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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
5bnw12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
5bnw12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/1.000
5c1d12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.613
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.610
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.500
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.497
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.487
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.486
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.483
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.482
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.481
3p62FMNPentaerythritol tetranitrate reductase/0.480
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.479
4jicFMNGTN Reductase/0.478
4df2FMNNADPH dehydrogenase/0.477
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.476
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.476
1h50FMNPentaerythritol tetranitrate reductase/0.475
4araC56Acetylcholinesterase3.1.1.70.472
1w6hTITPlasmepsin-23.4.23.390.470
3h3qH13Collagen type IV alpha-3-binding protein/0.469
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.469
4k6fNAPPutative Acetoacetyl-CoA reductase/0.467
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.466
1q84TZ4Acetylcholinesterase3.1.1.70.466
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
5czySAMEukaryotic huntingtin interacting protein B/0.466
1towCRZFatty acid-binding protein, adipocyte/0.465
1ra3MTXDihydrofolate reductase1.5.1.30.463
1xe65FPPlasmepsin-23.4.23.390.463
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.463
2xpc051UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.462
4loi1YCStimulator of interferon genes protein/0.462
4j0v1H7Beta-secretase 13.4.23.460.461
4tqgNDPPutative dTDP-d-glucose 4 6-dehydratase/0.461
1b5eDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.460
3d91REMRenin3.4.23.150.460
4ycpFMNtRNA-dihydrouridine(16) synthase/0.460
3f03FMNPentaerythritol tetranitrate reductase/0.459
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.458
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.458
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.457
2iibC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.457
2v16C47Renin3.4.23.150.457
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
4m83ERYOleandomycin glycosyltransferase2.4.10.457
4q0kGA3Phytohormone-binding protein/0.457
1vyrFMNPentaerythritol tetranitrate reductase/0.456
3bgsDIHPurine nucleoside phosphorylase2.4.2.10.456
3dziRGTADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.456
3p74FMNPentaerythritol tetranitrate reductase/0.456
1rzuADPGlycogen synthase 12.4.1.210.455
2zsiGA4Gibberellin receptor GID1A30.455
1umkFADNADH-cytochrome b5 reductase 31.6.2.20.454
1vi2NADQuinate/shikimate dehydrogenase/0.454
1yw8A75Methionine aminopeptidase 2/0.454
2rqfJH3Hemolymph juvenile hormone binding protein/0.454
1kh3ANPArgininosuccinate synthase/0.453
2cv2GSUGlutamate--tRNA ligase6.1.1.170.453
2iyfERYOleandomycin glycosyltransferase2.4.10.453
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.453
1h63FMNPentaerythritol tetranitrate reductase/0.452
1rneC60Renin3.4.23.150.452
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.452
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.451
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.451
1dyiFOLDihydrofolate reductase1.5.1.30.450
2hs8FMN12-oxophytodienoate reductase 31.3.1.420.450
3rpeFADPutative modulator of drug activity/0.450
4e2bFMNDehydrogenase/0.450
1dmyAZMCarbonic anhydrase 5A, mitochondrial4.2.1.10.449
2ab8MTPAdenosine kinase2.7.1.200.449
3b9xNOSPyrimidine-specific ribonucleoside hydrolase RihB3.2.2.80.449
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.449
4qxp1YEStimulator of interferon genes protein/0.449
2i7pACOPantothenate kinase 32.7.1.330.448
2v2zADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.448
