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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
1kbiFMNCytochrome b2, mitochondrial1.1.2.3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1kbiFMNCytochrome b2, mitochondrial1.1.2.31.000
1kbjFMNCytochrome b2, mitochondrial1.1.2.30.630
1szgFNSCytochrome b2, mitochondrial1.1.2.30.612
1szfFMNCytochrome b2, mitochondrial1.1.2.30.609
1goxFMNPeroxisomal (S)-2-hydroxy-acid oxidase1.1.3.150.572
2oz0FMNCytochrome b2, mitochondrial1.1.2.30.570
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.560
2nliFMNLactate oxidase/0.558
1qcwFNSCytochrome b2, mitochondrial1.1.2.30.552
5ebuFMNLactate oxidase/0.538
2e77FMNLactate oxidase/0.537
2j6xFMNLactate oxidase/0.525
3p62FMNPentaerythritol tetranitrate reductase/0.518
1h63FMNPentaerythritol tetranitrate reductase/0.516
1h50FMNPentaerythritol tetranitrate reductase/0.510
4rjeFNRLactate oxidase/0.507
1icqFMN12-oxophytodienoate reductase 11.3.1.420.502
3f03FMNPentaerythritol tetranitrate reductase/0.500
3p74FMNPentaerythritol tetranitrate reductase/0.500
4yl2FMNLactate oxidase/0.500
3hf3FMNChromate reductase/0.487
1z44FMNNADPH dehydrogenase/0.483
3p82FMNPentaerythritol tetranitrate reductase/0.481
1h51FMNPentaerythritol tetranitrate reductase/0.480
2abbFMNPentaerythritol tetranitrate reductase/0.479
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.478
3p84FMNPentaerythritol tetranitrate reductase/0.475
1vyrFMNPentaerythritol tetranitrate reductase/0.472
3p67FMNPentaerythritol tetranitrate reductase/0.472
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.472
1bwlFMNNADPH dehydrogenase 11.6.99.10.471
2du2FMNLactate oxidase/0.471
4tmbFMNOld yellow enzyme/0.471
1adfTADAlcohol dehydrogenase E chain1.1.1.10.470
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.470
4jicFMNGTN Reductase/0.470
3t4eNADQuinate/shikimate dehydrogenase/0.468
1a72PADAlcohol dehydrogenase E chain1.1.1.10.467
1icsFMN12-oxophytodienoate reductase 11.3.1.420.465
2q3rFMN12-oxophytodienoate reductase 11.3.1.420.465
3gkaFMNN-ethylmaleimide reductase/0.462
3hgrFMN12-oxophytodienoate reductase 11.3.1.420.462
3p8jFMNPentaerythritol tetranitrate reductase/0.461
4h6kFMNNADPH dehydrogenase 11.6.99.10.461
4rnwFMNNADPH dehydrogenase 11.6.99.10.461
3enkUPGUDP-glucose 4-epimerase/0.459
3l5lFMNXenobiotic reductase/0.459
4loi1YCStimulator of interferon genes protein/0.458
4m5pFMNNADPH dehydrogenase/0.458
4uthFMNXenobiotic reductase/0.458
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.457
3p8iFMNPentaerythritol tetranitrate reductase/0.457
4a0rDTBBifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial6.3.3.30.456
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.455
3tr05GPGuanylate kinase/0.455
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.455
2gesCOKPantothenate kinase2.7.1.330.454
1o9bNAIQuinate/shikimate dehydrogenase/0.453
1p9wANPType II secretion system protein E/0.453
1vjiFMN12-oxophytodienoate reductase 11.3.1.420.453
2f3rG5PGuanylate kinase2.7.4.80.453
2zfaFMNLactate oxidase/0.453
3nl6TPSUncharacterized protein/0.453
1w6hTITPlasmepsin-23.4.23.390.452
4e2bFMNDehydrogenase/0.452
4g74FADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.452
4giu636Anthranilate phosphoribosyltransferase/0.452
1p4aPCPPur operon repressor/0.451
2cy0NAPShikimate dehydrogenase (NADP(+))/0.451
4dfrMTXDihydrofolate reductase1.5.1.30.451
2ien017Gag-Pol polyprotein3.4.23.160.450
1joaFADNADH peroxidase1.11.1.10.449
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.449
3b70NAPEnoyl reductase LovC10.449
4df2FMNNADPH dehydrogenase/0.449
1bwkFMNNADPH dehydrogenase 11.6.99.10.448
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.448
3v2uATPProtein GAL3/0.448
4yaiNAIC alpha-dehydrogenase/0.448
2c29NAPDihydroflavonol 4-reductase/0.447
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.447
3tvqDQHMultifunctional cyclase-dehydratase-3-O-methyl transferase TcmN2.1.10.447
4awtFMNNADH:flavin oxidoreductase Sye1/0.447
4e2dFMNDehydrogenase/0.447
4qaiFMNNADPH dehydrogenase/0.447
1rneC60Renin3.4.23.150.446
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.446
3qt62P0Mevalonate diphosphate decarboxylase/0.446
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.446
5agaANPDNA polymerase theta/0.446
3lqfNADGalactitol dehydrogenase/0.445
4dbzNDPPutative ketoacyl reductase1.3.10.445
4yagNAIC alpha-dehydrogenase/0.445
1oycFMNNADPH dehydrogenase 11.6.99.10.444
1xe65FPPlasmepsin-23.4.23.390.444
1xvaSAMGlycine N-methyltransferase2.1.1.200.444
1p0hACOMycothiol acetyltransferase2.3.1.1890.443
1bwsNDPGDP-L-fucose synthase/0.442
2b4tAESGlyceraldehyde-3-phosphate dehydrogenase/0.442
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
5c3aURMHisto-blood group ABO system transferase/0.442
1rfvADPPyridoxal kinase2.7.1.350.441
2iibC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.441
3lpkZ76Beta-secretase 13.4.23.460.441
3tjlFMNNADPH dehydrogenase/0.441
4fj0NAP17beta-hydroxysteroid dehydrogenase/0.441
4k28NADShikimate dehydrogenase family protein/0.441
4ycpFMNtRNA-dihydrouridine(16) synthase/0.441
2qzlIXSBeta-secretase 13.4.23.460.440
2y0mACOHistone acetyltransferase KAT8/0.440