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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1umkFADNADH-cytochrome b5 reductase 31.6.2.2

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1umkFADNADH-cytochrome b5 reductase 31.6.2.21.000
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.601
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.600
1qx4FADNADH-cytochrome b5 reductase 31.6.2.20.575
1cnfFADNitrate reductase [NADH]1.7.1.10.573
2cndFADNitrate reductase [NADH]1.7.1.10.573
2eixFADNADH-cytochrome b5 reductase/0.553
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.533
1cneFADNitrate reductase [NADH]1.7.1.10.499
1rz1NADPhenol 2-hydroxylase component B/0.474
1x1aSAMC-20 methyltransferase/0.471
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.471
1x1cSAHC-20 methyltransferase/0.469
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.469
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.469
2dhfDZFDihydrofolate reductase1.5.1.30.464
1icsFMN12-oxophytodienoate reductase 11.3.1.420.462
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.461
3zeiAWHO-acetylserine sulfhydrylase/0.460
4bfzZVZPantothenate kinase2.7.1.330.460
1bwsNDPGDP-L-fucose synthase/0.459
4xrbNDPPossible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc/0.459
4bb3KKAIsopenicillin N synthase1.21.3.10.454
1tllFMNNitric oxide synthase, brain1.14.13.390.453
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.453
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.451
2wvlGDDMannosyl-3-phosphogylcerate synthase/0.451
1o9bNAIQuinate/shikimate dehydrogenase/0.449
2zvcSAHPrecorrin-3 C17-methyltransferase/0.449
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.448
1j9zFADNADPH--cytochrome P450 reductase/0.447
3l5lFMNXenobiotic reductase/0.447
3p62FMNPentaerythritol tetranitrate reductase/0.447
3t4eNADQuinate/shikimate dehydrogenase/0.447
1x1bSAHC-20 methyltransferase/0.446
2gh5FADGlutathione reductase, mitochondrial1.8.1.70.446
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.446
1h50FMNPentaerythritol tetranitrate reductase/0.445
2ejzSAHDiphthine synthase/0.445
2hfuMEVMevalonate kinase/0.445
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.445
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.445
2i3gNAPN-acetyl-gamma-glutamyl-phosphate reductase1.2.1.380.444
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.444
3lqsPSZD-alanine aminotransferase2.6.1.210.444
3tr05GPGuanylate kinase/0.444
1vhzAPRADP compounds hydrolase NudE3.6.10.442
2qbuSAHPrecorrin-2 methyltransferase/0.442
3n0hTOPDihydrofolate reductase1.5.1.30.442
3tozNADShikimate dehydrogenase (NADP(+))/0.442
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.442
4wecNADShort chain dehydrogenase/0.442
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.441
3k5c0BIBeta-secretase 13.4.23.460.441
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.441
1mvtDTMDihydrofolate reductase1.5.1.30.440
2iyfERYOleandomycin glycosyltransferase2.4.10.440
3n14FMNXenobiotic reductase/0.440
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.440