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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
4mq5TPPBenzoylformate decarboxylase4.1.1.7

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
4mq5TPPBenzoylformate decarboxylase4.1.1.71.000
4ju8TZDBenzoylformate decarboxylase4.1.1.70.700
4mprTPPBenzoylformate decarboxylase4.1.1.70.675
4ju9TZDBenzoylformate decarboxylase4.1.1.70.666
5dgtTZDBenzoylformate decarboxylase4.1.1.70.655
2fwnTDPBenzoylformate decarboxylase4.1.1.70.648
4gg1TZDBenzoylformate decarboxylase4.1.1.70.640
4k9nTZDBenzoylformate decarboxylase4.1.1.70.637
4jufTPPBenzoylformate decarboxylase4.1.1.70.636
4gm4TZDBenzoylformate decarboxylase4.1.1.70.631
1mczTDPBenzoylformate decarboxylase4.1.1.70.627
4k9oTPPBenzoylformate decarboxylase4.1.1.70.619
4gm0TZDBenzoylformate decarboxylase4.1.1.70.603
4jd5TZDBenzoylformate decarboxylase4.1.1.70.591
4qelTZDBenzoylformate decarboxylase4.1.1.70.590
1po7TZDBenzoylformate decarboxylase4.1.1.70.586
1bfdTPPBenzoylformate decarboxylase4.1.1.70.580
4jubTPPBenzoylformate decarboxylase4.1.1.70.563
4jucTPPBenzoylformate decarboxylase4.1.1.70.551
4k9pTPPBenzoylformate decarboxylase4.1.1.70.549
4mppTZDBenzoylformate decarboxylase4.1.1.70.523
4mzxTZDBenzoylformate decarboxylase4.1.1.70.500
4fj2NAP17beta-hydroxysteroid dehydrogenase/0.499
4bfxZVXPantothenate kinase2.7.1.330.497
2v3wTPPBenzoylformate decarboxylase4.1.1.70.494
3fhyATPPyridoxal kinase2.7.1.350.494
4gddNAIUDP-galactopyranose mutase/0.494
4fj1NAP17beta-hydroxysteroid dehydrogenase/0.491
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.491
2ou2ACOHistone acetyltransferase KAT5/0.490
4is3NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 21.17.98.10.489
4gm1TZDBenzoylformate decarboxylase4.1.1.70.487
2givACOHistone acetyltransferase KAT8/0.485
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.482
2vhxNADAlanine dehydrogenase1.4.1.10.481
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.481
1fduNAPEstradiol 17-beta-dehydrogenase 11.1.1.620.479
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.479
2yxuATPPyridoxal kinase2.7.1.350.479
3r3sNADPutative oxidoreductase/0.478
3f63GTXGlutathione transferase GST1-4/0.477
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.476
2xtnGTPGTPase IMAP family member 2/0.476
2y05NAPProstaglandin reductase 1/0.476
3kpbSAMUncharacterized protein MJ0100/0.476
3imgBZ2Pantothenate synthetase6.3.2.10.475
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.473
5cfpC2EStimulator of interferon genes protein/0.473
1qyvNAPEstradiol 17-beta-dehydrogenase 11.1.1.620.471
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.471
1mjaCOAHistone acetyltransferase ESA1/0.470
1w5sADPORC1-type DNA replication protein 2/0.470
3qwfNAP17beta-hydroxysteroid dehydrogenase/0.470
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.470
4uugPXGBranched-chain amino acid aminotransferase, putative/0.470
2rc3NADCBS domain/0.469
1n7hNDPGDP-mannose 4,6 dehydratase 24.2.1.470.468
3ieuGDPGTPase Era/0.468
2ztlNADD(-)-3-hydroxybutyrate dehydrogenase/0.467
4ambDUDPutative glycosyl transferase/0.467
1oc1ASVIsopenicillin N synthase1.21.3.10.466
2gesCOKPantothenate kinase2.7.1.330.466
3d3wNAPL-xylulose reductase1.1.1.100.466
3keuATPPyridoxal kinase2.7.1.350.466
3nxxNDPDihydrofolate reductase1.5.1.30.465
4kqwNAPKetol-acid reductoisomerase (NADP(+))/0.465
1gcoNADGlucose 1-dehydrogenase1.1.1.470.464
1nvmNADAcetaldehyde dehydrogenase1.2.1.100.464
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.464
3fpzAHZThiamine thiazole synthase/0.464
4iqgNAPShort-chain dehydrogenase/reductase SDR/0.464
1geeNADGlucose 1-dehydrogenase1.1.1.470.463
2geuCOKPantothenate kinase2.7.1.330.463
2po7CHDFerrochelatase, mitochondrial4.99.1.10.463
2vtbFADCryptochrome DASH, chloroplastic/mitochondrial/0.463
4df2FMNNADPH dehydrogenase/0.463
1edoNAP3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic1.1.1.1000.462
