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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
2o4cNADErythronate-4-phosphate dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2o4cNADErythronate-4-phosphate dehydrogenase/1.000
4p63NADProbable deoxyhypusine synthase2.5.1.460.506
4q71FADBifunctional protein PutA/0.491
3p62FMNPentaerythritol tetranitrate reductase/0.490
3rueNADUDP-N-acetylglucosamine 4-epimerase/0.485
4nxuADPMitochondrial dynamics protein MID51/0.485
2y3sTIRTamL/0.483
3f03FMNPentaerythritol tetranitrate reductase/0.480
4ipw1G7Mycocyclosin synthase1.14.21.90.476
3oetNADErythronate-4-phosphate dehydrogenase/0.473
2y3rTRKTamL/0.472
3rucNADUDP-N-acetylglucosamine 4-epimerase/0.468
1xddAAYIntegrin alpha-L/0.467
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.467
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.466
3toxNAPPutative oxidoreductase/0.466
1hdoNAPFlavin reductase (NADPH)/0.465
4djaFAD(6-4) photolyase/0.462
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.462
4xguADPPutative pachytene checkpoint protein 2/0.461
1u3dFADCryptochrome-1/0.460
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
4g3jVNTLanosterol 14-alpha-demethylase/0.460
4g6gFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.460
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.459
2c20NADUDP-glucose 4-epimerase/0.459
2y4gTIRTamL/0.458
4jicFMNGTN Reductase/0.458
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.457
3lqfNADGalactitol dehydrogenase/0.456
4oqyNDP(S)-imine reductase/0.456
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.456
2ylrNAPPhenylacetone monooxygenase1.14.13.920.455
4ambDUDPutative glycosyl transferase/0.455
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.454
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.454
3zhbNAPPutative dehydrogenase/0.454
3ru7NADUDP-N-acetylglucosamine 4-epimerase/0.453
4g7gVFVLanosterol 14-alpha-demethylase/0.453
4hhz15SPoly [ADP-ribose] polymerase 12.4.2.300.453
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.452
4k6fNAPPutative Acetoacetyl-CoA reductase/0.452
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.451
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.451
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
4m83ERYOleandomycin glycosyltransferase2.4.10.451
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.451
1bwsNDPGDP-L-fucose synthase/0.450
1u4oNDDL-lactate dehydrogenase1.1.1.270.450
3atyFMNProstaglandin F2a synthase/0.450
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
1g6kNADGlucose 1-dehydrogenase1.1.1.470.449
2ed3SAHDiphthine synthase/0.449
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.449
2gjlFMNNitronate monooxygenase1.13.12.160.449
3own3OXRenin3.4.23.150.449
3uylTYDProbable NDP-rhamnosyltransferase/0.449
4dbzNDPPutative ketoacyl reductase1.3.10.449
4q72FADBifunctional protein PutA/0.449
4q73FADBifunctional protein PutA/0.449
1t2cNAIL-lactate dehydrogenase1.1.1.270.448
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.448
3b70NAPEnoyl reductase LovC10.448
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.160.448
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.448
1h63FMNPentaerythritol tetranitrate reductase/0.447
1hkuNADC-terminal-binding protein 11.1.10.447
1xe55FEPlasmepsin-23.4.23.390.447
2g1n1IGRenin3.4.23.150.447
2g76NADD-3-phosphoglycerate dehydrogenase1.1.1.950.447
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.447
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.446
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.446
3oeyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.446
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.446
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.445
2h9iEADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.445
3s1dZIRCytokinin dehydrogenase 11.5.99.120.445
1bil0IURenin3.4.23.150.444
2dftADPShikimate kinase2.7.1.710.444
4e2bFMNDehydrogenase/0.444
4g9kFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.444
4qecNAPElxO/0.444
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.443
1o0sNAINAD-dependent malic enzyme, mitochondrial1.1.1.380.443
1zeoC01Peroxisome proliferator-activated receptor gamma/0.443
2f1kNAPPrephenate dehydrogenase/0.443
3c1y2BADNA integrity scanning protein DisA/0.443
4fmxCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.443
4ktoFADPutative isovaleryl-CoA dehydrogenase protein/0.443
4uymVOR14-alpha sterol demethylase Cyp51B/0.443
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
2iyfERYOleandomycin glycosyltransferase2.4.10.442
3f3sNADLambda-crystallin homolog/0.442
3k4nFADPyranose 2-oxidase/0.442
3qt62P0Mevalonate diphosphate decarboxylase/0.442
5d3qGDPDynamin-13.6.5.50.442
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1tehNADAlcohol dehydrogenase class-31.1.1.10.441
2dfvNADL-threonine 3-dehydrogenase/0.441
3a3gDLZLumazine protein/0.441
3c212BADNA integrity scanning protein DisA/0.441
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.441
3lu1NADUDP-N-acetylglucosamine 4-epimerase/0.441
1sq5ADPPantothenate kinase2.7.1.330.440
1udbUFGUDP-glucose 4-epimerase5.1.3.20.440
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.440
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.440
2ikuLIYRenin3.4.23.150.440
3icrFADCoenzyme A disulfide reductase/0.440
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.440