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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1bfdTPPBenzoylformate decarboxylase4.1.1.7

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1bfdTPPBenzoylformate decarboxylase4.1.1.71.000
2fwnTDPBenzoylformate decarboxylase4.1.1.70.761
4qelTZDBenzoylformate decarboxylase4.1.1.70.756
5dgtTZDBenzoylformate decarboxylase4.1.1.70.756
4ju8TZDBenzoylformate decarboxylase4.1.1.70.716
4mzxTZDBenzoylformate decarboxylase4.1.1.70.659
4jd5TZDBenzoylformate decarboxylase4.1.1.70.623
4mq5TPPBenzoylformate decarboxylase4.1.1.70.608
4gm0TZDBenzoylformate decarboxylase4.1.1.70.593
4ju9TZDBenzoylformate decarboxylase4.1.1.70.591
4gm4TZDBenzoylformate decarboxylase4.1.1.70.587
4mprTPPBenzoylformate decarboxylase4.1.1.70.574
3fznD7KBenzoylformate decarboxylase4.1.1.70.573
4jubTPPBenzoylformate decarboxylase4.1.1.70.570
4k9pTPPBenzoylformate decarboxylase4.1.1.70.563
4k9oTPPBenzoylformate decarboxylase4.1.1.70.560
4jufTPPBenzoylformate decarboxylase4.1.1.70.548
1mczTDPBenzoylformate decarboxylase4.1.1.70.536
4jucTPPBenzoylformate decarboxylase4.1.1.70.527
4gm1TZDBenzoylformate decarboxylase4.1.1.70.502
4frkDWDBeta-secretase 13.4.23.460.492
4mppTZDBenzoylformate decarboxylase4.1.1.70.491
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.486
1f0xFADD-lactate dehydrogenase1.1.1.280.482
3phiNDPShikimate dehydrogenase (NADP(+))/0.482
4wdgA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.481
2c1zU2FAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.480
4eph0RKCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.480
5c2tFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.480
2ztlNADD(-)-3-hydroxybutyrate dehydrogenase/0.478
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.478
4zolGTPTubulin alpha-1B chain/0.477
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.476
2v3wTPPBenzoylformate decarboxylase4.1.1.70.474
3w8eNAD3-hydroxybutyrate dehydrogenase/0.474
4y380A9Endothiapepsin3.4.23.220.474
5dbfNDPIridoid synthase1.3.1.990.474
4wbnGTPTubulin alpha-1B chain/0.473
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.472
3pmy41LEndothiapepsin3.4.23.220.471
1w6hTITPlasmepsin-23.4.23.390.469
1zthADPRIO-type serine/threonine-protein kinase Rio12.7.11.10.469
2w9hTOPDihydrofolate reductase1.5.1.30.469
4yagNAIC alpha-dehydrogenase/0.469
5ckuFADL-ornithine N(5)-monooxygenase/0.469
1iy8NADLevodione reductase/0.468
2uyiADPKinesin-like protein KIF11/0.468
2yphQQY2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.468
3zcsCAWGlycogen phosphorylase, muscle form2.4.1.10.468
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.467
5idwNAPShort-chain dehydrogenase/reductase SDR/0.467
2ou2ACOHistone acetyltransferase KAT5/0.466
3ua808WGlutamate receptor 2/0.466
2fonFADAcyl-coenzyme A oxidase/0.465
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.465
5eyuNADBetaine-aldehyde dehydrogenase/0.465
2gesCOKPantothenate kinase2.7.1.330.464
2yxuATPPyridoxal kinase2.7.1.350.464
3clbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.464
1zk7FADMercuric reductase1.16.1.10.463
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.463
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.463
4oztP1AEcdysone receptor, putative/0.463
3daaPDDD-alanine aminotransferase2.6.1.210.462
3kpbSAMUncharacterized protein MJ0100/0.462
4nauAGSPhosphopantetheine adenylyltransferase/0.462
4o4lGTPTubulin alpha-1B chain/0.462
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.460
2e0nSAHPrecorrin-2 C20-methyltransferase/0.460
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.460
2wb2FADRE11660p/0.460
4d5gFADCyclohexane-1,2-dione hydrolase3.7.1.110.460
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.460
4ihjGTPTubulin alpha-1B chain/0.460
3gqvNAPEnoyl reductase LovC10.459
4is3NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 21.17.98.10.459
4ytnFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.459
5dldUD1UDP-N-Acetylglucosamine 2-epimerase/0.459
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.458
3q9tFAYUncharacterized protein/0.458
3r1rATPRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.458
4b722FBBeta-secretase 13.4.23.460.458
4fhf0TTSpore photoproduct lyase/0.458
2cvzNDP3-hydroxyisobutyrate dehydrogenase/0.457
