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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
4e5n NAD Phosphonate dehydrogenase 1.20.1.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4e5n NADPhosphonate dehydrogenase 1.20.1.1 1.129
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 1.003
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.973
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.918
4nu6 NADPhosphonate dehydrogenase 1.20.1.1 0.917
2gsd NADFormate dehydrogenase / 0.807
3oet NADErythronate-4-phosphate dehydrogenase / 0.779
2nad NADFormate dehydrogenase / 0.756
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.751
4njo NADD-3-phosphoglycerate dehydrogenase, putative / 0.733
2ome NADC-terminal-binding protein 2 / 0.732
4xq9 NADHomospermidine synthase 2.5.1.44 0.727
4tvb NADHomospermidine synthase 2.5.1.44 0.724
1pzg A3DLactate dehydrogenase / 0.723
4xrg NADHomospermidine synthase 2.5.1.44 0.723
4plp NADHomospermidine synthase 2.5.1.44 0.719
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.717
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.717
4j49 NADUncharacterized protein / 0.717
1pzh NADLactate dehydrogenase / 0.716
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.715
3kb6 NADD-lactate dehydrogenase / 0.714
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.714
1hku NADC-terminal-binding protein 1 1.1.1 0.713
4xqc NADHomospermidine synthase 2.5.1.44 0.712
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.711
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.710
4jk3 NADUncharacterized protein / 0.707
1pzf A3DLactate dehydrogenase / 0.704
4lcj NADC-terminal-binding protein 2 / 0.702
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.701
2dc1 NADProbable L-aspartate dehydrogenase / 0.699
2x0i NAIMalate dehydrogenase / 0.699
1pjc NADAlanine dehydrogenase / 0.691
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.691
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.690
3wv7 ADPHmd co-occurring protein HcgE / 0.690
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.688
2dbq NAPGlyoxylate reductase 1.1.1.26 0.687
4weq NAPNAD-dependent dehydrogenase / 0.685
4ebf NADPhosphonate dehydrogenase 1.20.1.1 0.683
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.682
1sow NADL-lactate dehydrogenase 1.1.1.27 0.682
1yl7 NAI4-hydroxy-tetrahydrodipicolinate reductase / 0.682
1yqx NAPSinapyl alcohol dehydrogenase / 0.682
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.682
4i1i NADMalate dehydrogenase / 0.682
4j4b NAIUncharacterized protein / 0.682
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.680
2pv7 NADT-protein 1.3.1.12 0.678
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.678
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.677
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.677
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.677
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.676
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.676
3baz NAPHydroxyphenylpyruvate reductase 1.1.1.237 0.676
4xye NADFormate dehydrogenase / 0.676
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.674
2vhx NADAlanine dehydrogenase 1.4.1.1 0.671
5a1t NAIL-lactate dehydrogenase / 0.671
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.670
1xq6 NAPUncharacterized protein At5g02240 / 0.670
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.670
2y05 NAPProstaglandin reductase 1 / 0.670
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.669
1guy NADMalate dehydrogenase / 0.667
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.667
3uko NADAlcohol dehydrogenase class-3 / 0.667
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.667
1c1d NAIPhenylalanine dehydrogenase / 0.665
4j49 NAIUncharacterized protein / 0.665
4xcv NDPProbable hydroxyacid dehydrogenase protein / 0.665
2j3k NAPNADPH-dependent oxidoreductase 2-alkenal reductase 1.3.1.74 0.664
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.663
1h6c NDPGlucose--fructose oxidoreductase 1.1.99.28 0.662
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.662
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.662
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.662
2eer NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.662
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.662
4j43 NADUncharacterized protein / 0.662
5a02 NAPGlucose-fructose oxidoreductase / 0.662
3f3s NADLambda-crystallin homolog / 0.661
1emd NADMalate dehydrogenase / 0.660
2hu2 NADC-terminal binding protein 1 / 0.660
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.660
4k28 NADShikimate dehydrogenase family protein / 0.660
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.660
2c29 NAPDihydroflavonol 4-reductase / 0.659
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.658
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.658
1x7d NADPutative ornithine cyclodeaminase / 0.657
3wbb NAPMeso-diaminopimelate D-dehydrogenase / 0.657
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.657
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.656
2p5y NADUDP-glucose 4-epimerase / 0.656
1u7h NADPutative ornithine cyclodeaminase / 0.655
1y7t NDPMalate dehydrogenase / 0.654
1yqd NAPSinapyl alcohol dehydrogenase / 0.654
3tqh NDPQuinone oxidoreductase / 0.654
3mje NDPAmphB / 0.653
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.653
4c4o NADSADH / 0.653
4cuk NAID-lactate dehydrogenase / 0.653
4wlv NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.653
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.652
1p0f NAPNADP-dependent alcohol dehydrogenase 1.1.1.2 0.652
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.652
2j3i NAPNADPH-dependent oxidoreductase 2-alkenal reductase 1.3.1.74 0.651
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.651
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.651
1b8u NADMalate dehydrogenase / 0.650
2o4c NADErythronate-4-phosphate dehydrogenase / 0.650
2v7g NADUrocanate hydratase 4.2.1.49 0.650
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.650
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.650
4xr9 TMPCalS8 / 0.650