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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
3kb6 NAD D-lactate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3kb6 NADD-lactate dehydrogenase / 0.986
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.792
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.786
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.779
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.766
3baz NAPHydroxyphenylpyruvate reductase 1.1.1.237 0.763
4xcv NDPProbable hydroxyacid dehydrogenase protein / 0.749
5bqf NAPProbable hydroxyacid dehydrogenase protein / 0.748
4z0p NDPNAD-dependent dehydrogenase / 0.740
2nad NADFormate dehydrogenase / 0.735
4weq NAPNAD-dependent dehydrogenase / 0.731
2gsd NADFormate dehydrogenase / 0.729
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.724
2hu2 NADC-terminal binding protein 1 / 0.722
3oet NADErythronate-4-phosphate dehydrogenase / 0.722
4xye NADFormate dehydrogenase / 0.720
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 0.719
2dbq NAPGlyoxylate reductase 1.1.1.26 0.715
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.714
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.714
1uxk NADMalate dehydrogenase / 0.707
2aa3 AP0L-lactate dehydrogenase / 0.706
2dc1 NADProbable L-aspartate dehydrogenase / 0.706
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.704
2dbr NAPGlyoxylate reductase 1.1.1.26 0.704
4j43 NADUncharacterized protein / 0.700
1uxj NADMalate dehydrogenase / 0.699
2vhx NADAlanine dehydrogenase 1.4.1.1 0.698
4j49 NADUncharacterized protein / 0.696
5dt9 NADErythronate-4-phosphate dehydrogenase / 0.694
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.693
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.693
1pzh NADLactate dehydrogenase / 0.692
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.691
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.691
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.690
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.690
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.690
4c4o NADSADH / 0.690
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.688
4oaq NDPR-specific carbonyl reductase / 0.686
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.684
1j49 NADD-lactate dehydrogenase 1.1.1.28 0.684
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.684
6adh NADAlcohol dehydrogenase E chain 1.1.1.1 0.684
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.682
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.680
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.680
1f8f NADBenzyl alcohol dehydrogenase / 0.679
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.679
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.679
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.679
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.679
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.679
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.679
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.679
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.679
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.679
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.679
1ib6 NADMalate dehydrogenase / 0.678
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.678
2w2l NADD-mandelate dehydrogenase / 0.678
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.678
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.678
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.677
2a92 NAIL-lactate dehydrogenase / 0.675
2dbz NAPGlyoxylate reductase 1.1.1.26 0.675
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.675
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.675
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.674
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.674
2voj NADAlanine dehydrogenase 1.4.1.1 0.674
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.674
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.673
1wze NADMalate dehydrogenase / 0.672
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.672
3two NDPMannitol dehydrogenase / 0.672
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.672
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.672
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.672
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.671
1ie3 NADMalate dehydrogenase / 0.669
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.669
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.668
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.668
4nu6 NADPhosphonate dehydrogenase 1.20.1.1 0.667
5a1t NAIL-lactate dehydrogenase / 0.667
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.665
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.665
4njo NADD-3-phosphoglycerate dehydrogenase, putative / 0.665
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.664
1pjc NADAlanine dehydrogenase / 0.664
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.664
4jk3 NADUncharacterized protein / 0.664
3nx4 NAPPutative oxidoreductase / 0.663
4k28 NADShikimate dehydrogenase family protein / 0.663
2gcg NDPGlyoxylate reductase/hydroxypyruvate reductase 1.1.1.79 0.662
2p9c NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.661
1adc PADAlcohol dehydrogenase E chain 1.1.1.1 0.660
4ebf NADPhosphonate dehydrogenase 1.20.1.1 0.660
2eer NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.659
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.659
4cpd NADAlcohol dehydrogenase / 0.659
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.657
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.657
2o4c NADErythronate-4-phosphate dehydrogenase / 0.656
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.656
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.655
1h2h NADL-aspartate dehydrogenase 1.4.1.21 0.654
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.654
1yqx NAPSinapyl alcohol dehydrogenase / 0.654
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.654
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.653
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.653
1axg NADAlcohol dehydrogenase E chain 1.1.1.1 0.652
4w6z 8IDAlcohol dehydrogenase 1 1.1.1.1 0.652
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.651
1hku NADC-terminal-binding protein 1 1.1.1 0.651
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.651
2dph NADFormaldehyde dismutase / 0.651
3wle NAD(R)-specific carbonyl reductase / 0.651
4b7x NAPProbable oxidoreductase / 0.650