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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
4rgsV55Repressor protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4rgsV55Repressor protein/1.000
4twnB96Ephrin type-A receptor 32.7.10.10.499
1u1jC2F5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 12.1.1.140.495
1ipeNDPTropinone reductase 21.1.1.2360.492
4bftZVTPantothenate kinase2.7.1.330.487
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.484
2yphQQY2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.475
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.475
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.475
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.475
1ot7IU5Bile acid receptor/0.474
3arvSAUChitinase A/0.474
3rgaILDEpoxide hydrolase LasB5.5.10.474
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.473
1lkeDOGBilin-binding protein/0.472
2ekaSAHDiphthine synthase/0.472
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.472
2ejkSAHDiphthine synthase/0.471
2geuCOKPantothenate kinase2.7.1.330.470
2hpsCTZCa2+-triggered coelenterazine-binding protein 1/0.470
4bfwZVWPantothenate kinase2.7.1.330.470
1pq944BOxysterols receptor LXR-beta/0.469
3uk6ADPRuvB-like 23.6.4.120.469
5dp2NAPCurF/0.469
1f8gNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.468
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.468
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.468
1d3dBZTProthrombin3.4.21.50.466
4jln18VDeoxycytidine kinase2.7.1.740.466
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.464
2eeqSAHDiphthine synthase/0.464
2v58LZJBiotin carboxylase6.3.4.140.464
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.464
4e32DWNMethyltransferase/0.464
1d3pBT3Prothrombin3.4.21.50.463
1upw444Oxysterols receptor LXR-beta/0.463
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.463
2owuSAHDiphthine synthase/0.463
2yvgNADFerredoxin reductase/0.463
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
3q9bB3NAcetylpolyamine amidohydrolase/0.463
4fxfATPPyruvate kinase PKM2.7.1.400.463
4oztP1AEcdysone receptor, putative/0.463
2ehlSAHDiphthine synthase/0.462
2flhZEACytokinin-specific binding protein/0.462
2x9dITCTetracycline repressor protein class D/0.462
4e2yJHZMethyltransferase/0.462
4xbjIN5Alanine racemase, biosynthetic/0.462
5fm7ADPRuvB-like helicase/0.462
1nhtPGSAdenylosuccinate synthetase/0.461
2ociTYCValacyclovir hydrolase3.10.461
1hb1OCVIsopenicillin N synthase1.21.3.10.460
1obnASVIsopenicillin N synthase1.21.3.10.460
2ejzSAHDiphthine synthase/0.460
3o4rNAPDehydrogenase/reductase SDR family member 41.1.1.1840.460
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.460
4at0FADPossible succinate dehydrogenase/0.460
1mewXMPInosine-5'-monophosphate dehydrogenase/0.459
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.459
3pqbVGPPutative oxidoreductase/0.459
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.459
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.459
2dxxSAHDiphthine synthase/0.458
3owuEQUSteroid Delta-isomerase5.3.3.10.458
4bqyFNTEgl nine homolog 1/0.458
4jsr1NQNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.458
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.458
2eleSAHDiphthine synthase/0.457
2hv9SFGmRNA cap guanine-N7 methyltransferase2.1.1.560.457
2xlrFADPutative flavin-containing monooxygenase/0.457
3m13FADMonomeric sarcosine oxidase1.5.3.10.457
3ntrNADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.457
1k4hAPQQueuine tRNA-ribosyltransferase2.4.2.290.456
