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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
1a59COA2-methylcitrate synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1a59COA2-methylcitrate synthase/1.000
6ctsCICCitrate synthase, mitochondrial2.3.3.10.619
5ctsCMCCitrate synthase, mitochondrial2.3.3.10.609
1cscCMCCitrate synthase, mitochondrial2.3.3.10.605
3cscACOCitrate synthase, mitochondrial2.3.3.10.605
2r26CMCCitrate synthase2.3.3.160.593
2r9eSDXCitrate synthase2.3.3.160.578
2ctsCOACitrate synthase, mitochondrial2.3.3.10.552
2h12CMXCitrate synthase/0.542
1aj8COACitrate synthase/0.506
2fy4COACholine O-acetyltransferase2.3.1.60.496
3a3gDLZLumazine protein/0.493
4m83ERYOleandomycin glycosyltransferase2.4.10.489
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.486
3qt62P0Mevalonate diphosphate decarboxylase/0.485
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.481
4jicFMNGTN Reductase/0.480
1culFOKAdenylate cyclase type 2/0.476
1culFOKAdenylate cyclase type 5/0.476
4lcjNADC-terminal-binding protein 2/0.475
1xvaSAMGlycine N-methyltransferase2.1.1.200.474
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.474
1xddAAYIntegrin alpha-L/0.471
3b1dPLSBetaC-S lyase/0.471
2gvdFKPAdenylate cyclase type 2/0.470
2gvdFKPAdenylate cyclase type 5/0.470
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.470
2w6zL21Biotin carboxylase6.3.4.140.470
4df2FMNNADPH dehydrogenase/0.470
4dptAGSMevalonate diphosphate decarboxylase/0.470
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.470
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.469
2q85973UDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.469
3gkaFMNN-ethylmaleimide reductase/0.469
3q9bB3NAcetylpolyamine amidohydrolase/0.469
1h50FMNPentaerythritol tetranitrate reductase/0.468
1x1bSAHC-20 methyltransferase/0.468
1xe55FEPlasmepsin-23.4.23.390.468
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.468
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.468
2g8yNADHydroxycarboxylate dehydrogenase B/0.467
2yd0BESEndoplasmic reticulum aminopeptidase 13.4.110.467
3in6FMNUncharacterized protein/0.467
3td7FADProbable FAD-linked sulfhydryl oxidase R5961.8.3.20.467
4qaiFMNNADPH dehydrogenase/0.467
4xbjIN5Alanine racemase, biosynthetic/0.467
1udaUFGUDP-glucose 4-epimerase5.1.3.20.466
1vbiNADMalate/L-lactate dehydrogenase family protein/0.465
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
5dn1AMZPhosphoribosyl isomerase A5.3.1.160.464
2huxSAHDiphthine synthase/0.463
2q7vFADThioredoxin reductase/0.463
3fr5I4AFatty acid-binding protein, adipocyte/0.463
4dpy2P0Mevalonate diphosphate decarboxylase/0.463
2iyfERYOleandomycin glycosyltransferase2.4.10.462
3gegNADShort-chain dehydrogenase/reductase SDR/0.462
3junAKDPhenazine biosynthesis protein A/B/0.462
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.462
1rszDIHPurine nucleoside phosphorylase2.4.2.10.461
2oapANPType II secretion system protein (GspE-2)/0.461
2omeNADC-terminal-binding protein 2/0.461
3aezGDPPantothenate kinase2.7.1.330.461
3v2uATPProtein GAL3/0.461
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3hlwCE3Beta-lactamase/0.460
3p62FMNPentaerythritol tetranitrate reductase/0.460
2bb3SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE)/0.459
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.459
4bfzZVZPantothenate kinase2.7.1.330.459
4du82P0Mevalonate diphosphate decarboxylase/0.459
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.458
1xe65FPPlasmepsin-23.4.23.390.458
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.458
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.458
3hyoADPPyridoxal kinase/0.458
4m5pFMNNADPH dehydrogenase/0.458
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.457
2zsaADPPantothenate kinase2.7.1.330.457
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.457
3kb1ADPIron-sulfur cluster carrier protein/0.457
3uylTYDProbable NDP-rhamnosyltransferase/0.457
4ebfNADPhosphonate dehydrogenase1.20.1.10.457
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.457
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.457
1a9yUPGUDP-glucose 4-epimerase5.1.3.20.456
1w6hTITPlasmepsin-23.4.23.390.456
2c29NAPDihydroflavonol 4-reductase/0.456
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.456
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.456
3tjzGNPADP-ribosylation factor 1/0.456
1ma0NADAlcohol dehydrogenase class-31.1.1.10.455
1nzfUPGDNA beta-glucosyltransferase/0.455
1psa0ZLPepsin A3.4.23.10.455
1v0jFADUDP-galactopyranose mutase5.4.99.90.455
2ejzSAHDiphthine synthase/0.455
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.455
