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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
4njoNADD-3-phosphoglycerate dehydrogenase, putative

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4njoNADD-3-phosphoglycerate dehydrogenase, putative/1.000
2w2lNADD-mandelate dehydrogenase/0.524
3kb6NADD-lactate dehydrogenase/0.511
2g76NADD-3-phosphoglycerate dehydrogenase1.1.1.950.495
2dbzNAPGlyoxylate reductase1.1.1.260.492
2omeNADC-terminal-binding protein 2/0.476
4z34ON7Lysophosphatidic acid receptor 1/0.475
4lcjNADC-terminal-binding protein 2/0.474
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.469
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.463
4nu6NADPhosphonate dehydrogenase1.20.1.10.462
4e5kNADPhosphonate dehydrogenase1.20.1.10.461
4nu5NADPhosphonate dehydrogenase1.20.1.10.461
3bazNAPHydroxyphenylpyruvate reductase1.1.1.2370.460
4z35ON9Lysophosphatidic acid receptor 1/0.460
2dbqNAPGlyoxylate reductase1.1.1.260.459
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.458
3f03FMNPentaerythritol tetranitrate reductase/0.457
5js6NAD17-beta-hydroxysteroid dehydrogenase 141.1.10.457
2dbrNAPGlyoxylate reductase1.1.1.260.456
4dpuAGSMevalonate diphosphate decarboxylase/0.456
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.454
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.452
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.452
4hwkNAPSepiapterin reductase1.1.1.1530.452
1hkuNADC-terminal-binding protein 11.1.10.451
4e5mNAPPhosphonate dehydrogenase1.20.1.10.450
4weqNAPNAD-dependent dehydrogenase/0.450
1h50FMNPentaerythritol tetranitrate reductase/0.447
2abbFMNPentaerythritol tetranitrate reductase/0.447
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.446
3drcMTXDihydrofolate reductase1.5.1.30.446
3triNAPPyrroline-5-carboxylate reductase/0.446
4bb3KKAIsopenicillin N synthase1.21.3.10.446
1b5dDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.445
1h63FMNPentaerythritol tetranitrate reductase/0.445
2cig1DGDihydrofolate reductase1.5.1.30.445
1ci7UMPThymidylate synthase2.1.1.450.444
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.444
3wv7ADPHmd co-occurring protein HcgE/0.444
4z0pNDPNAD-dependent dehydrogenase/0.444
5jlaNADPutative short-chain dehydrogenase/reductase/0.444
2gv8FADThiol-specific monooxygenase1.14.130.442
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
3p62FMNPentaerythritol tetranitrate reductase/0.441
1culFOKAdenylate cyclase type 2/0.440
1culFOKAdenylate cyclase type 5/0.440
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.440
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.440