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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
3gl2D3MDdmC

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3gl2D3MDdmC/1.000
3gtsD3MDdmC/0.586
3gb4D3MDdmC/0.539
3gobHXXDdmC/0.510
1zdwFLVPrenyltransferase/0.490
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.478
2iyaZIOOleandomycin glycosyltransferase/0.472
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.470
2zjmF1MBeta-secretase 13.4.23.460.470
4iarERM5-hydroxytryptamine receptor 1B/0.470
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.469
3vrwYS5Vitamin D3 receptor/0.469
1xddAAYIntegrin alpha-L/0.468
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.468
2y0mACOHistone acetyltransferase KAT8/0.468
2jb4A14Isopenicillin N synthase1.21.3.10.467
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.467
4l8u9AZSerum albumin/0.467
1qrpHH0Pepsin A-43.4.23.10.466
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.466
1pq944BOxysterols receptor LXR-beta/0.465
4ocvANPAminoglycoside phosphotransferase/0.465
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.464
2g1r3IGRenin3.4.23.150.461
4bfxZVXPantothenate kinase2.7.1.330.461
3br3ETHTH-type transcriptional regulator QacR/0.460
4ambDUDPutative glycosyl transferase/0.460
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.459
2ejzSAHDiphthine synthase/0.459
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.459
3vt5YI2Vitamin D3 receptor/0.458
1hfqMOTDihydrofolate reductase1.5.1.30.457
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.457
2zevB71Geranylgeranyl pyrophosphate synthase/0.457
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1mj9COAHistone acetyltransferase ESA1/0.456
1qiqACCIsopenicillin N synthase1.21.3.10.456
3sf6FDAGlutaryl-CoA dehydrogenase/0.456
3uqdADPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.456
2gesCOKPantothenate kinase2.7.1.330.455
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.455
3ohh3HHBeta-secretase 13.4.23.460.455
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.455
1h6dNDPGlucose--fructose oxidoreductase1.1.99.280.454
1upw444Oxysterols receptor LXR-beta/0.454
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.453
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1pqc444Oxysterols receptor LXR-beta/0.452
1zg32HIIsoflavone 4'-O-methyltransferase/0.452
3c1tMYCDihydroflavonol 4-reductase1.1.1.2190.452
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.451
3p62FMNPentaerythritol tetranitrate reductase/0.450
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.450
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.449
3hl0NADMaleylacetate reductase/0.449
3rueNADUDP-N-acetylglucosamine 4-epimerase/0.449
4twnB96Ephrin type-A receptor 32.7.10.10.449
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.448
3ru7NADUDP-N-acetylglucosamine 4-epimerase/0.448
1synF89Thymidylate synthase/0.447
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.447
3ruhNADUDP-N-acetylglucosamine 4-epimerase/0.447
4bb3KKAIsopenicillin N synthase1.21.3.10.447
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.447
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.447
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.447
2x7hPFNProstaglandin reductase 310.446
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.446
3pm1ETHTH-type transcriptional regulator QacR/0.446
3wagTYDGlycosyltransferase/0.446
4ruoBIVVitamin D3 receptor A/0.446
1p8dCO1Oxysterols receptor LXR-beta/0.445
2ebaFADPutative glutaryl-CoA dehydrogenase/0.445
3vcyUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.445
4u7wNDPMxaA/0.445
4yaiNAIC alpha-dehydrogenase/0.445
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.445
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1fxsNAPGDP-L-fucose synthase/0.444
1ie8KH1Vitamin D3 receptor/0.444
1nytNAPShikimate dehydrogenase (NADP(+))/0.444
2rl1UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.444
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.444
4rvgTYDD-mycarose 3-C-methyltransferase/0.444
1culFOKAdenylate cyclase type 2/0.443
1culFOKAdenylate cyclase type 5/0.443
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.443
3nmpPYVAbscisic acid receptor PYL2/0.443
3o6o94MHeat shock protein 83/0.443
3qfrFMNNADPH--cytochrome P450 reductase/0.443
3rucNADUDP-N-acetylglucosamine 4-epimerase/0.443
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.443
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3w0yDS4Vitamin D3 receptor/0.443
4l9kEHFSerum albumin/0.443
5dozNDPJamJ/0.443
5hs1VORLanosterol 14-alpha demethylase/0.443
3d91REMRenin3.4.23.150.442
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
1fm4DXCMajor pollen allergen Bet v 1-L/0.441
1hb3SCVIsopenicillin N synthase1.21.3.10.441
1uydPU8Heat shock protein HSP 90-alpha/0.441
2a94AP0L-lactate dehydrogenase1.1.1.270.441
2g8yNADHydroxycarboxylate dehydrogenase B/0.441
2ieaTDPPyruvate dehydrogenase E1 component1.2.4.10.441
3hwxTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.441
3oqkS52Renin3.4.23.150.441
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
4hy6FJ1Heat shock protein HSP 90-alpha/0.441
1psa0ZLPepsin A3.4.23.10.440
2getCOKPantothenate kinase2.7.1.330.440
3c1oNAPEugenol synthase/0.440
3o4rNAPDehydrogenase/reductase SDR family member 41.1.1.1840.440
4a83DXCMajor pollen allergen Bet v 1-A/0.440
4at0FADPossible succinate dehydrogenase/0.440
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4jq4IMNAldo-keto reductase family 1 member C2/0.440
5dp2NAPCurF/0.440