3enkUPGUDP-glucose 4-epimerase/0.455
4lol1YEStimulator of interferon genes protein/0.455
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.455
5eioNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.455
1mjbACOHistone acetyltransferase ESA1/0.454
2dsgSAHDiphthine synthase/0.454
2he5NDPAldo-keto reductase family 1 member C211.1.10.454
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.454
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3h06VBPGlutamate receptor 2/0.454
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.454
4mlp2CXCryptochrome-2/0.454
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.453
2il2LIXRenin3.4.23.150.453
2o12FMNChorismate synthase/0.453
3bk2U5PRibonuclease J/0.453
3h3t16HCollagen type IV alpha-3-binding protein/0.453
4bfxZVXPantothenate kinase2.7.1.330.453
2iqgF2IBeta-secretase 13.4.23.460.452
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.452
2zbaZBATrichothecene 3-O-acetyltransferase/0.452
3w8qAGSDual specificity mitogen-activated protein kinase kinase 12.7.12.20.452
4a6cQG9Gag-Pol polyprotein3.4.23.160.452
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.452
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.451
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.451
2ohvNHLGlutamate racemase/0.451
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.451
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.451
3p67FMNPentaerythritol tetranitrate reductase/0.451
4exg916Beta-secretase 13.4.23.460.451
1h63FMNPentaerythritol tetranitrate reductase/0.450
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.450
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.450
2hfuMEVMevalonate kinase/0.450
3dv5BAVBeta-secretase 13.4.23.460.450
3f3sNADLambda-crystallin homolog/0.450
3lpiZ74Beta-secretase 13.4.23.460.450
3lqsPSZD-alanine aminotransferase2.6.1.210.450
4a802ANMajor pollen allergen Bet v 1-A/0.450
1f8fNADBenzyl alcohol dehydrogenase/0.449
1jdtMTAPurine nucleoside phosphorylase/0.449
1tj0FADBifunctional protein PutA1.5.5.20.449
1x27ASP_TYR_VAL_HIS_PTRTyrosine-protein kinase Lck2.7.10.20.449
2c20NADUDP-glucose 4-epimerase/0.449
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.449
3ensENSCoagulation factor X3.4.21.60.449
3o7bSAHRibosomal RNA small subunit methyltransferase Nep1/0.449
3r2fPB0Beta-secretase 13.4.23.460.449
3tqxPLP2-amino-3-ketobutyrate coenzyme A ligase/0.449
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.449
1ee9NADMethylenetetrahydrofolate dehydrogenase [NAD(+)]1.5.1.150.448
1fy7COAHistone acetyltransferase ESA1/0.448
1jdzFMBPurine nucleoside phosphorylase/0.448
1kp3ATPArgininosuccinate synthase6.3.4.50.448
1me6IVSPlasmepsin-23.4.23.390.448
1pjcNADAlanine dehydrogenase/0.448
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.448
2ed3SAHDiphthine synthase/0.448
2eldSAHDiphthine synthase/0.448
2ien017Gag-Pol polyprotein3.4.23.160.448
3d3xARG_ILE_MET_GLU_NH2Type E botulinum toxin/0.448
3f03FMNPentaerythritol tetranitrate reductase/0.448
3h3qH13Collagen type IV alpha-3-binding protein/0.448
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.448
3pgtGBXGlutathione S-transferase P2.5.1.180.448
4fduIHSPutative multiple inositol polyphosphate histidine phosphatase 1/0.448
4g74FADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.448
4tyqAP5Adenylate kinase/0.448
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.448
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.448
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.447
1gtrATPGlutamine--tRNA ligase6.1.1.180.447
1h51FMNPentaerythritol tetranitrate reductase/0.447
4ii4BYC1,2-phenylacetyl-CoA epoxidase, subunit A1.14.13.1490.447
4nbwNADShort-chain dehydrogenase/reductase SDR/0.447
4oztP1AEcdysone receptor, putative/0.447
1ds7FMNOxygen-insensitive NAD(P)H nitroreductase/0.446
1qpl587Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.446
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.446
2b4tAESGlyceraldehyde-3-phosphate dehydrogenase/0.446
2g247IGRenin3.4.23.150.446
2ii6C5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.446
2p83MR0Beta-secretase 13.4.23.460.446
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.446
2qimZEAClass 10 plant pathogenesis-related protein/0.446
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3kr6UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.446
3lqfNADGalactitol dehydrogenase/0.446
3nsh957Beta-secretase 13.4.23.460.446
3oqfS51Renin3.4.23.150.446
4blrUTPNTPase P4/0.446
4ejmNAPPutative zinc-binding dehydrogenase/0.446
4i0i957Beta-secretase 13.4.23.460.446