1ve3SAMUncharacterized protein/0.456
2clfF6FTryptophan synthase alpha chain/0.456
2dsgSAHDiphthine synthase/0.456
2e7rSAHDiphthine synthase/0.456
2gcqDOIAdenylosuccinate synthetase/0.456
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.456
4jzr4JREgl nine homolog 1/0.456
4qmpDKISerine/threonine-protein kinase 242.7.11.10.456
4xxvNAD3-isopropylmalate dehydrogenase/0.456
1je1GMPPurine nucleoside phosphorylase/0.455
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.455
2emuSAHDiphthine synthase/0.455
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.455
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.455
2rlcCHDCholoylglycine hydrolase3.5.1.240.455
3qlrNDPDihydrofolate reductase1.5.1.30.455
4b4vL34Bifunctional protein FolD/0.455
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.455
1rneC60Renin3.4.23.150.454
3sf6FDAGlutaryl-CoA dehydrogenase/0.454
1jnrFADAdenylylsulfate reductase, subunit A (AprA)/0.453
1pqc444Oxysterols receptor LXR-beta/0.453
2pchSAHDiphthine synthase/0.453
2r0pK2CPutative FAD-monooxygenase/0.453
3ndjJHZMethyltransferase/0.453
3pyzANPDihydrofolate synthase/folylpolyglutamate synthase/0.453
3rpeFADPutative modulator of drug activity/0.453
4bfvZVVPantothenate kinase2.7.1.330.453
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.453
1jpaANPEphrin type-B receptor 22.7.10.10.452
1ngiANPHeat shock cognate 71 kDa protein/0.452
1oc1ASVIsopenicillin N synthase1.21.3.10.452
2v6gNAP3-oxo-Delta(4,5)-steroid 5-beta-reductase/0.452
2xveFADPutative flavin-containing monooxygenase/0.452
2xvfFADPutative flavin-containing monooxygenase/0.452
3lqfNADGalactitol dehydrogenase/0.452
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.452
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.452
3up0D7SaceDAF-12/0.452
4bfyZVYPantothenate kinase2.7.1.330.452
5irnADPNucleotide binding oligomerization domain containing 2/0.452
1b87ACOAac(6')-Ii protein/0.451
1eioGCHGastrotropin/0.451
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
1qorNDPQuinone oxidoreductase 1/0.451
2fjbSFDAdenylylsulfate reductase, subunit A (AprA)/0.451
2iviACWIsopenicillin N synthase1.21.3.10.451
2pckSAHDiphthine synthase/0.451
4f7iNAD3-isopropylmalate dehydrogenase1.1.1.850.451
4jlk1NODeoxycytidine kinase2.7.1.740.451
4jlm1NNDeoxycytidine kinase2.7.1.740.451
4jt81NRNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.451
4jx1CAHCamphor 5-monooxygenase1.14.15.10.451
1fcbFMNCytochrome b2, mitochondrial1.1.2.30.450
1jdvADNPurine nucleoside phosphorylase/0.450
1zeoC01Peroxisome proliferator-activated receptor gamma/0.450
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.450
3h3r14HCollagen type IV alpha-3-binding protein/0.450
3lpiZ74Beta-secretase 13.4.23.460.450
3rkuNAPNADP-dependent 3-hydroxy acid dehydrogenase/0.450
3v0p4GWHisto-blood group ABO system transferase/0.450
4bqwQNMEgl nine homolog 1/0.450
4dbs0HVAldo-keto reductase family 1 member C3/0.450
4n3l2FNProthrombin3.4.21.50.450
4psbGA3Cytokinin-specific binding protein/0.450
4r1lADPPhenylacetate-coenzyme A ligase/0.450
2dgnDOIAdenylosuccinate synthetase isozyme 1/0.449
2dv3SAHDiphthine synthase/0.449
2e8rSAHDiphthine synthase/0.449
2ydd2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.449
3zhvTDWMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.449
4bfzZVZPantothenate kinase2.7.1.330.449
4dvi2IWTankyrase-12.4.2.300.449
4kxjP34Nucleoprotein/0.449
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.449
1bwlFMNNADPH dehydrogenase 11.6.99.10.448