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.462
1szgFNSCytochrome b2, mitochondrial1.1.2.30.462
2dteNAIGlucose 1-dehydrogenase related protein/0.462
2qbuSAHPrecorrin-2 methyltransferase/0.462
3l77NJPShort-chain alcohol dehydrogenase/0.462
4fj0NAP17beta-hydroxysteroid dehydrogenase/0.462
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.461
2ahrNAPPyrroline-5-carboxylate reductase/0.461
2fonFADAcyl-coenzyme A oxidase/0.461
2g1n1IGRenin3.4.23.150.461
4djaFAD(6-4) photolyase/0.461
4fse0VABeta-secretase 13.4.23.460.461
4oztP1AEcdysone receptor, putative/0.461
1mjbACOHistone acetyltransferase ESA1/0.460
1psa0ZLPepsin A3.4.23.10.460
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.460
1fm4DXCMajor pollen allergen Bet v 1-L/0.459
1fy7COAHistone acetyltransferase ESA1/0.459
2ekpNAD2-deoxy-D-gluconate 3-dehydrogenase/0.459
2v13C40Renin3.4.23.150.459
3c3eGDP2-phospho-L-lactate transferase/0.459
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.459
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.459
4i521HA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.459
1iy8NADLevodione reductase/0.458
1jqiFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial/0.458
1m8kNADNicotinamide-nucleotide adenylyltransferase2.7.7.10.458
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.458
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.458
5jydNADShort chain dehydrogenase/0.458
2p41SAHGenome polyprotein/0.457
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.457
4hwkNAPSepiapterin reductase1.1.1.1530.457
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.456
1y0s331Peroxisome proliferator-activated receptor delta/0.456
2vojNADAlanine dehydrogenase1.4.1.10.456
3elySAHMethyltransferase/0.456
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.456
4irnFADAnaB/0.456
1e3sNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.455
2c12FADNitroalkane oxidase1.7.3.10.455
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.455
2y99NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase1.3.1.560.455
2yutNAPPutative short-chain oxidoreductase/0.455
3eksCY9Actin-5C/0.455
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.455
3q43D66M1 family aminopeptidase3.4.110.455
1bdbNADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase/0.454
1p0hACOMycothiol acetyltransferase2.3.1.1890.454
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.454
1rwbNADGlucose 1-dehydrogenase1.1.1.470.454
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.454
3c8bARG_ARG_GLY_ILE_NH2Botulinum neurotoxin type A3.4.24.690.454
3x2wATPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.454
4hfmNAP2-alkenal reductase (NADP(+)-dependent)/0.454
4o1mNADEnoyl-acyl carrier reductase/0.454
4yaoFMNNADPH--cytochrome P450 reductase/0.454
5ftfADPTPR domain protein/0.454
1rv1IMZE3 ubiquitin-protein ligase Mdm26.3.20.453
4acxS8ZBeta-secretase 13.4.23.460.453
5jscFADPutative acyl-CoA dehydrogenase/0.453
1jjeBYSBeta-lactamase/0.452
1zdwFLVPrenyltransferase/0.452
2g8yNADHydroxycarboxylate dehydrogenase B/0.452
3p8z36AGenome polyprotein2.1.1.560.452
5idwNAPShort-chain dehydrogenase/reductase SDR/0.452
5ig2NADShort-chain dehydrogenase/reductase SDR/0.452
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.452
1f8wFADNADH peroxidase1.11.1.10.451
1kvkATPMevalonate kinase2.7.1.360.451
2ctsCOACitrate synthase, mitochondrial2.3.3.10.451
2ebaFADPutative glutaryl-CoA dehydrogenase/0.451
2p83MR0Beta-secretase 13.4.23.460.451
3ijoB4DGlutamate receptor 2/0.451
3ivgFG5Pantothenate synthetase6.3.2.10.451
3toxNAPPutative oxidoreductase/0.451
4yaiNAIC alpha-dehydrogenase/0.451
1ld7U66Protein farnesyltransferase subunit beta2.5.1.580.450
2g1o2IGRenin3.4.23.150.450
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.450
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.450
