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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
5dt9NADErythronate-4-phosphate dehydrogenase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
5dt9NADErythronate-4-phosphate dehydrogenase/1.000
3oetNADErythronate-4-phosphate dehydrogenase/0.509
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.481
2p9gNAID-3-phosphoglycerate dehydrogenase1.1.1.950.478
3atzFMNProstaglandin F2a synthase/0.475
2pa3NAID-3-phosphoglycerate dehydrogenase1.1.1.950.474
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.471
4b65FADL-ornithine N(5)-monooxygenase/0.471
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.466
2eklNADD-3-phosphoglycerate dehydrogenase/0.466
2ylrNAPPhenylacetone monooxygenase1.14.13.920.466
4zgsNADPutative D-lactate dehydrogenase/0.466
2cy0NAPShikimate dehydrogenase (NADP(+))/0.465
2d8aNADL-threonine 3-dehydrogenase/0.463
4q72FADBifunctional protein PutA/0.462
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.460
4q73FADBifunctional protein PutA/0.459
4yau2AMNADPH--cytochrome P450 reductase/0.459
4q71FADBifunctional protein PutA/0.458
3ksdNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.457
2ohvNHLGlutamate racemase/0.456
4y9uNAPNADPH--cytochrome P450 reductase/0.456
4nxuADPMitochondrial dynamics protein MID51/0.455
1o9bNAIQuinate/shikimate dehydrogenase/0.454
4i1iNADMalate dehydrogenase/0.454
5a3bAPRSIR2 family protein/0.452
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
1nzdUPGDNA beta-glucosyltransferase/0.448
1u4oNDDL-lactate dehydrogenase1.1.1.270.447
2aa3AP0L-lactate dehydrogenase/0.446
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.446
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.446
4tqgNDPPutative dTDP-d-glucose 4 6-dehydratase/0.446
1psdNADD-3-phosphoglycerate dehydrogenase1.1.1.950.445
2x0rNADMalate dehydrogenase/0.445
2yxuATPPyridoxal kinase2.7.1.350.445
4ejmNAPPutative zinc-binding dehydrogenase/0.445
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.445
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
5kgpACOPredicted acetyltransferase/0.444
1h51FMNPentaerythritol tetranitrate reductase/0.443
2bpoNAPNADPH--cytochrome P450 reductase/0.443
3h4lANPDNA mismatch repair protein PMS1/0.443
4ctaATPCinA-like protein/0.443
4jicFMNGTN Reductase/0.443
1nytNAPShikimate dehydrogenase (NADP(+))/0.442
2ep7NADGlyceraldehyde-3-phosphate dehydrogenase/0.442
2ok7FADFerredoxin--NADP reductase, apicoplast/0.442
4a99FADTetX family tetracycline inactivation enzyme/0.442
4dtiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4jhz1KVBeta-glucuronidase3.2.1.310.442
1a72PADAlcohol dehydrogenase E chain1.1.1.10.441
1enyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
1j49NADD-lactate dehydrogenase1.1.1.280.441
3gviADPMalate dehydrogenase/0.441
4yaf2AMNADPH--cytochrome P450 reductase/0.441
1nptNADGlyceraldehyde-3-phosphate dehydrogenase/0.440
2hs8FMN12-oxophytodienoate reductase 31.3.1.420.440
2nv6ZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
2p5uNADUDP-glucose 4-epimerase/0.440
4p8rNADGlyceraldehyde-3-phosphate dehydrogenase/0.440
4qxq1YEStimulator of interferon genes protein/0.440