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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
2dfd NAD Malate dehydrogenase, mitochondrial 1.1.1.37

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 1.085
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.996
4wlv NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.983
1ib6 NADMalate dehydrogenase / 0.921
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.844
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.826
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.822
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.820
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.815
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.813
1bmd NADMalate dehydrogenase / 0.806
1ie3 NADMalate dehydrogenase / 0.801
1wze NADMalate dehydrogenase / 0.797
1pzh NADLactate dehydrogenase / 0.796
4wlo NAIMalate dehydrogenase, mitochondrial 1.1.1.37 0.791
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.786
1gv0 NADMalate dehydrogenase / 0.781
1pzf A3DLactate dehydrogenase / 0.779
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.776
1uxk NADMalate dehydrogenase / 0.775
1bdm NAXMalate dehydrogenase / 0.771
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.771
1wzi NDPMalate dehydrogenase / 0.770
4i1i NADMalate dehydrogenase / 0.770
1o6z NADMalate dehydrogenase / 0.767
1b8v NADMalate dehydrogenase / 0.763
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.760
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.758
2a92 NAIL-lactate dehydrogenase / 0.756
4ros APRMalate dehydrogenase / 0.755
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.754
1emd NADMalate dehydrogenase / 0.748
1sow NADL-lactate dehydrogenase 1.1.1.27 0.745
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.744
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.742
4j49 NADUncharacterized protein / 0.742
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.742
1pzg A3DLactate dehydrogenase / 0.740
4j43 NADUncharacterized protein / 0.739
3jv7 NADSecondary alcohol dehydrogenase / 0.738
1uxj NADMalate dehydrogenase / 0.736
5a1t NAIL-lactate dehydrogenase / 0.734
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.731
5mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.731
4mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.730
2aa3 AP0L-lactate dehydrogenase / 0.729
4c4o NADSADH / 0.729
2x0i NAIMalate dehydrogenase / 0.728
1hdz NADAlcohol dehydrogenase 1B 1.1.1.1 0.726
1axg NADAlcohol dehydrogenase E chain 1.1.1.1 0.725
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.725
2vhx NADAlanine dehydrogenase 1.4.1.1 0.725
2x0r NADMalate dehydrogenase / 0.724
3wsw NADL-lactate dehydrogenase / 0.718
4jk3 NADUncharacterized protein / 0.718
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.717
2xaa NADSecondary alcohol dehydrogenase / 0.716
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.716
2hjr APRMalate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase / 0.715
1u7h NADPutative ornithine cyclodeaminase / 0.714
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.713
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.706
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.705
2dvm NAD439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme] / 0.704
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.702
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.702
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.702
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.702
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.701
4b7x NAPProbable oxidoreductase / 0.701
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.701
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.701
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.701
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.701
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.700
2nad NADFormate dehydrogenase / 0.698
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.696
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.696
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.696
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.694
2eer NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.692
1bw9 NADPhenylalanine dehydrogenase / 0.691
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.691
4lcj NADC-terminal-binding protein 2 / 0.691
4xcv NDPProbable hydroxyacid dehydrogenase protein / 0.690
5bqf NAPProbable hydroxyacid dehydrogenase protein / 0.690
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.689
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.687
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.687
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.686
4j49 NAIUncharacterized protein / 0.686
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.685
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.684
3wv7 ADPHmd co-occurring protein HcgE / 0.682
3m6i NADL-arabinitol 4-dehydrogenase 1.1.1.12 0.681
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.681
4cpd NADAlcohol dehydrogenase / 0.680
4k28 NADShikimate dehydrogenase family protein / 0.680
1x7d NADPutative ornithine cyclodeaminase / 0.679
3kb6 NADD-lactate dehydrogenase / 0.679
3wv8 ATPHmd co-occurring protein HcgE / 0.679
1ez4 NADL-lactate dehydrogenase 1.1.1.27 0.678
3tqh NDPQuinone oxidoreductase / 0.678
4jji NADAlcohol dehydrogenase class-3 / 0.678
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.678
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.677
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.677
3two NDPMannitol dehydrogenase / 0.677
3wle NAD(R)-specific carbonyl reductase / 0.677
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.676
2voj NADAlanine dehydrogenase 1.4.1.1 0.675
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.675
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.675
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.674
1yqd NAPSinapyl alcohol dehydrogenase / 0.674
3uko NADAlcohol dehydrogenase class-3 / 0.674
4j4b NAIUncharacterized protein / 0.673
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.672
3q3c NADNAD-dependent L-serine dehydrogenase / 0.671
4xqc NADHomospermidine synthase 2.5.1.44 0.671
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.669
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.668
1o8c NDPProbable acrylyl-CoA reductase AcuI 1.3.1.84 0.667
1heu NADAlcohol dehydrogenase E chain 1.1.1.1 0.665
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.665
1piw NAPNADP-dependent alcohol dehydrogenase 6 1.1.1.2 0.665
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.664
2y05 NAPProstaglandin reductase 1 / 0.664
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.663
2dfv NADL-threonine 3-dehydrogenase / 0.663
3gvh NADMalate dehydrogenase / 0.663
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.663
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.663
1yqx NAPSinapyl alcohol dehydrogenase / 0.662
1h2h NADL-aspartate dehydrogenase 1.4.1.21 0.661
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.660
2cda NAPGlucose 1-dehydrogenase / 0.660
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.660
1guy NADMalate dehydrogenase / 0.659
1agn NADAlcohol dehydrogenase class 4 mu/sigma chain 1.1.1.1 0.658
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.658
3ggo NAIPrephenate dehydrogenase / 0.658
6adh NADAlcohol dehydrogenase E chain 1.1.1.1 0.658
1y7t NDPMalate dehydrogenase / 0.656
2cvq NDPMalate dehydrogenase / 0.656
1e3l NADAlcohol dehydrogenase 4 1.1.1.1 0.655
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.655
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.655
4gi2 NAPCrotonyl-CoA carboxylase/reductase / 0.655
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.654
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.653
1hzz NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.652
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.652
1ky4 NADAdenosylhomocysteinase 3.3.1.1 0.651
2fze APRAlcohol dehydrogenase class-3 1.1.1.1 0.651
3h3f NAIL-lactate dehydrogenase A chain 1.1.1.27 0.651
2pv7 NADT-protein 1.3.1.12 0.650
4l0q NADAlcohol dehydrogenase class-3 / 0.650