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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
3eon341Glutaryl-CoA dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3eon341Glutaryl-CoA dehydrogenase/1.000
3gncQQQGlutaryl-CoA dehydrogenase/0.622
1xddAAYIntegrin alpha-L/0.520
2rhrEMOPutative ketoacyl reductase1.3.10.502
5c1mCLRMu-type opioid receptor/0.493
2vcmM11Isopenicillin N synthase1.21.3.10.491
4l5b1UXDeoxycytidine kinase2.7.1.740.489
4dch4DCGlucokinase2.7.1.20.488
1oc1ASVIsopenicillin N synthase1.21.3.10.485
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.485
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.483
4isf1FXGlucokinase2.7.1.20.479
4iah1DXAlr2278 protein/0.476
1yw8A75Methionine aminopeptidase 2/0.475
4ybnFADFlavin-nucleotide-binding protein/0.475
4qx5CMPcGMP-dependent protein kinase 12.7.11.120.474
3h3sH15Collagen type IV alpha-3-binding protein/0.472
2vbpVB1Isopenicillin N synthase1.21.3.10.471
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.471
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.471
3s41S41Glucokinase2.7.1.20.471
1cqp803Integrin alpha-L/0.470
2rqfJH3Hemolymph juvenile hormone binding protein/0.470
3gwfFADCyclohexanone monooxygenase/0.470
3iktNADRedox-sensing transcriptional repressor Rex/0.470
1qv0CZHObelin/0.469
3l6jZ90Alr2278 protein/0.469
1c7oPPGHemolysin/0.468
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.468
2y3sTIRTamL/0.468
2yj5ATPCopper-transporting ATPase/0.467
4isg1FYGlucokinase2.7.1.20.467
4h6uACOAlpha-tubulin N-acetyltransferase 1/0.466
2po7CHDFerrochelatase, mitochondrial4.99.1.10.465
1kqwRTLCellular retinol-binding protein type II/0.464
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.464
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.464
2cy0NAPShikimate dehydrogenase (NADP(+))/0.463
3pn1IVHDNA ligase/0.463
4da6GA2Purine nucleoside phosphorylase DeoD-type2.4.2.10.463
2vbdV10Isopenicillin N synthase1.21.3.10.462
4h6zACOAlpha-tubulin N-acetyltransferase 1/0.462
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.461
2uxpCLMHTH-type transcriptional regulator TtgR/0.461
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.460
2ga2A19Methionine aminopeptidase 2/0.460
2puiADPMethylthioribose kinase2.7.1.1000.460
3h3t16HCollagen type IV alpha-3-binding protein/0.460
4ap1NAPSteroid monooxygenase/0.460
4jlm1NNDeoxycytidine kinase2.7.1.740.460
2bu9HFVIsopenicillin N synthase1.21.3.10.459
3occDIHPurine nucleoside phosphorylase DeoD-type/0.459
4a83DXCMajor pollen allergen Bet v 1-A/0.459
4dhyS41Glucokinase2.7.1.20.459
4fewPP2Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.459
4s1iPLPPyridoxal kinase, putative/0.459
1hb3SCVIsopenicillin N synthase1.21.3.10.458
1p33MTXPteridine reductase 11.5.1.330.458
1pkfEPDEpothilone C/D epoxidase1.140.458
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.458
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.458
2ea2F77Methionine aminopeptidase 2/0.458
2npaMMBPeroxisome proliferator-activated receptor alpha/0.458
2pl0STITyrosine-protein kinase Lck2.7.10.20.458
2uxoTACHTH-type transcriptional regulator TtgR/0.458
1hb1OCVIsopenicillin N synthase1.21.3.10.457
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.457
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.457
3njoPYVAbscisic acid receptor PYR1/0.457
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
4ipw1G7Mycocyclosin synthase1.14.21.90.457
1uhhCZPAequorin-2/0.456
1ygkRRCPyridoxal kinase2.7.1.350.456
2b365PPEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.456
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.456
2zbaZBATrichothecene 3-O-acetyltransferase/0.456
1hfqMOTDihydrofolate reductase1.5.1.30.455
1jf2CZHObelin/0.455
1pq6965Oxysterols receptor LXR-beta/0.455
2e8hSAHDiphthine synthase/0.455
2yhuWHFPteridine reductase/0.455
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.455
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.455
3uzaT4GAdenosine receptor A2a/0.455
1rgsCMPcAMP-dependent protein kinase type I-alpha regulatory subunit/0.454
3lxiCAMCytochrome P450/0.454
4twnB96Ephrin type-A receptor 32.7.10.10.454
1rd4L08Integrin alpha-L/0.453
1synF89Thymidylate synthase/0.453
2dv3SAHDiphthine synthase/0.453
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.453
2y60M8FIsopenicillin N synthase1.21.3.10.453
3zoiM2WIsopenicillin N synthase1.21.3.10.453
4i421HA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.453
4j6cSTRCytochrome P450 monooxygenase/0.453
4jlk1NODeoxycytidine kinase2.7.1.740.453
4jln18VDeoxycytidine kinase2.7.1.740.453
1pqc444Oxysterols receptor LXR-beta/0.452
1qjfACSIsopenicillin N synthase1.21.3.10.452
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.452
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
3c3xNAPEugenol synthase 11.1.1.3180.452
4ia2BIVVitamin D3 receptor A/0.452
1el4CTZObelin/0.451
1rdtL79Retinoic acid receptor RXR-alpha/0.451
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.451
2rlcCHDCholoylglycine hydrolase3.5.1.240.451
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.451
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.451
4ixd1HVIntegrin alpha-L/0.451
4lgaA2OAbscisic acid receptor PYL2/0.451
4qzuRTLRetinol-binding protein 2/0.451
5d1bTSNHistone deacetylase 83.5.1.980.451
1pd9CO4Dihydrofolate reductase1.5.1.30.450
3d4pNADL-lactate dehydrogenase 11.1.1.270.450
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
3lnbCOAN-acetyltransferase family protein/0.450
3nx2FERFerulic acid decarboxylase/0.450
4klaCHDFerrochelatase, mitochondrial4.99.1.10.450
