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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
4ubtCOASteroid 3-ketoacyl-CoA thiolase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4ubtCOASteroid 3-ketoacyl-CoA thiolase/1.000
4ubvCOASteroid 3-ketoacyl-CoA thiolase/0.530
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.489
3w6hAZMCarbonic anhydrase 14.2.1.10.487
4o701QKBromodomain-containing protein 4/0.486
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.485
1xddAAYIntegrin alpha-L/0.484
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.483
3w0gW07Vitamin D3 receptor/0.483
4c2jCOA3-ketoacyl-CoA thiolase, mitochondrial2.3.1.160.480
1qorNDPQuinone oxidoreductase 1/0.477
2c29NAPDihydroflavonol 4-reductase/0.477
4twnB96Ephrin type-A receptor 32.7.10.10.475
1g4kHQQStromelysin-13.4.24.170.474
2gv8NDPThiol-specific monooxygenase1.14.130.474
2x7hPFNProstaglandin reductase 310.474
4bizADPSensor histidine kinase CpxA/0.473
4phlPILPhosphodiesterase/0.473
4ubuCOASteroid 3-ketoacyl-CoA thiolase/0.472
3b1dPLSBetaC-S lyase/0.471
3rpeFADPutative modulator of drug activity/0.470
4ipw1G7Mycocyclosin synthase1.14.21.90.470
1eveE20Acetylcholinesterase3.1.1.70.469
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.469
2ou2ACOHistone acetyltransferase KAT5/0.468
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.468
4ambDUDPutative glycosyl transferase/0.468
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.467
2vcmM11Isopenicillin N synthase1.21.3.10.466
3lqfNADGalactitol dehydrogenase/0.466
4l4xNDPAmphI/0.466
4q71FADBifunctional protein PutA/0.465
2po7CHDFerrochelatase, mitochondrial4.99.1.10.464
2uuvFADAlkyldihydroxyacetonephosphate synthase2.5.1.260.464
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.464
3uylTYDProbable NDP-rhamnosyltransferase/0.464
4bftZVTPantothenate kinase2.7.1.330.464
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.464
3q9bB3NAcetylpolyamine amidohydrolase/0.463
5dp2NAPCurF/0.463
3cz7ACOHistone acetyltransferase RTT1092.3.1.480.462
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.462
3hl0NADMaleylacetate reductase/0.462
4bfxZVXPantothenate kinase2.7.1.330.462
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.461
2cy0NAPShikimate dehydrogenase (NADP(+))/0.461
3jynNDPQuinone oxidoreductase/0.461
1wdkACO3-ketoacyl-CoA thiolase/0.460
1zidZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
3bg7FADPyranose 2-oxidase/0.460
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
1dghNDPCatalase1.11.1.60.459
3zbsOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.459
4b4vL34Bifunctional protein FolD/0.459
4ktl1CQCytochrome P450/0.459
1i3mUD1UDP-glucose 4-epimerase/0.458
2bu9HFVIsopenicillin N synthase1.21.3.10.458
4pd6URINucleoside permease/0.458
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.457
1qjfACSIsopenicillin N synthase1.21.3.10.457
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.457
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.457
3c1oNAPEugenol synthase/0.457
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3k4nFADPyranose 2-oxidase/0.457
4g95OAGDihydrofolate reductase1.5.1.30.457
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.457
5dozNDPJamJ/0.457
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.456
3mjeNDPAmphB/0.456
4oztP1AEcdysone receptor, putative/0.456
1dhrNADDihydropteridine reductase1.5.1.340.455
1f8gNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.455
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.455
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.455
2gr1FADFerredoxin reductase/0.455
3bbtFMMReceptor tyrosine-protein kinase erbB-42.7.10.10.455
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
4ips1G4Mycocyclosin synthase1.14.21.90.455
4irnFADAnaB/0.455
1u2gAPRNAD(P) transhydrogenase subunit alpha part 11.6.1.20.454
2ntvP1HEnoyl-[acyl-carrier-protein] reductase [NADH]/0.454
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.454
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.454
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4hjoAQ4Epidermal growth factor receptor2.7.10.10.454
4jlm1NNDeoxycytidine kinase2.7.1.740.454
4jx1CAHCamphor 5-monooxygenase1.14.15.10.454
