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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
4kotCE3Uncharacterized protein

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4kotCE3Uncharacterized protein/1.000
4koxCLSUncharacterized protein/0.773
4kovKOVUncharacterized protein/0.711
4kos4KOUncharacterized protein/0.663
4kouC04Uncharacterized protein/0.649
4kowCFXUncharacterized protein/0.584
3pgpACOUncharacterized protein/0.561
4klvKLVUncharacterized protein/0.526
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.496
3v0p4GWHisto-blood group ABO system transferase/0.488
1dr2TAPDihydrofolate reductase1.5.1.30.479
4b4dFADFerredoxin-NADP reductase/0.475
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.474
3qlsNDPDihydrofolate reductase1.5.1.30.471
2vbdV10Isopenicillin N synthase1.21.3.10.470
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.469
3v0o4GWHisto-blood group ABO system transferase/0.467
4e2dFMNDehydrogenase/0.466
4kubCOAUncharacterized protein/0.463
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.463
5ex0SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.463
1h2bNAJNAD-dependent alcohol dehydrogenase/0.462
2iviACWIsopenicillin N synthase1.21.3.10.462
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.462
1mvtDTMDihydrofolate reductase1.5.1.30.460
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.460
4dc0NDPPutative ketoacyl reductase1.3.10.459
1a8pFADFerredoxin--NADP reductase/0.458
1dr3TAPDihydrofolate reductase1.5.1.30.458
3mtwM3RXaa-Pro dipeptidase, putative/0.458
3s3vTOPDihydrofolate reductase1.5.1.30.458
2wo7ASVIsopenicillin N synthase1.21.3.10.457
1mrqSTRAldo-keto reductase family 1 member C1/0.456
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.456
4fk8FADFerredoxin--NADP reductase/0.456
1dfoPLGSerine hydroxymethyltransferase2.1.2.10.455
1hb1OCVIsopenicillin N synthase1.21.3.10.455
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.454
3p62FMNPentaerythritol tetranitrate reductase/0.454
3qwbNDPProbable quinone oxidoreductase1.6.5.50.454
3zoiM2WIsopenicillin N synthase1.21.3.10.454
4lnbED5CaaX farnesyltransferase beta subunit Ram1/0.454
4xrbNDPPossible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc/0.454
1d6w00RProthrombin3.4.21.50.453
1obnASVIsopenicillin N synthase1.21.3.10.453
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.453
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.453
4zu44TGWxcM-like protein/0.453
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.452
1bwlFMNNADPH dehydrogenase 11.6.99.10.451
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.451
1rd7FOLDihydrofolate reductase1.5.1.30.450
3otwCOAPhosphopantetheine adenylyltransferase/0.450
3w5hFADNADH-cytochrome b5 reductase 31.6.2.20.450
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.449
4kc4WS3Histo-blood group ABO system transferase/0.449
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.449
1o9bNAIQuinate/shikimate dehydrogenase/0.448
2e1zB4PPropionate kinase/0.448
2f98NGVAklanonic acid methyl ester cyclase AcmA5.5.1.230.448
3eksCY9Actin-5C/0.448
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.448
3toxNAPPutative oxidoreductase/0.448
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.448
1gthFADDihydropyrimidine dehydrogenase [NADP(+)]1.3.1.20.447
1vi2NADQuinate/shikimate dehydrogenase/0.447
2bgjFADNADPH:ferredoxin reductase/0.447
2qtaTDPPyruvate dehydrogenase E1 component1.2.4.10.447
3h3r14HCollagen type IV alpha-3-binding protein/0.447
3nxxNDPDihydrofolate reductase1.5.1.30.447
3p74FMNPentaerythritol tetranitrate reductase/0.446
1ddrMTXDihydrofolate reductase1.5.1.30.445
1rd4L08Integrin alpha-L/0.445
2vnkFADNADPH:ferredoxin reductase/0.445
2xlpFADPutative flavin-containing monooxygenase/0.445
2z9dFMNFMN-dependent NADH-azoreductase/0.445
4bfxZVXPantothenate kinase2.7.1.330.445
5c3aURMHisto-blood group ABO system transferase/0.445
1a27ESTEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1hb3SCVIsopenicillin N synthase1.21.3.10.444
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.444
2qdxFADFerredoxin--NADP+ reductase/0.444
2vbpVB1Isopenicillin N synthase1.21.3.10.444
3hz5Z64Heat shock protein HSP 90-alpha/0.444
4demYS4Farnesyl pyrophosphate synthase2.5.1.100.444
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.443
1qyvNAPEstradiol 17-beta-dehydrogenase 11.1.1.620.443
1s5kCOAAminoglycoside N(6')-acetyltransferase type 1/0.443
1szgFNSCytochrome b2, mitochondrial1.1.2.30.443
2dhfDZFDihydrofolate reductase1.5.1.30.443
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.443
3bw4FMNPutative 2-nitropropane dioxygenase/0.443
3q43D66M1 family aminopeptidase3.4.110.443
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.443
3up3XCAaceDAF-12/0.443
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.443
4b4w9L9Bifunctional protein FolD/0.443
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.443
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.443
4i4z2NE1,4-dihydroxy-2-naphthoyl-CoA synthase/0.443
4jeyPLPAcetylornithine/succinyldiaminopimelate aminotransferase2.6.1.110.443
1ay0TPPTransketolase 12.2.1.10.442
1ddsMTXDihydrofolate reductase1.5.1.30.442
1rx7FOLDihydrofolate reductase1.5.1.30.442
2aclL05Oxysterols receptor LXR-alpha/0.442
3qt62P0Mevalonate diphosphate decarboxylase/0.442
3t3r9PLCytochrome P450 2A61.14.130.442
4bb3KKAIsopenicillin N synthase1.21.3.10.442
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.442
1pq944BOxysterols receptor LXR-beta/0.441
2zseACPPantothenate kinase2.7.1.330.441
3gqvNAPEnoyl reductase LovC10.441
3ppoDCKGlycine betaine/carnitine/choline-binding protein OpuCC/0.441
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
4c4oNADSADH/0.441
1bk0ACVIsopenicillin N synthase1.21.3.10.440
1kfbIGPTryptophan synthase alpha chain/0.440
1u1gBBBUridine phosphorylase2.4.2.30.440
1x2hLPALipoate-protein ligase A6.3.1.200.440
2b4rNADGlyceraldehyde-3-phosphate dehydrogenase/0.440
2ft0ACOdTDP-fucosamine acetyltransferase/0.440
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.440
2gd2CAAProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.440
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.440
3oetNADErythronate-4-phosphate dehydrogenase/0.440
3q8hAO92-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.440
3tozNADShikimate dehydrogenase (NADP(+))/0.440
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4b79NADProbable short-chain dehydrogenase/0.440
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.440