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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
5dgtTZDBenzoylformate decarboxylase4.1.1.7

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
5dgtTZDBenzoylformate decarboxylase4.1.1.71.000
2fwnTDPBenzoylformate decarboxylase4.1.1.70.766
4ju8TZDBenzoylformate decarboxylase4.1.1.70.764
4ju9TZDBenzoylformate decarboxylase4.1.1.70.698
1bfdTPPBenzoylformate decarboxylase4.1.1.70.687
4mq5TPPBenzoylformate decarboxylase4.1.1.70.671
4qelTZDBenzoylformate decarboxylase4.1.1.70.620
4mzxTZDBenzoylformate decarboxylase4.1.1.70.582
4k9nTZDBenzoylformate decarboxylase4.1.1.70.573
4jd5TZDBenzoylformate decarboxylase4.1.1.70.561
4gm0TZDBenzoylformate decarboxylase4.1.1.70.541
1mczTDPBenzoylformate decarboxylase4.1.1.70.537
4jubTPPBenzoylformate decarboxylase4.1.1.70.532
4gm1TZDBenzoylformate decarboxylase4.1.1.70.501
3fznD7KBenzoylformate decarboxylase4.1.1.70.500
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.496
1xe55FEPlasmepsin-23.4.23.390.489
4k9pTPPBenzoylformate decarboxylase4.1.1.70.485
2g76NADD-3-phosphoglycerate dehydrogenase1.1.1.950.484
3ieuGDPGTPase Era/0.484
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.478
1la2NADInositol-3-phosphate synthase5.5.1.40.476
3otwCOAPhosphopantetheine adenylyltransferase/0.476
3owaFADAcyl-CoA dehydrogenase/0.473
2givACOHistone acetyltransferase KAT8/0.467
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.467
2g8yNADHydroxycarboxylate dehydrogenase B/0.466
1g1aNADdTDP-glucose 4,6-dehydratase/0.465
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.464
1zk7FADMercuric reductase1.16.1.10.464
1kqgHQOFormate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit/0.461
4frkDWDBeta-secretase 13.4.23.460.461
1dyjDDFDihydrofolate reductase1.5.1.30.460
2vtbFADCryptochrome DASH, chloroplastic/mitochondrial/0.460
4iv6FDAIsovaleryl-CoA dehydrogenase/0.460
2c1zU2FAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.459
2ebaFADPutative glutaryl-CoA dehydrogenase/0.459
4fhf0TTSpore photoproduct lyase/0.459
1c9k5GPBifunctional adenosylcobalamin biosynthesis protein CobU/0.458
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.457
1x1aSAMC-20 methyltransferase/0.457
2y0mACOHistone acetyltransferase KAT8/0.457
3ctyFADProbable thioredoxin reductase/0.457
1po7TZDBenzoylformate decarboxylase4.1.1.70.456
2j3nFADThioredoxin reductase 1, cytoplasmic1.8.1.90.456
4dyn0MRNucleoprotein/0.456
3f1kNAPUncharacterized oxidoreductase YciK10.455
4i02CMPcAMP-activated global transcriptional regulator CRP/0.455
1k6vXN2Gag-Pol polyprotein3.4.23.160.454
1kkq471Peroxisome proliferator-activated receptor alpha/0.453
1kvuUPGUDP-glucose 4-epimerase5.1.3.20.453
2qbmCAMCamphor 5-monooxygenase1.14.15.10.453
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.453
4emdC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.453
2qblCAMCamphor 5-monooxygenase1.14.15.10.452
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.452
2wb2FADRE11660p/0.451
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.451
4uugPXGBranched-chain amino acid aminotransferase, putative/0.451
1oc1ASVIsopenicillin N synthase1.21.3.10.450
1t85CAMCamphor 5-monooxygenase1.14.15.10.450
3b70NAPEnoyl reductase LovC10.450
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.450
3ut5LOCTubulin beta chain/0.450
4ph9IBPProstaglandin G/H synthase 21.14.99.10.450
2dftADPShikimate kinase2.7.1.710.449
2vhxNADAlanine dehydrogenase1.4.1.10.449
2po7CHDFerrochelatase, mitochondrial4.99.1.10.448
2qbnCAMCamphor 5-monooxygenase1.14.15.10.448
3m30COMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.448
3m30COMMethyl-coenzyme M reductase I subunit beta2.8.4.10.448
3sx2NADUncharacterized protein/0.448
5dbfNDPIridoid synthase1.3.1.990.448
5itzGTPTubulin alpha-1B chain/0.448
5jscFADPutative acyl-CoA dehydrogenase/0.448
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.447
1t2aNDPGDP-mannose 4,6 dehydratase4.2.1.470.447
3cinNADMyo-inositol-1-phosphate synthase-related protein/0.447
2irzI02Beta-secretase 13.4.23.460.446
2r26CMCCitrate synthase2.3.3.160.446
4fizCUE17beta-hydroxysteroid dehydrogenase/0.446
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.445
4b7754MBeta-secretase 13.4.23.460.445
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.445
1x1cSAHC-20 methyltransferase/0.444
2gjlFMNNitronate monooxygenase1.13.12.160.444
2ou2ACOHistone acetyltransferase KAT5/0.444
2ylzFADPhenylacetone monooxygenase1.14.13.920.444
2ztlNADD(-)-3-hydroxybutyrate dehydrogenase/0.444
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.444
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.444
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.443
1mj9COAHistone acetyltransferase ESA1/0.443
1n7hNDPGDP-mannose 4,6 dehydratase 24.2.1.470.443
1w4xFADPhenylacetone monooxygenase1.14.13.920.443
2gh5FADGlutathione reductase, mitochondrial1.8.1.70.443
3l9hEMQKinesin-like protein KIF11/0.443
3q43D66M1 family aminopeptidase3.4.110.443
4xr9NADCalS8/0.443
1a72PADAlcohol dehydrogenase E chain1.1.1.10.442
1kszPGSAdenylosuccinate synthetase/0.442
1npdNADQuinate/shikimate dehydrogenase/0.442
3a28NADL-2,3-butanediol dehydrogenase1.1.1.760.442
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.442
3vyeVYERenin3.4.23.150.442
4bqtC5ESoluble acetylcholine receptor/0.442
4dldTZGGlutamate receptor ionotropic, kainate 1/0.442
4wecNADShort chain dehydrogenase/0.442
1cg3IMOAdenylosuccinate synthetase/0.441
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1wn3HXCPhenylacetic acid degradation protein PaaI/0.441
2ahrNAPPyrroline-5-carboxylate reductase/0.441
3ad9FADSubunit beta of sarcosine oxidase/0.441
3lqfNADGalactitol dehydrogenase/0.441
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.441
4hmvWUBPhenazine biosynthesis protein PhzG1.40.441
4l4xNDPAmphI/0.441
4rvdSAMD-mycarose 3-C-methyltransferase/0.441
1mjaCOAHistone acetyltransferase ESA1/0.440
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/0.440
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.440
2j09FMNDeoxyribodipyrimidine photo-lyase4.1.99.30.440
2ywlFADThioredoxin reductase related protein/0.440
2znnS44Peroxisome proliferator-activated receptor alpha/0.440
3zl8ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.440
4b0qGMFBeta-secretase 13.4.23.460.440
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.440
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.440
6cp4CAMCamphor 5-monooxygenase1.14.15.10.440