4r20AERCytochrome P450 family 17 polypeptide 2/0.454
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.453
1o76CAMCamphor 5-monooxygenase1.14.15.10.453
1ur5NADMalate dehydrogenase/0.453
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.453
3qfrFMNNADPH--cytochrome P450 reductase/0.453
3vtbTKAVitamin D3 receptor/0.453
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.453
4kxjP34Nucleoprotein/0.453
4r21STRCytochrome P450 family 17 polypeptide 2/0.453
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.452
1zgbA1EAcetylcholinesterase3.1.1.70.452
3kozZ97D-ornithine 4,5-aminomutase subunit beta/0.452
3t4nADP5'-AMP-activated protein kinase subunit gamma/0.452
3zoiM2WIsopenicillin N synthase1.21.3.10.452
4kbyC2EStimulator of interferon genes protein/0.452
4xguADPPutative pachytene checkpoint protein 2/0.452
4y8vADPAcyl-CoA synthetase (NDP forming)/0.452
1zdgUPGGlycogenin-12.4.1.1860.451
3p3zP3ZPutative cytochrome P450/0.451
4qxr1YEStimulator of interferon genes protein/0.451
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.451
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.450
1o8cNDPProbable acrylyl-CoA reductase AcuI1.3.1.840.450
1obnASVIsopenicillin N synthase1.21.3.10.450
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.450
2c12FADNitroalkane oxidase1.7.3.10.450
2jb4A14Isopenicillin N synthase1.21.3.10.450
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.450
3o4rNAPDehydrogenase/reductase SDR family member 41.1.1.1840.450
4g3jVNTLanosterol 14-alpha-demethylase/0.450
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.449
1gvv0GMEndothiapepsin3.4.23.220.449
2wo7ASVIsopenicillin N synthase1.21.3.10.449
2xtnGTPGTPase IMAP family member 2/0.449
2zb3NDPProstaglandin reductase 21.3.1.480.449
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3ekuCY9Actin-5C/0.449
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.449
3qe2FMNNADPH--cytochrome P450 reductase/0.449
3zxsFADDeoxyribodipyrimidine photolyase-related protein/0.449
4enhFVXCholesterol 24-hydroxylase/0.449
4g7gVFVLanosterol 14-alpha-demethylase/0.449
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.449
4otwDB8Receptor tyrosine-protein kinase erbB-32.7.10.10.449
4udrFAD5-(hydroxymethyl)furfural oxidase/0.449
5irnADPNucleotide binding oligomerization domain containing 2/0.449
1bk0ACVIsopenicillin N synthase1.21.3.10.448
1g1aNADdTDP-glucose 4,6-dehydratase/0.448
1n83CLRNuclear receptor ROR-alpha/0.448
1tqf32PBeta-secretase 13.4.23.460.448
1u4oNDDL-lactate dehydrogenase1.1.1.270.448
1wl4COAAcetyl-CoA acetyltransferase, cytosolic2.3.1.90.448
1xtsGTPGTP-binding protein Rheb/0.448
1yb5NAPQuinone oxidoreductase1.6.5.50.448
2d29FADAcyl-CoA dehydrogenase/0.448
2geuCOKPantothenate kinase2.7.1.330.448
2ggsNDPdTDP-4-dehydrorhamnose reductase/0.448
2xx413IATP-dependent molecular chaperone HSP82/0.448
4c0bATPmRNA cleavage and polyadenylation factor CLP1/0.448
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
4j491J1Uncharacterized protein/0.448
4l7j1W2Beta-secretase 13.4.23.460.448
5a0112VO-glycosyltransferase/0.448
5c93ACPTwo-component system histidine protein kinase/0.448
3gwfNAPCyclohexanone monooxygenase/0.447
3m6iNADL-arabinitol 4-dehydrogenase1.1.1.120.447
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.447
3ohh3HHBeta-secretase 13.4.23.460.447
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.447
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.447
4ead0NPThymidine phosphorylase2.4.2.40.447
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.447
4iae1DXAlr2278 protein/0.447
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.447
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.447
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.447
5kgpACOPredicted acetyltransferase/0.447
1n2sNAIdTDP-4-dehydrorhamnose reductase1.1.1.1330.446
1xe55FEPlasmepsin-23.4.23.390.446
2bjhFERFeruloyl esterase A3.1.1.730.446
2c20NADUDP-glucose 4-epimerase/0.446
2dv3SAHDiphthine synthase/0.446
2he5NDPAldo-keto reductase family 1 member C211.1.10.446
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.446
2q9fC3SCholesterol 24-hydroxylase/0.446
3u8k09PAcetylcholine-binding protein/0.446
4fehFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.446
