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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
2p3qSAHGenome polyprotein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2p3qSAHGenome polyprotein/1.000
2p41SAHGenome polyprotein/0.620
1l9kSAHGenome polyprotein2.7.7.480.595
3p97SAMGenome polyprotein2.1.1.560.582
4k6mSAHGenome polyprotein/0.576
3p8zSAHGenome polyprotein2.1.1.560.574
2xbmSAHGenome polyprotein/0.563
2p1dSAHGenome polyprotein2.7.7.480.559
4ctjSAMGenome polyprotein/0.555
1r6aSAHGenome polyprotein2.7.7.480.554
2pxaSAHGenome polyprotein2.7.7.480.548
5dtoSAHGenome polyprotein/0.543
3eluSAMMethyltransferase/0.534
3eldSFGMethyltransferase/0.528
3elySAHMethyltransferase/0.522
3p8z36AGenome polyprotein2.1.1.560.522
5cuqNSCGenome polyprotein/0.516
5jjrSAHGenome polyprotein/0.515
3evaSAHGenome polyprotein2.1.1.560.503
1oc1ASVIsopenicillin N synthase1.21.3.10.498
2px5SAHGenome polyprotein2.7.7.480.498
3evcSAHGenome polyprotein2.1.1.560.496
3evbSAHGenome polyprotein2.1.1.560.494
1vyrFMNPentaerythritol tetranitrate reductase/0.492
5jjsSAHGenome polyprotein/0.490
1obnASVIsopenicillin N synthase1.21.3.10.485
2vbdV10Isopenicillin N synthase1.21.3.10.484
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.483
4bb3KKAIsopenicillin N synthase1.21.3.10.481
4ctkSAMGenome polyprotein/0.477
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.475
4g3pUD1Bifunctional protein GlmU/0.475
2px2SAHGenome polyprotein2.7.7.480.473
3gwfNAPCyclohexanone monooxygenase/0.473
4h6rFDAProline dehydrogenase/0.472
2oxtSAMGenome polyprotein/0.471
3f03FMNPentaerythritol tetranitrate reductase/0.471
5eccNAPDehydrofolate reductase type I/0.469
1hb1OCVIsopenicillin N synthase1.21.3.10.467
1hb3SCVIsopenicillin N synthase1.21.3.10.467
3r6sCMPCRP-like cAMP-activated global transcriptional regulator/0.467
4dtiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.467
4ddhMS0Pantothenate synthetase6.3.2.10.466
1bk0ACVIsopenicillin N synthase1.21.3.10.464
1bwsNDPGDP-L-fucose synthase/0.464
2qblCAMCamphor 5-monooxygenase1.14.15.10.463
2y6fM9FIsopenicillin N synthase1.21.3.10.463
3p82FMNPentaerythritol tetranitrate reductase/0.463
2vcmM11Isopenicillin N synthase1.21.3.10.462
4bfvZVVPantothenate kinase2.7.1.330.462
5fs7FADApoptosis-inducing factor 1, mitochondrial1.1.10.462
1qiqACCIsopenicillin N synthase1.21.3.10.461
3fwyADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein/0.460
3lqfNADGalactitol dehydrogenase/0.460
3p67FMNPentaerythritol tetranitrate reductase/0.460
3p62FMNPentaerythritol tetranitrate reductase/0.458
4j95ACPFibroblast growth factor receptor 2/0.457
1blzACVIsopenicillin N synthase1.21.3.10.456
2w9hTOPDihydrofolate reductase1.5.1.30.456
2jb4A14Isopenicillin N synthase1.21.3.10.455
2wo7ASVIsopenicillin N synthase1.21.3.10.455
3zoiM2WIsopenicillin N synthase1.21.3.10.455
4i02CMPcAMP-activated global transcriptional regulator CRP/0.455
1qjfACSIsopenicillin N synthase1.21.3.10.454
4ikeADPAdenylate kinase/0.454
4jldADPAdenylate kinase/0.454
3iaeD7KBenzaldehyde lyase/0.453
1dliUDXUDP-glucose 6-dehydrogenase/0.452
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.452
2abbFMNPentaerythritol tetranitrate reductase/0.452
4e2bFMNDehydrogenase/0.452
2iviACWIsopenicillin N synthase1.21.3.10.451
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.451
3gfbNADL-threonine 3-dehydrogenase/0.451
3nl6TPSUncharacterized protein/0.451
4anwO92Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
1m78NDPDihydrofolate reductase1.5.1.30.450
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.450
3ggj25HHypoxanthine-guanine phosphoribosyltransferase2.4.2.80.450