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.450
3pfdFDAAcyl-CoA dehydrogenase FadE25/0.450
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.450
4i6gFADCryptochrome-2/0.450
4n3cUD1UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.450
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.450
1la2NADInositol-3-phosphate synthase5.5.1.40.449
1x7gNAPPutative ketoacyl reductase1.3.10.449
3ekuCY9Actin-5C/0.449
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.449
3phiNDPShikimate dehydrogenase (NADP(+))/0.449
3w6hAZMCarbonic anhydrase 14.2.1.10.449
4b78KGGBeta-secretase 13.4.23.460.449
4bfyZVYPantothenate kinase2.7.1.330.449
4q73FADBifunctional protein PutA/0.449
4z44FADFlavin-dependent tryptophan halogenase PrnA1.14.19.90.449
1hyhNADL-2-hydroxyisocaproate dehydrogenase/0.448
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.448
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.448
1kvuUPGUDP-glucose 4-epimerase5.1.3.20.448
1me6IVSPlasmepsin-23.4.23.390.448
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.448
2npaMMBPeroxisome proliferator-activated receptor alpha/0.448
2y4gTIRTamL/0.448
3owaFADAcyl-CoA dehydrogenase/0.448
3sx2NADUncharacterized protein/0.448
4fhf0TTSpore photoproduct lyase/0.448
4mihFADPyranose 2-oxidase1.1.3.100.448
4phlPILPhosphodiesterase/0.448
5dldUD1UDP-N-Acetylglucosamine 2-epimerase/0.448
5irnADPNucleotide binding oligomerization domain containing 2/0.448
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.447
1oaaNAPSepiapterin reductase1.1.1.1530.447
1zk7FADMercuric reductase1.16.1.10.447
2b3dFADModulator of drug activity B/0.447
2wdzNADGalactitol dehydrogenase/0.447
3lpiZ74Beta-secretase 13.4.23.460.447
3qd03Q43-phosphoinositide-dependent protein kinase 12.7.11.10.447
3to6LYS_CMCHistone acetyltransferase ESA1/0.447
4j7xNAPSepiapterin reductase1.1.1.1530.447
4wdgA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.447
1f0xFADD-lactate dehydrogenase1.1.1.280.446
1qjfACSIsopenicillin N synthase1.21.3.10.446
2g76NADD-3-phosphoglycerate dehydrogenase1.1.1.950.446
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.446
3gobHXXDdmC/0.446
3idbANPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
3lpkZ76Beta-secretase 13.4.23.460.446
3mddFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.446
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.446
3mx5UTPNucleoprotein/0.446
3t7tSAHUncharacterized protein/0.446
3w8eNAD3-hydroxybutyrate dehydrogenase/0.446
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.446
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.446
4h6rFDAProline dehydrogenase/0.446
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.445
1lbcCYZGlutamate receptor 2/0.445
1tehNADAlcohol dehydrogenase class-31.1.1.10.445
1x1dSAHC-20 methyltransferase/0.445
2a94AP0L-lactate dehydrogenase1.1.1.270.445
2ag5NAD3-hydroxybutyrate dehydrogenase type 2/0.445
2vhwNAIAlanine dehydrogenase1.4.1.10.445
3a37ADPATPase GET3/0.445
3hyoADPPyridoxal kinase/0.445
3iocA5DPantothenate synthetase6.3.2.10.445
3q9bB3NAcetylpolyamine amidohydrolase/0.445
4bmvNAPShort-chain dehydrogenase/0.445
4djy0KRBeta-secretase 13.4.23.460.445
4xguADPPutative pachytene checkpoint protein 2/0.445
5ckuFADL-ornithine N(5)-monooxygenase/0.445
1bzlFADTrypanothione reductase1.8.1.120.444
1galFADGlucose oxidase1.1.3.40.444
1k7l544Peroxisome proliferator-activated receptor alpha/0.444
1pl1ABYGlutathione S-transferase A12.5.1.180.444
1xddAAYIntegrin alpha-L/0.444
2gjlFMNNitronate monooxygenase1.13.12.160.444
2vijC44Beta-secretase 13.4.23.460.444
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.444
2wa2SAMGenome polyprotein/0.444
2xgs44PUncharacterized protein/0.444
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.444
3clsFADElectron transfer flavoprotein subunit alpha/0.444
3coy53HPantothenate synthetase6.3.2.10.444
3oadLPORenin3.4.23.150.444