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.446
4ke11R6Beta-secretase 13.4.23.460.446
1a8rGTPGTP cyclohydrolase 13.5.4.160.445
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.445
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.445
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.445
2cftPLPPyridoxal phosphate phosphatase/0.445
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.445
2gmjFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.445
2rlcCHDCholoylglycine hydrolase3.5.1.240.445
3gqvNAPEnoyl reductase LovC10.445
3hyg099A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.445
3pm1ETHTH-type transcriptional regulator QacR/0.445
3u9eCOALmo1369 protein/0.445
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.445
4dd8BATDisintegrin and metalloproteinase domain-containing protein 83.4.240.445
4de00JBBeta-lactamase/0.445
1b5eDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.444
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.444
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.444
1xl5190Gag-Pol polyprotein3.4.23.160.444
1yqsBSAD-alanyl-D-alanine carboxypeptidase3.4.16.40.444
2dv3SAHDiphthine synthase/0.444
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.444
2gjnFMNNitronate monooxygenase1.13.12.160.444
2w6qOA5Biotin carboxylase6.3.4.140.444
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.444
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3lxiCAMCytochrome P450/0.444
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.444
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.444
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.444
4lutDCSAlanine racemase/0.444
4z5wILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.444
1bdlIM1Gag-Pol polyprotein3.4.23.160.443
1pagFMPAntiviral protein I3.2.2.220.443
2b53D23Cyclin-dependent kinase 22.7.11.220.443
2g1s4IGRenin3.4.23.150.443
2gnhH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
2z1mNDPGDP-mannose 4,6-dehydratase/0.443
3ai3NDPNADPH-sorbose reductase/0.443
3bgsDIHPurine nucleoside phosphorylase2.4.2.10.443
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3h6vNS6Glutamate receptor 2/0.443
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.443
3mauEXTPutative sphingosine-1-phosphate lyase/0.443
3vg10GTBeta-secretase 13.4.23.460.443
3vyfVYFRenin3.4.23.150.443
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.443
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.442
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1rywEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.442
1tsxUMPThymidylate synthase/0.442
1uxyEPUUDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.442
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.442
2i7nACOPantothenate kinase 12.7.1.330.442
2ilvC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.442
3b2sB2STrichothecene 3-O-acetyltransferase/0.442
4ambDUDPutative glycosyl transferase/0.442
4eb7PLPCysteine desulfurase IscS 2/0.442
4mr92BXGamma-aminobutyric acid type B receptor subunit 1/0.442
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.442
4wriOKAOkadaic acid binding protein 2-alpha/0.442
4zseANPEpidermal growth factor receptor2.7.10.10.442
5d3qGDPDynamin-13.6.5.50.442
5ftfADPTPR domain protein/0.442
2ea2F77Methionine aminopeptidase 2/0.441
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.441
2qdxFADFerredoxin--NADP+ reductase/0.441
3e23SAMUncharacterized protein/0.441
3eldSFGMethyltransferase/0.441
3i25MV7Beta-secretase 13.4.23.460.441
3mx5UTPNucleoprotein/0.441
3o0o5ADVitamin B12-dependent ribonucleotide reductase/0.441
4f9gC2EStimulator of interferon genes protein/0.441
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4l0qNADAlcohol dehydrogenase class-3/0.441
4wrkDUPDUTPase/0.441
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.441
1g1aNADdTDP-glucose 4,6-dehydratase/0.440
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.440
1s63778Protein farnesyltransferase subunit beta2.5.1.580.440
1thyUMPThymidylate synthase/0.440
2bjfDXCCholoylglycine hydrolase3.5.1.240.440
2f81017Gag-Pol polyprotein3.4.23.160.440
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.440
2hu2NADC-terminal binding protein 1/0.440
2vprTDCTetracycline repressor protein class H/0.440
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.440
3h3r14HCollagen type IV alpha-3-binding protein/0.440
3zvmADPBifunctional polynucleotide phosphatase/kinase2.7.1.780.440
4dpuAGSMevalonate diphosphate decarboxylase/0.440
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.440
4wudANPDNA gyrase subunit B/0.440
4xymCOAAcyl-CoA synthetase (NDP forming)/0.440