2vyqFADFerredoxin--NADP reductase1.18.1.20.448
3p67FMNPentaerythritol tetranitrate reductase/0.448
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.448
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.448
4kbyC2EStimulator of interferon genes protein/0.448
1n4qLYS_CYS_VAL_ILE_LEUGeranylgeranyl transferase type-1 subunit beta2.5.1.590.447
1txtCAAHMG-CoA synthase/0.447
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.447
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3opmLUIDipeptidyl peptidase 4/0.447
3vdqNAD3-hydroxybutyrate dehydrogenase/0.447
1zdwFLVPrenyltransferase/0.446
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.446
2zvbSAHPrecorrin-3 C17-methyltransferase/0.446
3apwDP0Alpha-1-acid glycoprotein 2/0.446
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3jyqNADQuinate/shikimate dehydrogenase (NAD(+))/0.446
3k8q22APurine nucleoside phosphorylase2.4.2.10.446
4a862ANMajor pollen allergen Bet v 1-A/0.446
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.446
1owe675Urokinase-type plasminogen activator3.4.21.730.445
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.445
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.445
2nnqT4BFatty acid-binding protein, adipocyte/0.445
2qbuSAHPrecorrin-2 methyltransferase/0.445
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3vsxR32Renin3.4.23.150.445
4bfzZVZPantothenate kinase2.7.1.330.445
1icpFMN12-oxophytodienoate reductase 11.3.1.420.444
1mxfMTXPutative pteridine reductase 2/0.444
1o9bNAIQuinate/shikimate dehydrogenase/0.444
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.444
1udaUFGUDP-glucose 4-epimerase5.1.3.20.444
1wklATPNucleoside diphosphate kinase/0.444
2hrbNAPCarbonyl reductase [NADPH] 31.1.1.1840.444
3hgoFMN12-oxophytodienoate reductase 31.3.1.420.444
3k5c0BIBeta-secretase 13.4.23.460.444
4rp8ASCAscorbate-specific PTS system EIIC component/0.444
1b8oIMHPurine nucleoside phosphorylase2.4.2.10.443
1npdNADQuinate/shikimate dehydrogenase/0.443
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.443
1t7o152Carnitine O-acetyltransferase2.3.1.70.443
2gv8NDPThiol-specific monooxygenase1.14.130.443
2gyuHI6Acetylcholinesterase3.1.1.70.443
2p9gNAID-3-phosphoglycerate dehydrogenase1.1.1.950.443
2pa7TYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.443
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.443
3atzFMNProstaglandin F2a synthase/0.443
3o7bSAHRibosomal RNA small subunit methyltransferase Nep1/0.443
3zmg6Z0Beta-secretase 13.4.23.460.443
4jiq1L5GTN Reductase/0.443
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.442
1nzdUPGDNA beta-glucosyltransferase/0.442
2geuCOKPantothenate kinase2.7.1.330.442
2j3qTFLAcetylcholinesterase3.1.1.70.442
3ed1GA3Gibberellin receptor GID1/0.442
3eu5GBOProtein farnesyltransferase subunit beta2.5.1.580.442
3gqvNAPEnoyl reductase LovC10.442
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.442
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.441
1w34FADFerredoxin--NADP reductase1.18.1.20.441
2dxdANPNucleoside diphosphate kinase2.7.4.60.441
2g1n1IGRenin3.4.23.150.441
2il2LIXRenin3.4.23.150.441
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.441
3fr28CAFatty acid-binding protein, adipocyte/0.441
3fr5I4AFatty acid-binding protein, adipocyte/0.441
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.441
3tozNADShikimate dehydrogenase (NADP(+))/0.441
3zoiM2WIsopenicillin N synthase1.21.3.10.441
4g95OAGDihydrofolate reductase1.5.1.30.441
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.441
1bil0IURenin3.4.23.150.440
1yqzCOACoenzyme A disulfide reductase/0.440
2dfvNADL-threonine 3-dehydrogenase/0.440
2e0nSAHPrecorrin-2 C20-methyltransferase/0.440
2ex1C5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.440
2g1r3IGRenin3.4.23.150.440
3b2sB2STrichothecene 3-O-acetyltransferase/0.440
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3q9bB3NAcetylpolyamine amidohydrolase/0.440
3v2uATPProtein GAL3/0.440
4a8v2ANMajor pollen allergen Bet v 1-J/0.440
4p9dTMPDeoxycytidylate deaminase/0.440