligase6.1.1.180.440
4xouACPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.440