2ilvC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.457
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.457
5a3bAPRSIR2 family protein/0.457
5la6GTPTubulin alpha-1B chain/0.457
1bdbNADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase/0.456
1xkdNAPIsocitrate dehydrogenase [NADP]/0.456
1zemNADXylitol dehydrogenase/0.456
3ieuGDPGTPase Era/0.456
4y4jLNREndothiapepsin3.4.23.220.456
1lbcCYZGlutamate receptor 2/0.455
1tehNADAlcohol dehydrogenase class-31.1.1.10.455
2g8yNADHydroxycarboxylate dehydrogenase B/0.455
2givACOHistone acetyltransferase KAT8/0.455
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.455
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.455
4o4iGTPTubulin alpha-1B chain/0.455
5jscFADPutative acyl-CoA dehydrogenase/0.455
1f20NAPNitric oxide synthase, brain1.14.13.390.454
1h73ANPHomoserine kinase2.7.1.390.454
1qyvNAPEstradiol 17-beta-dehydrogenase 11.1.1.620.454
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.454
2pg0FADAcyl-CoA dehydrogenase/0.454
2zjmF1MBeta-secretase 13.4.23.460.454
3tqxPLP2-amino-3-ketobutyrate coenzyme A ligase/0.454
5a3cNADSIR2 family protein/0.454
1e3sNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.453
1mj9COAHistone acetyltransferase ESA1/0.453
1o01NADAldehyde dehydrogenase, mitochondrial1.2.1.30.453
2rlcCHDCholoylglycine hydrolase3.5.1.240.453
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.453
3ll9ADPIsopentenyl phosphate kinase/0.453
3o3pGDDGlycosyl transferase, family 2/0.453
1fduNAPEstradiol 17-beta-dehydrogenase 11.1.1.620.452
1mjbACOHistone acetyltransferase ESA1/0.452
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.452
1bwsNDPGDP-L-fucose synthase/0.451
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.451
2ekpNAD2-deoxy-D-gluconate 3-dehydrogenase/0.451
2ex1C5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.451
3b70NAPEnoyl reductase LovC10.451
3x2wATPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
1j49NADD-lactate dehydrogenase1.1.1.280.450
1xddAAYIntegrin alpha-L/0.450
2g76NADD-3-phosphoglycerate dehydrogenase1.1.1.950.450
2pauD5M5'-deoxynucleotidase YfbR/0.450
2pk3GDDGDP-6-deoxy-D-mannose reductase/0.450
3d3wNAPL-xylulose reductase1.1.1.100.450
3dzkNMNADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.450
3kruFMNNADH:flavin oxidoreductase/NADH oxidase/0.450
3r6c17NAnthranilate phosphoribosyltransferase/0.450
5c3jUQ1Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.450
5c3jUQ1Succinate dehydrogenase cytochrome b560/0.450
1fy7COAHistone acetyltransferase ESA1/0.449
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.449
2igyA2TPlasmepsin 2/0.449
2ykeYKEHeat shock protein HSP 90-alpha/0.449
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.449
3q43D66M1 family aminopeptidase3.4.110.449
4jtqNAPAldo-keto reductase family 1 member C2/0.449
4m10ICDProstaglandin G/H synthase 21.14.99.10.449
4n9iPCGCatabolite expression activator/0.449
1kkq471Peroxisome proliferator-activated receptor alpha/0.448
1txiTX5Vitamin D3 receptor/0.448
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.448
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.448
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.448
3pm4F5NEndothiapepsin3.4.23.220.448
3r3sNADPutative oxidoreductase/0.448
4a8v2ANMajor pollen allergen Bet v 1-J/0.448
4lnbED5CaaX farnesyltransferase beta subunit Ram1/0.448
5dp2NAPCurF/0.448
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.447
1jqiFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial/0.447
1m8kNADNicotinamide-nucleotide adenylyltransferase2.7.7.10.447
1vl8NAPOxidoreductase, short chain dehydrogenase/reductase family/0.447
2bjfDXCCholoylglycine hydrolase3.5.1.240.447
2hu4G39Neuraminidase/0.447
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.447
3k4cFADPyranose 2-oxidase/0.447
3oibFDAPutative acyl-CoA dehydrogenase/0.447
4l7j1W2Beta-secretase 13.4.23.460.447
1nzyBCA4-chlorobenzoyl coenzyme A dehalogenase3.8.1.70.446
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
2gv8FADThiol-specific monooxygenase1.14.130.446
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.446
2xlrFADPutative flavin-containing monooxygenase/0.446
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.446
3a3gDLZLumazine protein/0.446
3gegNADShort-chain dehydrogenase/reductase SDR/0.446
