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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
4e5m NAP Phosphonate dehydrogenase 1.20.1.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 1.222
4e5n NADPhosphonate dehydrogenase 1.20.1.1 1.003
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.923
4nu6 NADPhosphonate dehydrogenase 1.20.1.1 0.902
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.879
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.795
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.781
2gsd NADFormate dehydrogenase / 0.758
2nad NADFormate dehydrogenase / 0.756
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.752
4xyb NDPFormate dehydrogenase / 0.731
3oet NADErythronate-4-phosphate dehydrogenase / 0.724
4z0p NDPNAD-dependent dehydrogenase / 0.723
4xcv NDPProbable hydroxyacid dehydrogenase protein / 0.722
4ebf NADPhosphonate dehydrogenase 1.20.1.1 0.721
4weq NAPNAD-dependent dehydrogenase / 0.720
3kb6 NADD-lactate dehydrogenase / 0.719
4tvb NADHomospermidine synthase 2.5.1.44 0.717
4njo NADD-3-phosphoglycerate dehydrogenase, putative / 0.716
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.710
4jbi NDPAlcohol dehydrogenase (Zinc) / 0.707
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.706
4xq9 NADHomospermidine synthase 2.5.1.44 0.706
4plp NADHomospermidine synthase 2.5.1.44 0.704
2j3k NAPNADPH-dependent oxidoreductase 2-alkenal reductase 1.3.1.74 0.701
4xrg NADHomospermidine synthase 2.5.1.44 0.697
2dc1 NADProbable L-aspartate dehydrogenase / 0.694
4xye NADFormate dehydrogenase / 0.694
3baz NAPHydroxyphenylpyruvate reductase 1.1.1.237 0.693
2o4c NADErythronate-4-phosphate dehydrogenase / 0.692
2dbq NAPGlyoxylate reductase 1.1.1.26 0.689
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.688
5bqf NAPProbable hydroxyacid dehydrogenase protein / 0.688
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.687
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.682
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.681
1i36 NAPConserved protein / 0.680
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.680
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.680
1hku NADC-terminal-binding protein 1 1.1.1 0.679
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.678
5doz NDPJamJ / 0.678
4xqc NADHomospermidine synthase 2.5.1.44 0.676
1yqx NAPSinapyl alcohol dehydrogenase / 0.674
2dbz NAPGlyoxylate reductase 1.1.1.26 0.674
1gq2 NAPNADP-dependent malic enzyme 1.1.1.40 0.673
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.673
4j4b NAIUncharacterized protein / 0.672
5j23 A2RPutative 2-hydroxyacid dehydrogenase / 0.672
4b7x NAPProbable oxidoreductase / 0.671
4j49 NADUncharacterized protein / 0.671
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.671
2voj NADAlanine dehydrogenase 1.4.1.1 0.670
4j43 NADUncharacterized protein / 0.670
4j49 NAIUncharacterized protein / 0.670
4jk3 NADUncharacterized protein / 0.669
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.668
3wsw NADL-lactate dehydrogenase / 0.668
2yyy NAPGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.667
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.666
2c29 NAPDihydroflavonol 4-reductase / 0.666
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.666
2vhx NADAlanine dehydrogenase 1.4.1.1 0.665
3wle NAD(R)-specific carbonyl reductase / 0.664
1e5q NDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming] 1.5.1.10 0.663
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.662
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.659
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.659
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.659
2p5y NADUDP-glucose 4-epimerase / 0.659
1pzh NADLactate dehydrogenase / 0.658
1yb5 NAPQuinone oxidoreductase 1.6.5.5 0.658
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.658
1u7h NADPutative ornithine cyclodeaminase / 0.657
1yqd NAPSinapyl alcohol dehydrogenase / 0.657
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.656
1sow NADL-lactate dehydrogenase 1.1.1.27 0.656
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.656
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.655
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.654
1j49 NADD-lactate dehydrogenase 1.1.1.28 0.653
1pjc NADAlanine dehydrogenase / 0.653
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.653
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.653
5bsg NAPPyrroline-5-carboxylate reductase / 0.653
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.652
1sny NAPLD36273p / 0.652
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.652
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.652
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.652
1pzf A3DLactate dehydrogenase / 0.651
2p9c NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.651
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.651
3s5w NAPL-ornithine N(5)-monooxygenase / 0.651
4ej0 NAPADP-L-glycero-D-manno-heptose-6-epimerase / 0.651
1teh NADAlcohol dehydrogenase class-3 1.1.1.1 0.650
3rj9 NADAlcohol dehydrogenase 1.1.1.1 0.650
4oaq NDPR-specific carbonyl reductase / 0.650