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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4xb2 NDP 319aa long hypothetical homoserine dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 1.154
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.897
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.760
4xgi NADGlutamate dehydrogenase / 0.744
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.740
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.736
2ph5 NADHomospermidine synthase / 0.714
2o4c NADErythronate-4-phosphate dehydrogenase / 0.713
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.711
1c1d NAIPhenylalanine dehydrogenase / 0.708
3zhb NAPPutative dehydrogenase / 0.702
4oqy NDP(S)-imine reductase / 0.701
4tvb NADHomospermidine synthase 2.5.1.44 0.701
1npd NADQuinate/shikimate dehydrogenase / 0.695
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.694
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.692
1vi2 NADQuinate/shikimate dehydrogenase / 0.691
4xq9 NADHomospermidine synthase 2.5.1.44 0.691
4nu6 NADPhosphonate dehydrogenase 1.20.1.1 0.690
3dtt NAPNADP oxidoreductase, coenzyme F420-dependent / 0.689
4u7w NDPMxaA / 0.688
4k28 NADShikimate dehydrogenase family protein / 0.686
2y05 NAPProstaglandin reductase 1 / 0.682
3tri NAPPyrroline-5-carboxylate reductase / 0.682
2zb3 NDPProstaglandin reductase 2 1.3.1.48 0.681
4b7x NAPProbable oxidoreductase / 0.681
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.680
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 0.680
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.678
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.678
3o26 NDPSalutaridine reductase / 0.678
1i36 NAPConserved protein / 0.676
2yut NAPPutative short-chain oxidoreductase / 0.676
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.675
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.674
4bmv NAPShort-chain dehydrogenase / 0.674
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.672
4pvd NDPNADPH-dependent methylglyoxal reductase GRE2 / 0.669
1e5q NDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming] 1.5.1.10 0.668
4jbi NDPAlcohol dehydrogenase (Zinc) / 0.668
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.667
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.666
1emd NADMalate dehydrogenase / 0.665
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.665
2nnl NAPDihydroflavonol 4-reductase 1.1.1.219 0.665
3q3c NADNAD-dependent L-serine dehydrogenase / 0.665
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.664
4z0p NDPNAD-dependent dehydrogenase / 0.663
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.662
3t4e NADQuinate/shikimate dehydrogenase / 0.662
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.662
4xrg NADHomospermidine synthase 2.5.1.44 0.662
2czc NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.661
3wmx NADNAD dependent epimerase/dehydratase / 0.661
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.661
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.661
3ean NAPThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.660
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.659
3nx4 NAPPutative oxidoreductase / 0.659
2yjz NAPMetalloreductase STEAP4 1.16.1 0.658
3ggp NADPrephenate dehydrogenase / 0.658
3tnl NADShikimate dehydrogenase (NADP(+)) / 0.658
3wds NADNADH-dependent quinuclidinone reductase / 0.658
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.657
1ipe NDPTropinone reductase 2 1.1.1.236 0.657
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.657
1zid ZIDEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.657
2gcg NDPGlyoxylate reductase/hydroxypyruvate reductase 1.1.1.79 0.657
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.657
1h5q NAPNADP-dependent mannitol dehydrogenase 1.1.1.138 0.655
2c29 NAPDihydroflavonol 4-reductase / 0.655
3a28 NADL-2,3-butanediol dehydrogenase 1.1.1.76 0.655
3w8f NAD3-hydroxybutyrate dehydrogenase / 0.655
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.654
3rj9 NADAlcohol dehydrogenase 1.1.1.1 0.654
5j23 A2RPutative 2-hydroxyacid dehydrogenase / 0.654
2ahr NAPPyrroline-5-carboxylate reductase / 0.653
3cea NADMyo-inositol 2-dehydrogenase-like (Promiscuous) / 0.653
1o9b NAIQuinate/shikimate dehydrogenase / 0.652
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.652
3phi NDPShikimate dehydrogenase (NADP(+)) / 0.652
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.652
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.651
3tqh NDPQuinone oxidoreductase / 0.651
4dpl NAPMalonyl-CoA reductase 1.2.1.75 0.651
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.651
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.651
5bsf NADPyrroline-5-carboxylate reductase / 0.651
4xyb NDPFormate dehydrogenase / 0.650