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.446
3prsRITEndothiapepsin3.4.23.220.446
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.446
4bb3KKAIsopenicillin N synthase1.21.3.10.446
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.446
1by5GLY_GLY_GLY_AHO_AHO_AHO_FEFerrichrome-iron receptor/0.445
1kqgMGDFormate dehydrogenase, nitrate-inducible, major subunit1.1.5.60.445
2x8iX8ISerine/threonine-protein kinase Chk12.7.11.10.445
3iwjNADAminoaldehyde dehydrogenase/0.445
3jvvACPTwitching mobility protein/0.445
3wagTYDGlycosyltransferase/0.445
4fj0NAP17beta-hydroxysteroid dehydrogenase/0.445
4tuyGTPTubulin alpha-1B chain/0.445
4xw4ANPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
5a8aADPRiboflavin biosynthesis protein RibF2.7.1.260.445
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.444
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.444
1szgFNSCytochrome b2, mitochondrial1.1.2.30.444
1t9gFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.444
1z7yAA5Cysteine synthase 12.5.1.470.444
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.444
2wsbNADGalactitol dehydrogenase/0.444
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.444
3vdqNAD3-hydroxybutyrate dehydrogenase/0.444
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.444
4y35F90Endothiapepsin3.4.23.220.444
4yd7F5NEndothiapepsin3.4.23.220.444
5c3jFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.444
6req3CPMethylmalonyl-CoA mutase large subunit5.4.99.20.444
2a2sGSNGlutathione S-transferase P2.5.1.180.443
2he5NDPAldo-keto reductase family 1 member C211.1.10.443
2iibC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.443
2y0mACOHistone acetyltransferase KAT8/0.443
2zdyADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.443
3dgeADPSensor histidine kinase/0.443
3p8z36AGenome polyprotein2.1.1.560.443
3ska053Genome polyprotein2.7.7.480.443
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.443
4dmmNAP3-oxoacyl-[acyl-carrier-protein] reductase/0.443
4hxm1A8Bromodomain-containing protein 4/0.443
4kqqVPPPeptidoglycan D,D-transpeptidase FtsI/0.443
4l1xNAPAldo-keto reductase family 1 member C2/0.443
5esoTDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.443
1rf7DHFDihydrofolate reductase1.5.1.30.442
1tj0FADBifunctional protein PutA1.5.5.20.442
2bsxNOSPurine nucleoside phosphorylase/0.442
2dftADPShikimate kinase2.7.1.710.442
2gjnFMNNitronate monooxygenase1.13.12.160.442
2vprTDCTetracycline repressor protein class H/0.442
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.442
3aezGDPPantothenate kinase2.7.1.330.442
3fhyATPPyridoxal kinase2.7.1.350.442
4dfg0JVGag-Pol polyprotein3.4.23.160.442
4h3j10WBeta-secretase 13.4.23.460.442
4q71FADBifunctional protein PutA/0.442
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.442
4uugPXGBranched-chain amino acid aminotransferase, putative/0.442
1bim0QBRenin3.4.23.150.441
1xseNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
1zdwFLVPrenyltransferase/0.441
2g1s4IGRenin3.4.23.150.441
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.441
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.441
2xlpFADPutative flavin-containing monooxygenase/0.441
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.441
3ha7B32Hydroxymycolate synthase MmaA42.1.10.441
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.441
3wqmB29Diterpene synthase3.1.7.80.441
4bmvNAPShort-chain dehydrogenase/0.441
4h3i10VBeta-secretase 13.4.23.460.441
4j7xNAPSepiapterin reductase1.1.1.1530.441
1e1kFADNADPH:adrenodoxin oxidoreductase, mitochondrial1.18.1.60.440
1e2nRCAThymidine kinase/0.440
2ahrNAPPyrroline-5-carboxylate reductase/0.440
2ebaFADPutative glutaryl-CoA dehydrogenase/0.440
2ejzSAHDiphthine synthase/0.440
2hdjNDPAldo-keto reductase family 1 member C2/0.440
3gy0NAPNAD(P)-dependent oxidoreductase/0.440
3ju8NADN-succinylglutamate 5-semialdehyde dehydrogenase1.2.1.710.440
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.440
3pi0F91Endothiapepsin3.4.23.220.440
3qwbNDPProbable quinone oxidoreductase1.6.5.50.440
3wv7ADPHmd co-occurring protein HcgE/0.440
3x21FMNOxygen-insensitive NAD(P)H nitroreductase/0.440
4b63NAPL-ornithine N(5)-monooxygenase/0.440
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.440
5c3aURMHisto-blood group ABO system transferase/0.440
5c41ACPRibokinase/0.440