4g1d0VKVitamin D3 receptor A/0.446
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.446
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.446
1equEQIEstradiol 17-beta-dehydrogenase 11.1.1.620.445
1hb3SCVIsopenicillin N synthase1.21.3.10.445
1qy5NECEndoplasmin/0.445
1trgCB3Thymidylate synthase/0.445
1u3dFADCryptochrome-1/0.445
1u65CP0Acetylcholinesterase3.1.1.70.445
2a94AP0L-lactate dehydrogenase1.1.1.270.445
2b3dFADModulator of drug activity B/0.445
2belCBOCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
2bf4FMNNADPH--cytochrome P450 reductase/0.445
2emrSAHDiphthine synthase/0.445
2givACOHistone acetyltransferase KAT8/0.445
2vbpVB1Isopenicillin N synthase1.21.3.10.445
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.445
4gk3L87Ephrin type-A receptor 32.7.10.10.445
4kp5E1FCarbonic anhydrase 124.2.1.10.445
4obwSAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial/0.445
1a9yUPGUDP-glucose 4-epimerase5.1.3.20.444
1hvyD16Thymidylate synthase2.1.1.450.444
1i59ADPChemotaxis protein CheA2.7.13.30.444
1t2cNAIL-lactate dehydrogenase1.1.1.270.444
2gesCOKPantothenate kinase2.7.1.330.444
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.444
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.444
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3junAKDPhenazine biosynthesis protein A/B/0.444
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3lsiFADPyranose 2-oxidase/0.444
3tdaPN0Cytochrome P450 2D6/0.444
4e2zJHZMethyltransferase/0.444
4x2qNADRetinal dehydrogenase 21.2.1.360.444
4xg1LLPDiaminopimelate decarboxylase/0.444
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.444
1mvsDTMDihydrofolate reductase1.5.1.30.443
1piwNAPNADP-dependent alcohol dehydrogenase 61.1.1.20.443
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.443
1wngSAHDiphthine synthase/0.443
2c3qGTXGlutathione S-transferase theta-12.5.1.180.443
2huqSAHDiphthine synthase/0.443
2yj5ATPCopper-transporting ATPase/0.443
3q43D66M1 family aminopeptidase3.4.110.443
3w32W32Epidermal growth factor receptor2.7.10.10.443
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.443
4u8iFDAUDP-galactopyranose mutase/0.443
4yerADPAntibiotic ABC transporter, ATP-binding protein, putative/0.443
1ja0FMNNADPH--cytochrome P450 reductase/0.442
1mjbACOHistone acetyltransferase ESA1/0.442
1x27ASP_TYR_VAL_HIS_PTRTyrosine-protein kinase Lck2.7.10.20.442
1yqxNAPSinapyl alcohol dehydrogenase/0.442
2bifANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 42.7.1.1050.442
2g1n1IGRenin3.4.23.150.442
2y3rTRKTamL/0.442
3deyDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
3klmDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
4dc0NDPPutative ketoacyl reductase1.3.10.442
4g1z0VPVitamin D3 receptor A/0.442
4nd4NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.442
4rww2BALmo2692 protein/0.442
4y8wSTRSteroid 21-hydroxylase/0.442
5ch7MD1DMSO reductase family type II enzyme, molybdopterin subunit/0.442
1mjaCOAHistone acetyltransferase ESA1/0.441
1ygkRRCPyridoxal kinase2.7.1.350.441
2ozuACOHistone acetyltransferase KAT6A/0.441
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.441
2x06NADL-sulfolactate dehydrogenase/0.441
3c3xNAPEugenol synthase 11.1.1.3180.441
3flwFLWMitogen-activated protein kinase 14/0.441
3rk1ATPN-type ATP pyrophosphatase superfamily/0.441
3zkyWT4Isopenicillin N synthase1.21.3.10.441
4wdfA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
4yaiNAIC alpha-dehydrogenase/0.441
1bwsNDPGDP-L-fucose synthase/0.440
1dgfNDPCatalase1.11.1.60.440
1gc5ADPADP-dependent glucokinase2.7.1.1470.440
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.440
1qiqACCIsopenicillin N synthase1.21.3.10.440
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.440
2igoFADPyranose 2-oxidase/0.440
2y0mACOHistone acetyltransferase KAT8/0.440
3cppCAMCamphor 5-monooxygenase1.14.15.10.440
3d4pNADL-lactate dehydrogenase 11.1.1.270.440
3hcrCHDFerrochelatase, mitochondrial4.99.1.10.440
3pm1ETHTH-type transcriptional regulator QacR/0.440
4b4w9L9Bifunctional protein FolD/0.440
4bfvZVVPantothenate kinase2.7.1.330.440
4bfzZVZPantothenate kinase2.7.1.330.440
4i6gFADCryptochrome-2/0.440
4l4bCAMCamphor 5-monooxygenase1.14.15.10.440
4tuvCPZCytochrome P450 1191.140.440