1p33MTXPteridine reductase 11.5.1.330.448
1tysDHFThymidylate synthase/0.448
2e08SAHDiphthine synthase/0.448
2ed3SAHDiphthine synthase/0.448
2ek3SAHDiphthine synthase/0.448
2fjdSFDAdenylylsulfate reductase, subunit A (AprA)/0.448
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.448
2pg0FADAcyl-CoA dehydrogenase/0.448
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.448
3u4cNDPNADPH-dependent reductase BacG/0.448
3wqmB29Diterpene synthase3.1.7.80.448
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.448
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.448
1blzACVIsopenicillin N synthase1.21.3.10.447
1hb3SCVIsopenicillin N synthase1.21.3.10.447
1kt6RTLRetinol-binding protein 4/0.447
2cvzNDP3-hydroxyisobutyrate dehydrogenase/0.447
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.447
2dxvSAHDiphthine synthase/0.447
2el3SAHDiphthine synthase/0.447
2fa3ACOHydroxymethylglutaryl-CoA synthase/0.447
2hveADPNucleoside diphosphate kinase A2.7.4.60.447
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.447
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.447
2p6dSAHDiphthine synthase/0.447
2q2qNADBeta-D-hydroxybutyrate dehydrogenase/0.447
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3h7uNAPNADPH-dependent aldo-keto reductase, chloroplastic/0.447
3iogSDFMetallo-beta-lactamase type 2/0.447
3r96ACOMccE protein/0.447
3wznBTNStreptavidin/0.447
4ubvCOASteroid 3-ketoacyl-CoA thiolase/0.447
4uugPXGBranched-chain amino acid aminotransferase, putative/0.447
5epoTUD7-alpha-hydroxysteroid deydrogenase/0.447
5f54TMPSingle-stranded-DNA-specific exonuclease/0.447
1nghATPHeat shock cognate 71 kDa protein/0.446
1sriDMBStreptavidin/0.446
1w7kADPDihydrofolate synthase/folylpolyglutamate synthase6.3.2.120.446
2c42TPPPyruvate synthase/0.446
2e15SAHDiphthine synthase/0.446
2egbSAHDiphthine synthase/0.446
2eklNADD-3-phosphoglycerate dehydrogenase/0.446
3ha5SFGHydroxymycolate synthase MmaA42.1.10.446
3tfyMET_LEU_GLY_PRON-alpha-acetyltransferase 502.3.10.446
4mk728OGenome polyprotein2.7.7.480.446
1drhNAPDihydrofolate reductase1.5.1.30.445
1gtrATPGlutamine--tRNA ligase6.1.1.180.445
1kt3RTLRetinol-binding protein 4/0.445
1vf3GDNGlutathione S-transferase 32.5.1.180.445
1yryMSGPurine nucleoside phosphorylase2.4.2.10.445
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.445
2ek2SAHDiphthine synthase/0.445
2w6mOA1Biotin carboxylase6.3.4.140.445
2yk2YJXHeat shock protein HSP 90-alpha/0.445
3d28B34Genome polyprotein2.7.7.480.445
3ebiBEYM1 family aminopeptidase3.4.110.445
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.445
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.445
3h3qH13Collagen type IV alpha-3-binding protein/0.445
3oqkS52Renin3.4.23.150.445
3vf60H6Glucokinase2.7.1.20.445
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.445
4e2xTYDMethyltransferase/0.445
4m4922YL-lactate dehydrogenase A chain1.1.1.270.445
4qe6JN3Bile acid receptor/0.445
1di8DTQCyclin-dependent kinase 22.7.11.220.444
1wngSAHDiphthine synthase/0.444
2e95B75Geranylgeranyl pyrophosphate synthase/0.444
2owkSAHDiphthine synthase/0.444
2p5cSAHDiphthine synthase/0.444
2pcgSAHDiphthine synthase/0.444
2xviFADPutative flavin-containing monooxygenase/0.444
2ydbNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.444
2ym1FADPhenylacetone monooxygenase1.14.13.920.444
3d3wNAPL-xylulose reductase1.1.1.100.444
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.444
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.444
4fweFADLysine-specific histone demethylase 1B10.444