1pnvTYDdTDP-epi-vancosaminyltransferase2.4.1.3110.449
1r8cUTPCCA-adding enzyme2.7.7.720.449
2y60M8FIsopenicillin N synthase1.21.3.10.449
3c35KAIGlutamate receptor ionotropic, kainate 1/0.449
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
4b2wBZ0Glucose-1-phosphate thymidylyltransferase/0.449
4r7uUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.449
2ijgFADCryptochrome DASH, chloroplastic/mitochondrial/0.448
1ftlDNQGlutamate receptor 2/0.447
1u3dFADCryptochrome-1/0.447
1yreCOAUncharacterized protein/0.447
3enkUPGUDP-glucose 4-epimerase/0.447
3ijdC2FMethylenetetrahydrofolate reductase/0.447
3t1tGDPProbable gliding protein mglA/0.447
3zkyWT4Isopenicillin N synthase1.21.3.10.447
1bwkFMNNADPH dehydrogenase 11.6.99.10.446
2hamC33Vitamin D3 receptor/0.446
2zl9VDAVitamin D3 receptor/0.446
3fhxPLPPyridoxal kinase2.7.1.350.446
3zhrTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.446
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
1ia1NDPDihydrofolate reductase1.5.1.30.445
2ft9CHDFatty acid-binding protein 2, liver/0.445
3a783EVVitamin D3 receptor/0.445
3n8nN883-dehydroquinate dehydratase4.2.1.100.445
3r9iADPSeptum site-determining protein MinD/0.445
3vrvYSDVitamin D3 receptor/0.445
4g3qUD1Bifunctional protein GlmU/0.445
5bsgNAPPyrroline-5-carboxylate reductase/0.445
1enyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
1uu9BI33-phosphoinositide-dependent protein kinase 12.7.11.10.444
1uzwCDHIsopenicillin N synthase1.21.3.10.444
1w06W05Isopenicillin N synthase1.21.3.10.444
2bl4NADLactaldehyde reductase1.1.1.770.444
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
3eyhIZATyrosine-protein kinase JAK1/0.444
3oafOAGDihydrofolate reductase1.5.1.30.444
3upkUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.444
1dnpFADDeoxyribodipyrimidine photo-lyase4.1.99.30.443
1np7FADCryptochrome DASH/0.443
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.443
3b1jNADGlyceraldehyde-3-phosphate dehydrogenase/0.443
3ed1GA3Gibberellin receptor GID1/0.443
3p8iFMNPentaerythritol tetranitrate reductase/0.443
3qlrNDPDihydrofolate reductase1.5.1.30.443
4a6nFADTetX family tetracycline inactivation enzyme/0.443
4lutDCSAlanine racemase/0.443
1ddsMTXDihydrofolate reductase1.5.1.30.442
1dr2TAPDihydrofolate reductase1.5.1.30.442
1udcUFMUDP-glucose 4-epimerase5.1.3.20.442
2ad5ADPCTP synthase/0.442
3cluFADElectron transfer flavoprotein subunit alpha/0.442
3w1tWRODihydroorotate dehydrogenase (fumarate)1.3.98.10.442
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.442
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.442
4s0vSUVOrexin receptor type 2/0.442
1bsvNDPGDP-L-fucose synthase/0.441
1f8sFADL-amino-acid oxidase1.4.3.20.441
1h50FMNPentaerythritol tetranitrate reductase/0.441
1nzfUPGDNA beta-glucosyltransferase/0.441
1ykdCMPAdenylate cyclase/0.441
2qimZEAClass 10 plant pathogenesis-related protein/0.441
3emdSFGMethyltransferase/0.441
4a4zANPAntiviral helicase SKI23.6.4.130.441
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.441
4cf7ADPAdenylate kinase/0.441
4lt63ATPoly(A) polymerase gamma2.7.7.190.441
4wctFADFructosyl amine:oxygen oxidoreductase/0.441
1ai9NDPDihydrofolate reductase1.5.1.30.440
1qpjSTUTyrosine-protein kinase Lck2.7.10.20.440
2ql6ADPNicotinamide riboside kinase 1/0.440
2wpxACOOrf14/0.440
2x7gPVBSRSF protein kinase 22.7.11.10.440
3a6rFMNFMN-binding protein/0.440
3nmnPYVAbscisic acid receptor PYL1/0.440
4ehyADPTetraacyldisaccharide 4'-kinase/0.440
4lrzADPPEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL2.70.440
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.440