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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
4kotCE3Uncharacterized protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4kotCE3Uncharacterized protein/1.000
4koxCLSUncharacterized protein/0.773
4kovKOVUncharacterized protein/0.740
4kos4KOUncharacterized protein/0.688
4kouC04Uncharacterized protein/0.642
4koyCSCUncharacterized protein/0.606
4kowCFXUncharacterized protein/0.604
4klvKLVUncharacterized protein/0.534
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.504
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.503
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.500
3v0p4GWHisto-blood group ABO system transferase/0.492
2vbdV10Isopenicillin N synthase1.21.3.10.487
1dr2TAPDihydrofolate reductase1.5.1.30.483
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.483
2iviACWIsopenicillin N synthase1.21.3.10.479
2jb4A14Isopenicillin N synthase1.21.3.10.477
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.477
4b4dFADFerredoxin-NADP reductase/0.475
3v0o4GWHisto-blood group ABO system transferase/0.474
1hb1OCVIsopenicillin N synthase1.21.3.10.470
4jx1CAMCamphor 5-monooxygenase1.14.15.10.468
1hb3SCVIsopenicillin N synthase1.21.3.10.467
1obnASVIsopenicillin N synthase1.21.3.10.466
3qwbNDPProbable quinone oxidoreductase1.6.5.50.466
3zoiM2WIsopenicillin N synthase1.21.3.10.466
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.465
2bgjFADNADPH:ferredoxin reductase/0.464
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.464
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.463
5ex0SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.463
4c4oNADSADH/0.462
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.462
3wleNAD(R)-specific carbonyl reductase/0.461
1d6w00RProthrombin3.4.21.50.459
1a8pFADFerredoxin--NADP reductase/0.458
2gd2CAAProbable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )/0.457
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.457
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.457
3uovFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.456
4fk8FADFerredoxin--NADP reductase/0.456
1dr3TAPDihydrofolate reductase1.5.1.30.455
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.455
1u1gBBBUridine phosphorylase2.4.2.30.454
4kcfAKMFAD-dependent oxidoreductase/0.454
1bk0ACVIsopenicillin N synthase1.21.3.10.453
1qiqACCIsopenicillin N synthase1.21.3.10.453
3gqvNAPEnoyl reductase LovC10.453
4zu44TGWxcM-like protein/0.453
2z9dFMNFMN-dependent NADH-azoreductase/0.452
3f3sNADLambda-crystallin homolog/0.452
4bfxZVXPantothenate kinase2.7.1.330.452
2qimZEAClass 10 plant pathogenesis-related protein/0.451
2vnkFADNADPH:ferredoxin reductase/0.451
3b70NAPEnoyl reductase LovC10.451
3qlsNDPDihydrofolate reductase1.5.1.30.451
4b4w9L9Bifunctional protein FolD/0.451
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.451
1ve3SAMUncharacterized protein/0.450
2g8yNADHydroxycarboxylate dehydrogenase B/0.450
4bb3KKAIsopenicillin N synthase1.21.3.10.450
1h2bNAJNAD-dependent alcohol dehydrogenase/0.449
2ay95PVAromatic-amino-acid aminotransferase2.6.1.570.449
2vbpVB1Isopenicillin N synthase1.21.3.10.449
3d84NDPDihydrofolate reductase1.5.1.30.449
3eksCY9Actin-5C/0.449
3eufBAUUridine phosphorylase 1/0.449
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.449
2bu9HFVIsopenicillin N synthase1.21.3.10.448
1a5bIGPTryptophan synthase alpha chain/0.447
4uugPXGBranched-chain amino acid aminotransferase, putative/0.447
2wo7ASVIsopenicillin N synthase1.21.3.10.446
2xlpFADPutative flavin-containing monooxygenase/0.446
3oadLPORenin3.4.23.150.446
3ox4NADAlcohol dehydrogenase 21.1.1.10.446
3tm5SFGUncharacterized protein/0.446
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.446
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.446
1c7oPPGHemolysin/0.445
2e1zB4PPropionate kinase/0.445
3gw9VNILanosterol 14-alpha-demethylase/0.445
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.445
3oxfSAHHistone-lysine N-methyltransferase SMYD32.1.1.430.445
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.445
4kgmATPUncharacterized protein/0.445
5c3aURMHisto-blood group ABO system transferase/0.445
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.444
1s5kCOAAminoglycoside N(6')-acetyltransferase type 1/0.444
2h21SAMRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic2.1.1.1270.444
2qdxFADFerredoxin--NADP+ reductase/0.444
2vn1FK5Peptidylprolyl isomerase/0.444
3b7dCNIGlutamate receptor 2/0.444
4demYS4Farnesyl pyrophosphate synthase2.5.1.100.444
4i4z2NE1,4-dihydroxy-2-naphthoyl-CoA synthase/0.444
4kbyC2EStimulator of interferon genes protein/0.444
1qyvNAPEstradiol 17-beta-dehydrogenase 11.1.1.620.443
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
2gjlFMNNitronate monooxygenase1.13.12.160.443
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.443
2y60M8FIsopenicillin N synthase1.21.3.10.443
3aho3A2Oligopeptidase/0.443
3gwfNAPCyclohexanone monooxygenase/0.443
3lpfZ77Beta-glucuronidase3.2.1.310.443
3r1kCOAN-acetyltransferase Eis/0.443
3up3XCAaceDAF-12/0.443
1gthFADDihydropyrimidine dehydrogenase [NADP(+)]1.3.1.20.442
1h61PDNPentaerythritol tetranitrate reductase/0.442
2aclL05Oxysterols receptor LXR-alpha/0.442
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.442
2y6fM9FIsopenicillin N synthase1.21.3.10.442
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3toxNAPPutative oxidoreductase/0.442
4ambDUDPutative glycosyl transferase/0.442
4b79NADProbable short-chain dehydrogenase/0.442
1e3eNAIAlcohol dehydrogenase 41.1.1.10.441
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.441
4bftZVTPantothenate kinase2.7.1.330.441
4eb5PLPCysteine desulfurase IscS 2/0.441
4kc4WS3Histo-blood group ABO system transferase/0.441
4ktoFADPutative isovaleryl-CoA dehydrogenase protein/0.441
4ri1ACOUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase2.3.1.2020.441
4wriOKAOkadaic acid binding protein 2-alpha/0.441
1adfTADAlcohol dehydrogenase E chain1.1.1.10.440
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.440
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.440
1zdwFLVPrenyltransferase/0.440
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.440
3ei8PL5LL-diaminopimelate aminotransferase, chloroplastic/0.440
3q8hAO92-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.440
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4r21STRCytochrome P450 family 17 polypeptide 2/0.440
5e5h0T1Succinyl-CoA:acetate CoA-transferase/0.440
5fknTDCTetracycline repressor protein class D/0.440