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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
1mraAPGMandelate racemase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1mraAPGMandelate racemase/1.000
1mdrAPGMandelate racemase/0.551
1xddAAYIntegrin alpha-L/0.484
3bsyACOUDP-N-acetylbacillosamine N-acetyltransferase2.3.1.2030.482
1towCRZFatty acid-binding protein, adipocyte/0.476
3tm5SFGUncharacterized protein/0.472
2vq7NAPPutative flavin-containing monooxygenase/0.469
1foaUD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase2.4.1.1010.468
1cqp803Integrin alpha-L/0.467
4b4w9L9Bifunctional protein FolD/0.467
1ndzFR5Adenosine deaminase3.5.4.40.466
3nmpPYVAbscisic acid receptor PYL2/0.466
1kw8BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.465
1mrqSTRAldo-keto reductase family 1 member C1/0.464
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.463
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.462
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.462
4m4922YL-lactate dehydrogenase A chain1.1.1.270.462
3otwCOAPhosphopantetheine adenylyltransferase/0.461
4bfxZVXPantothenate kinase2.7.1.330.461
1tkaN3TTransketolase 12.2.1.10.460
3zeiAWHO-acetylserine sulfhydrylase/0.460
3cgbCOACoenzyme A disulfide reductase/0.459
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.459
3vilSA0Beta-glucosidase/0.459
3vy2FMNFMN-binding protein/0.458
4y0kNAPAntE/0.455
2gouFMNNADH:flavin oxidoreductase Sye1/0.454
2nnqT4BFatty acid-binding protein, adipocyte/0.454
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.454
3p62FMNPentaerythritol tetranitrate reductase/0.453
3qvrFADGlucose oxidase1.1.3.40.453
1r5hAO2Methionine aminopeptidase 2/0.452
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.452
1wxjIPLTryptophan synthase alpha chain/0.451
3ju8NADN-succinylglutamate 5-semialdehyde dehydrogenase1.2.1.710.451
3p74FMNPentaerythritol tetranitrate reductase/0.451
4bfsZVSPantothenate kinase2.7.1.330.451
4fqsLYAThymidylate synthase ThyA/0.451
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.451
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.450
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.450
5e8jSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.450
3fr4F8AFatty acid-binding protein, adipocyte/0.449
4u8iFDAUDP-galactopyranose mutase/0.449
1diuBDMDihydrofolate reductase1.5.1.30.448
1ej2NADNicotinamide-nucleotide adenylyltransferase2.7.7.10.447
1ftlDNQGlutamate receptor 2/0.447
1kw6BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.447
1trkTPPTransketolase 12.2.1.10.447
2a9y26AAdenosine kinase2.7.1.200.447
2ea2F77Methionine aminopeptidase 2/0.447
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.447
3ibqATPPyridoxal kinase/0.447
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.446
1yw8A75Methionine aminopeptidase 2/0.446
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.446
2zbaZBATrichothecene 3-O-acetyltransferase/0.446
3br3ETHTH-type transcriptional regulator QacR/0.446
4ba5PXGProbable aminotransferase/0.446
1o9bNAIQuinate/shikimate dehydrogenase/0.445
2clfF6FTryptophan synthase alpha chain/0.445
2w6zL21Biotin carboxylase6.3.4.140.445
3fr5I4AFatty acid-binding protein, adipocyte/0.445
3wv9FEGHmd co-occurring protein HcgE/0.445
4fevPP1Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.445
4u0sADPAdenosine monophosphate-protein transferase FICD2.7.7.n10.445
5kf2ACOPredicted acetyltransferase/0.445
1a4lDCFAdenosine deaminase3.5.4.40.444
1bo4COAAminoglycoside-(3)-N-acetyltransferase/0.444
1h50FMNPentaerythritol tetranitrate reductase/0.444
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1qxlFR8Adenosine deaminase3.5.4.40.444
2xviFADPutative flavin-containing monooxygenase/0.444
3hy310F5-formyltetrahydrofolate cyclo-ligase6.3.3.20.444
3iktNADRedox-sensing transcriptional repressor Rex/0.444
4bftZVTPantothenate kinase2.7.1.330.444
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
1z7yAA5Cysteine synthase 12.5.1.470.443
2ab8MTPAdenosine kinase2.7.1.200.443
2cy2ACOProbable acetyltransferase/0.443
2jl1NAPTriphenylmethane reductase/0.443
2rlcCHDCholoylglycine hydrolase3.5.1.240.443
3p8iFMNPentaerythritol tetranitrate reductase/0.443
3t4nADP5'-AMP-activated protein kinase subunit gamma/0.443
1cbqRE9Cellular retinoic acid-binding protein 2/0.442
1g7uPEP2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.442
1upw444Oxysterols receptor LXR-beta/0.442
2ejvNADL-threonine 3-dehydrogenase/0.442
2vbdV10Isopenicillin N synthase1.21.3.10.442
3gxfIFMGlucosylceramidase3.2.1.450.442
3rbqGLY_ALA_GLY_ALA_DAOProtein unc-119 homolog A/0.442
4hkfACOAlpha-tubulin N-acetyltransferase 1/0.442
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.442
1g8oU5PN-acetyllactosaminide alpha-1,3-galactosyltransferase/0.441
2g1n1IGRenin3.4.23.150.441
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.441
2r5nTPPTransketolase 1/0.441
3f03FMNPentaerythritol tetranitrate reductase/0.441
3pdqKC6Lysine-specific demethylase 4A1.14.110.441
1kqwRTLCellular retinol-binding protein type II/0.440
4k37SAMAnaerobic sulfatase-maturating enzyme1.8.980.440
4kbyC2EStimulator of interferon genes protein/0.440