4xoqF42Coenzyme F420:L-glutamate ligase/0.450
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.450
1n83CLRNuclear receptor ROR-alpha/0.449
1y5xE89Queuine tRNA-ribosyltransferase2.4.2.290.449
2oiqSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.449
3fkoFKOMitogen-activated protein kinase 14/0.449
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3qpg3QPAspartate aminotransferase2.6.1.10.449
4cdmFO1Deoxyribodipyrimidine photolyase/0.449
4rh10TTSpore photoproduct lyase/0.449
1m13HYFNuclear receptor subfamily 1 group I member 2/0.448
1qiqACCIsopenicillin N synthase1.21.3.10.448
1w06W05Isopenicillin N synthase1.21.3.10.448
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.448
2jn3JN3Fatty acid-binding protein, liver/0.448
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.448
4mv1ADPBiotin carboxylase6.3.4.140.448
1cbqRE9Cellular retinoic acid-binding protein 2/0.447
1o9bNAIQuinate/shikimate dehydrogenase/0.447
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.447
2eglSAHDiphthine synthase/0.447
2gbyBRNHTH-type transcriptional regulator QacR/0.447
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
3gw9VNILanosterol 14-alpha-demethylase/0.447
3t2yFADSulfide-quinone reductase/0.447
5bn4ANPV-type ATP synthase alpha chain/0.447
5dozNDPJamJ/0.447
1dliUDXUDP-glucose 6-dehydrogenase/0.446
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
1trgCB3Thymidylate synthase/0.446
2cy2ACOProbable acetyltransferase/0.446
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
3bsyACOUDP-N-acetylbacillosamine N-acetyltransferase2.3.1.2030.446
3k2fNKXCarbonic anhydrase 24.2.1.10.446
3k47D09Dihydrofolate reductase1.5.1.30.446
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.446
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
3w6hAZMCarbonic anhydrase 14.2.1.10.446
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.446
4iae1DXAlr2278 protein/0.446
4qa2SHHHistone deacetylase 83.5.1.980.446
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.446
1ej3CZHAequorin-2/0.445
1oj4CDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.445
1uzwCDHIsopenicillin N synthase1.21.3.10.445
2y6fM9FIsopenicillin N synthase1.21.3.10.445
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.445
2d09FLVBiflaviolin synthase CYP158A2/0.444
2e08SAHDiphthine synthase/0.444
2feuCAMCamphor 5-monooxygenase1.14.15.10.444
2he5NDPAldo-keto reductase family 1 member C211.1.10.444
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.444
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3fp0FP015-O-acetyltransferase/0.444
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3p3zP3ZPutative cytochrome P450/0.444
4a6eASEAcetylserotonin O-methyltransferase2.1.1.40.444
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.444
4g3jVNTLanosterol 14-alpha-demethylase/0.444
4hshQEIQueuine tRNA-ribosyltransferase2.4.2.290.444
5ab6CAANonspecific lipid-transfer protein, putative/0.444
5hs1VORLanosterol 14-alpha demethylase/0.444
1blzACVIsopenicillin N synthase1.21.3.10.443
1q9mROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.443
2dv5SAHDiphthine synthase/0.443
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
2p15EZTEstrogen receptor/0.443
2pnuENMAndrogen receptor/0.443
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.443
2qimZEAClass 10 plant pathogenesis-related protein/0.443
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
3mdvCL6Cholesterol 24-hydroxylase/0.443
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.443
3tk3CPZCytochrome P450 2B41.14.14.10.443
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.443
1k7l544Peroxisome proliferator-activated receptor alpha/0.442
1obnASVIsopenicillin N synthase1.21.3.10.442
1upw444Oxysterols receptor LXR-beta/0.442
1wpgADPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.442
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
2z97CAMCamphor 5-monooxygenase1.14.15.10.442
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
3oafOAGDihydrofolate reductase1.5.1.30.442
4bb3KKAIsopenicillin N synthase1.21.3.10.442
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4g7gVFVLanosterol 14-alpha-demethylase/0.442
1bk0ACVIsopenicillin N synthase1.21.3.10.441
1qv1CZHObelin/0.441
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
2bxqIMNSerum albumin/0.441
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.441
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.441
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.441
3jyqNADQuinate/shikimate dehydrogenase (NAD(+))/0.441
3lfeZ84Mitogen-activated protein kinase 14/0.441
3nn6HNK6-hydroxy-L-nicotine oxidase/0.441
4c9oCAMCytochrome P450/0.441
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.441
4qij1HA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.441
3rfmCFFAdenosine receptor A2a/0.441
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.440
1ivrCBAAspartate aminotransferase, mitochondrial2.6.1.10.440
2hxzH7JCathepsin S3.4.22.270.440
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.440
2jb4A14Isopenicillin N synthase1.21.3.10.440
2pchSAHDiphthine synthase/0.440
2pulACPMethylthioribose kinase2.7.1.1000.440
3csdEMOPutative ketoacyl reductase1.3.10.440
3da24MDCarbonic anhydrase 134.2.1.10.440
3hl0NADMaleylacetate reductase/0.440
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4ead0NPThymidine phosphorylase2.4.2.40.440
4jqh1MFAlr2278 protein/0.440
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.440
4mxeACON-acetyltransferase ESCO12.3.10.440
4tuvCPZCytochrome P450 1191.140.440
4tzt468Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440