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.444
4u9yCOAAlpha-tubulin N-acetyltransferase 1/0.444
1odcA8BAcetylcholinesterase3.1.1.70.443
1osvCHCBile acid receptor/0.443
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.443
1stdBFSScytalone dehydratase4.2.1.940.443
1sweBTNStreptavidin/0.443
1zdwFLVPrenyltransferase/0.443
2clmF6FTryptophan synthase alpha chain/0.443
2eh5SAHDiphthine synthase/0.443
2el0SAHDiphthine synthase/0.443
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.443
2hq9FADMll6688 protein/0.443
2x7jTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.443
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.443
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.443
3lfeZ84Mitogen-activated protein kinase 14/0.443
3zhuTD8Multifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.443
4b8wNAPGDP-L-fucose synthase1.1.1.2710.443
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4relKMPGlycosyltransferase/0.443
1ahiCHO7-alpha-hydroxysteroid dehydrogenase1.1.1.1590.442
1b5dDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.442
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.442
2ea2F77Methionine aminopeptidase 2/0.442
2huxSAHDiphthine synthase/0.442
2jgsBTNAvidin/0.442
2wksCB63-dehydroquinate dehydratase4.2.1.100.442
3cavCI23-oxo-5-beta-steroid 4-dehydrogenase/0.442
3h3sH15Collagen type IV alpha-3-binding protein/0.442
3q3cNADNAD-dependent L-serine dehydrogenase/0.442
3v2uATPProtein GAL3/0.442
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
4cfaWOPIntegrase/0.442
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.442
4jyzATPGlutamine--tRNA ligase6.1.1.180.442
5ej5TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.442
5emhNAPIridoid synthase1.3.1.990.442
1fvpFMANon-fluorescent flavoprotein/0.441
1ndzFR5Adenosine deaminase3.5.4.40.441
1ngeATPHeat shock cognate 71 kDa protein/0.441
2ejjSAHDiphthine synthase/0.441
2eniSAHDiphthine synthase/0.441
2ihvTPPN(2)-(2-carboxyethyl)arginine synthase/0.441
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.441
2uuvFADAlkyldihydroxyacetonephosphate synthase2.5.1.260.441
2xw7NDPDihydrofolate reductase/0.441
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
3gdpFAD(R)-mandelonitrile lyase 24.1.2.100.441
3ohh3HHBeta-secretase 13.4.23.460.441
3vri1KXHLA class I histocompatibility antigen, B-57 alpha chain/0.441
4ttjFMCPurine nucleoside phosphorylase DeoD-type/0.441
5dozNDPJamJ/0.441
1lcwSHMStreptavidin/0.440
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.440
2daaDCSD-alanine aminotransferase2.6.1.210.440
2dv4SAHDiphthine synthase/0.440
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2gv8NDPThiol-specific monooxygenase1.14.130.440
2o7pNAPRiboflavin biosynthesis protein RibD/0.440
2owfSAHDiphthine synthase/0.440
2w6qOA5Biotin carboxylase6.3.4.140.440
2zevB71Geranylgeranyl pyrophosphate synthase/0.440
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.440
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.440
3evcSAHGenome polyprotein2.1.1.560.440
3f03FMNPentaerythritol tetranitrate reductase/0.440
3q8hAO92-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.440
3w8dNAD3-hydroxybutyrate dehydrogenase/0.440
3zkyWT4Isopenicillin N synthase1.21.3.10.440
4cf1IY7Integrase/0.440
4ckrDI1Epithelial discoidin domain-containing receptor 12.7.10.10.440
4h7zGUNQueuine tRNA-ribosyltransferase2.4.2.290.440
4ho8THMGlucose-1-phosphate thymidylyltransferase/0.440
4tmcFMNOld yellow enzyme/0.440
4xybNDPFormate dehydrogenase/0.440