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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
3bbhSFGRibosomal RNA small subunit methyltransferase Nep12.1.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3bbhSFGRibosomal RNA small subunit methyltransferase Nep12.1.11.000
3bbdSAHRibosomal RNA small subunit methyltransferase Nep12.1.10.533
4dbzNDPPutative ketoacyl reductase1.3.10.483
3omuIBDHeat shock protein 83/0.476
4ips1G4Mycocyclosin synthase1.14.21.90.470
3o7bSAHRibosomal RNA small subunit methyltransferase Nep1/0.468
4g7gVFVLanosterol 14-alpha-demethylase/0.468
5ahsCOAAcyl-CoA dehydrogenase/0.467
1xe65FPPlasmepsin-23.4.23.390.466
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.465
1nooCAHCamphor 5-monooxygenase1.14.15.10.463
3ai3NDPNADPH-sorbose reductase/0.463
3qt62P0Mevalonate diphosphate decarboxylase/0.462
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.461
2uxhQUEHTH-type transcriptional regulator TtgR/0.461
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.461
2gjlFMNNitronate monooxygenase1.13.12.160.459
3h3r14HCollagen type IV alpha-3-binding protein/0.458
4jwfSAHtRNA (guanine(9)-N1)-methyltransferase/0.458
3t2zFADSulfide-quinone reductase/0.457
2uxoTACHTH-type transcriptional regulator TtgR/0.456
2gv8NDPThiol-specific monooxygenase1.14.130.455
3h06VBPGlutamate receptor 2/0.455
3h3t16HCollagen type IV alpha-3-binding protein/0.455
4kbyC2EStimulator of interferon genes protein/0.455
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.455
4i1iNADMalate dehydrogenase/0.454
1j9zFADNADPH--cytochrome P450 reductase/0.453
1xe55FEPlasmepsin-23.4.23.390.453
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.453
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4j16NAPNAD(P) transhydrogenase subunit beta/0.452
1t2cNAIL-lactate dehydrogenase1.1.1.270.451
1tj0FADBifunctional protein PutA1.5.5.20.450
3phiNDPShikimate dehydrogenase (NADP(+))/0.450
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.450
4nmdFDABifunctional protein PutA/0.450
3otwCOAPhosphopantetheine adenylyltransferase/0.449
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.449
2p20PRXAcetyl-coenzyme A synthetase/0.448
1g6kNADGlucose 1-dehydrogenase1.1.1.470.447
1lf2R37Plasmepsin-23.4.23.390.447
2fy4COACholine O-acetyltransferase2.3.1.60.447
2rlcCHDCholoylglycine hydrolase3.5.1.240.447
4c34STUcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
4kgnSAHtRNA (cytidine(34)-2'-O)-methyltransferase/0.447
2z9dFMNFMN-dependent NADH-azoreductase/0.446
3gqvNAPEnoyl reductase LovC10.446
4g3jVNTLanosterol 14-alpha-demethylase/0.446
6ctsCICCitrate synthase, mitochondrial2.3.3.10.446
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.445
4r81FMNPredicted NADH dehydrogenase/0.445
4xboSAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ2.1.1.2000.445
2g1n1IGRenin3.4.23.150.444
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.444
3r95ACOMccE protein/0.444
4eb7PLPCysteine desulfurase IscS 2/0.444
1rf7DHFDihydrofolate reductase1.5.1.30.443
2owfSAHDiphthine synthase/0.443
3s1dZIRCytokinin dehydrogenase 11.5.99.120.443
3ut5LOCTubulin beta chain/0.443
4ambDUDPutative glycosyl transferase/0.443
1cscCMCCitrate synthase, mitochondrial2.3.3.10.442
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.442
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.442
2hk9NAPShikimate dehydrogenase (NADP(+))/0.442
3f03FMNPentaerythritol tetranitrate reductase/0.442
4ktl1CQCytochrome P450/0.442
1culFOKAdenylate cyclase type 2/0.441
1culFOKAdenylate cyclase type 5/0.441
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.441
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.441
2i7pACOPantothenate kinase 32.7.1.330.441
4dc0NDPPutative ketoacyl reductase1.3.10.441
4rheFMNFlavin prenyltransferase UbiX/0.441
5ctsCMCCitrate synthase, mitochondrial2.3.3.10.441
1dr5NAPDihydrofolate reductase1.5.1.30.440
1gcoNADGlucose 1-dehydrogenase1.1.1.470.440
1me6IVSPlasmepsin-23.4.23.390.440
1qy8RDIEndoplasmin/0.440
2he5NDPAldo-keto reductase family 1 member C211.1.10.440
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.440
3gwfFADCyclohexanone monooxygenase/0.440
3qlrNDPDihydrofolate reductase1.5.1.30.440