3q8hAO92-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.444
3wagTYDGlycosyltransferase/0.444
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.444
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.444
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
4yagNAIC alpha-dehydrogenase/0.444
5cfn2BAStimulator of interferon genes protein/0.444
5dmhADP3-oxo-tetronate kinase/0.444
1nlmUD1UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase/0.443
1ofgNDPGlucose--fructose oxidoreductase1.1.99.280.443
1qzyTDEMethionine aminopeptidase 2/0.443
1sdwIYTPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.443
2dvlFADAcyl-CoA dehydrogenase/0.443
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.443
3fql79ZGenome polyprotein2.7.7.480.443
3mkhFADNitroalkane oxidase/0.443
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.443
4i4z2NE1,4-dihydroxy-2-naphthoyl-CoA synthase/0.443
4j7uNAPSepiapterin reductase1.1.1.1530.443
4p63NADProbable deoxyhypusine synthase2.5.1.460.443
4qlyFMNEnone reductase CLA-ER/0.443
5dp2NAPCurF/0.443
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.443
1cydNDPCarbonyl reductase [NADPH] 21.1.1.1840.442
1gsnFADGlutathione reductase, mitochondrial1.8.1.70.442
1obnASVIsopenicillin N synthase1.21.3.10.442
1w6hTITPlasmepsin-23.4.23.390.442
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.442
1xu7CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
1z7yAA5Cysteine synthase 12.5.1.470.442
2znnS44Peroxisome proliferator-activated receptor alpha/0.442
2zu8GDDMannosyl-3-phosphoglycerate synthase2.4.1.2170.442
3b7dCNIGlutamate receptor 2/0.442
3eldSFGMethyltransferase/0.442
3i0pNADMalate dehydrogenase, putative/0.442
3ut5LOCTubulin beta chain/0.442
3vdqNAD3-hydroxybutyrate dehydrogenase/0.442
3wbfNAPMeso-diaminopimelate D-dehydrogenase/0.442
4h1vGNPDynamin-1-like protein3.6.5.50.442
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.442
4nmdFDABifunctional protein PutA/0.442
4rvgTYDD-mycarose 3-C-methyltransferase/0.442
5burATP2-succinylbenzoate--CoA ligase/0.442
1ipeNDPTropinone reductase 21.1.1.2360.441
1odcA8BAcetylcholinesterase3.1.1.70.441
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.441
1t9gFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.441
2iqgF2IBeta-secretase 13.4.23.460.441
4b722FBBeta-secretase 13.4.23.460.441
4g3jVNTLanosterol 14-alpha-demethylase/0.441
4zp1TPPPyruvate decarboxylase4.1.1.10.441
5hxwFADL-amino acid deaminase/0.441
1fecFADTrypanothione reductase1.8.1.120.440
1o0sNAINAD-dependent malic enzyme, mitochondrial1.1.1.380.440
1qiqACCIsopenicillin N synthase1.21.3.10.440
1t2aNDPGDP-mannose 4,6 dehydratase4.2.1.470.440
2dshSAHDiphthine synthase/0.440
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.440
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.440
2gh5FADGlutathione reductase, mitochondrial1.8.1.70.440
2gv8NDPThiol-specific monooxygenase1.14.130.440
2yvfNADFerredoxin reductase/0.440
2z3nPHE_ARG_TYR_LEU_GLYLeucyl/phenylalanyl-tRNA--protein transferase2.3.2.60.440
3dh9FADThioredoxin reductase 1, mitochondrial1.8.1.90.440
3dk9FADGlutathione reductase, mitochondrial1.8.1.70.440
3f90FMNFlavodoxin/0.440
3ge6FMNNitroreductase/0.440
3gqvNAPEnoyl reductase LovC10.440
3nl6ACPUncharacterized protein/0.440
3nsh957Beta-secretase 13.4.23.460.440
3p8zSAHGenome polyprotein2.1.1.560.440
3rsv3RSBeta-secretase 13.4.23.460.440
3tn7NJPShort-chain alcohol dehydrogenase/0.440
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.440
4eb7PLPCysteine desulfurase IscS 2/0.440
4fvqATPTyrosine-protein kinase JAK2/0.440
4i0i957Beta-secretase 13.4.23.460.440
4ke01R8Beta-secretase 13.4.23.460.440
4n9iPCGCatabolite expression activator/0.440
4ohwATPProtein clpf-1/0.440
4q71FADBifunctional protein PutA/0.440
4x28FDAAcyl-CoA dehydrogenase FadE26/0.440
4x28FDAAcyl-CoA dehydrogenase FadE27/0.440
4xw4ANPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440