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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
2vyxFMNDodecin

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2vyxFMNDodecin/1.000
2v18FMNDodecin/0.764
2v19FMNDodecin/0.549
3nksACJProtoporphyrinogen oxidase1.3.3.40.495
1e79ATPATP synthase subunit alpha, mitochondrial/0.489
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.489
2vbpVB1Isopenicillin N synthase1.21.3.10.476
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.476
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.469
4uugPXGBranched-chain amino acid aminotransferase, putative/0.469
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.468
4psbGA3Cytokinin-specific binding protein/0.468
2qimZEAClass 10 plant pathogenesis-related protein/0.467
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
5dp2NAPCurF/0.465
2vd0D27Hematopoietic prostaglandin D synthase/0.464
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
2yac937Serine/threonine-protein kinase PLK12.7.11.210.460
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
1hb3SCVIsopenicillin N synthase1.21.3.10.459
4a2aATPCell division protein FtsA/0.459
2hk9NAPShikimate dehydrogenase (NADP(+))/0.458
4g8jTHMUridine phosphorylase/0.458
2bjsACVIsopenicillin N synthase1.21.3.10.457
2ejzSAHDiphthine synthase/0.456
3v0p4GWHisto-blood group ABO system transferase/0.456
4kbyC2EStimulator of interferon genes protein/0.455
1obnASVIsopenicillin N synthase1.21.3.10.454
3ox34X4Ribosyldihydronicotinamide dehydrogenase [quinone]/0.454
4b7754MBeta-secretase 13.4.23.460.454
4kw51W6Decaprenylphosphoryl-beta-D-ribose oxidase/0.454
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
5c1gGDUHisto-blood group ABO system transferase/0.453
1ja1FMNNADPH--cytochrome P450 reductase/0.452
3c1oNAPEugenol synthase/0.452
3kslSZHProtein farnesyltransferase subunit beta2.5.1.580.452
1akcPPEAspartate aminotransferase, mitochondrial2.6.1.10.451
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.451
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.451
4wctFADFructosyl amine:oxygen oxidoreductase/0.451
1hb1OCVIsopenicillin N synthase1.21.3.10.450
1x8lOXRRetinol dehydratase/0.450
1k7fIAVTryptophan synthase alpha chain/0.449
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4ntjAZJP2Y purinoceptor 12/0.449
2e16SAHDiphthine synthase/0.448
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.448
4bfxZVXPantothenate kinase2.7.1.330.448
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3phjDHKShikimate dehydrogenase (NADP(+))/0.447
3zkyWT4Isopenicillin N synthase1.21.3.10.447
4b0532DBeta-secretase 13.4.23.460.447
1ppjANYCytochrome b/0.446
1qiqACCIsopenicillin N synthase1.21.3.10.446
1vhzAPRADP compounds hydrolase NudE3.6.10.446
2vcmM11Isopenicillin N synthase1.21.3.10.446
3fktSIIBeta-secretase 13.4.23.460.446
3kkzSAMUncharacterized protein/0.446
3qiyQI1Botulinum neurotoxin type A3.4.24.690.446
2am22LGUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.445
2bu9HFVIsopenicillin N synthase1.21.3.10.445
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3qizQI2Botulinum neurotoxin type A3.4.24.690.445
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.444
1w0kADPATP synthase subunit alpha, mitochondrial/0.444
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.444
2g1n1IGRenin3.4.23.150.444
2iviACWIsopenicillin N synthase1.21.3.10.444
2jb4A14Isopenicillin N synthase1.21.3.10.444
2rfiSAHHistone-lysine N-methyltransferase EHMT1/0.444
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.444
4ead0NPThymidine phosphorylase2.4.2.40.444
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
1ex75GPGuanylate kinase2.7.4.80.443
4dymIYZActivin receptor type-12.7.11.300.443
1ascNPLAspartate aminotransferase2.6.1.10.442
1bjkFADFerredoxin--NADP reductase1.18.1.20.442
1s4oGDPGlycolipid 2-alpha-mannosyltransferase/0.442
3dtcVINMitogen-activated protein kinase kinase kinase 92.7.11.250.442
3fvqATPFe(3+) ions import ATP-binding protein FbpC/0.442
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.442
3oqkS52Renin3.4.23.150.442
4bfuZVUPantothenate kinase2.7.1.330.442
5bv3M7Gm7GpppX diphosphatase3.6.1.590.442
1fw0KAIGlutamate receptor 2/0.441
1qh0FADFerredoxin--NADP reductase1.18.1.20.441
1uzwCDHIsopenicillin N synthase1.21.3.10.441
2o3uNGDADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.441
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.441
2zevB71Geranylgeranyl pyrophosphate synthase/0.441
4cukNAID-lactate dehydrogenase/0.441
2owfSAHDiphthine synthase/0.440
2tsrUMPThymidylate synthase2.1.1.450.440
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3nhfVVVRibosyldihydronicotinamide dehydrogenase [quinone]/0.440
4b2gV1NUncharacterized protein/0.440
4mr92BXGamma-aminobutyric acid type B receptor subunit 1/0.440
5dozNDPJamJ/0.440