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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
2ekl NAD D-3-phosphoglycerate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ekl NADD-3-phosphoglycerate dehydrogenase / 1.120
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.831
2o4c NADErythronate-4-phosphate dehydrogenase / 0.821
3oet NADErythronate-4-phosphate dehydrogenase / 0.813
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.812
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.787
3kb6 NADD-lactate dehydrogenase / 0.786
1pjc NADAlanine dehydrogenase / 0.780
3baz NAPHydroxyphenylpyruvate reductase 1.1.1.237 0.779
4xq9 NADHomospermidine synthase 2.5.1.44 0.773
2ome NADC-terminal-binding protein 2 / 0.765
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.757
1pzg A3DLactate dehydrogenase / 0.753
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.752
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.751
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.745
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.744
4j43 NADUncharacterized protein / 0.743
1pzh NADLactate dehydrogenase / 0.742
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.738
1x7d NADPutative ornithine cyclodeaminase / 0.735
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.735
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.733
4xrg NADHomospermidine synthase 2.5.1.44 0.732
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.731
4tvb NADHomospermidine synthase 2.5.1.44 0.726
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.725
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.724
1c1d NAIPhenylalanine dehydrogenase / 0.718
2dbz NAPGlyoxylate reductase 1.1.1.26 0.717
2dbr NAPGlyoxylate reductase 1.1.1.26 0.716
2gsd NADFormate dehydrogenase / 0.716
4xye NADFormate dehydrogenase / 0.716
2voj NADAlanine dehydrogenase 1.4.1.1 0.715
4njo NADD-3-phosphoglycerate dehydrogenase, putative / 0.713
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.711
1u8x NADMaltose-6'-phosphate glucosidase 3.2.1.122 0.711
3jv7 NADSecondary alcohol dehydrogenase / 0.711
1gv0 NADMalate dehydrogenase / 0.709
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.708
4b7x NAPProbable oxidoreductase / 0.706
5a1t NAIL-lactate dehydrogenase / 0.705
1uxk NADMalate dehydrogenase / 0.704
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.703
1pzf A3DLactate dehydrogenase / 0.703
1ma0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.701
1yqd NAPSinapyl alcohol dehydrogenase / 0.701
1u7h NADPutative ornithine cyclodeaminase / 0.700
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.700
2p9c NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.699
4c4o NADSADH / 0.699
3wsw NADL-lactate dehydrogenase / 0.698
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.698
2a92 NAIL-lactate dehydrogenase / 0.697
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.696
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.696
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.695
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.694
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.694
2nad NADFormate dehydrogenase / 0.693
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.692
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.692
1hku NADC-terminal-binding protein 1 1.1.1 0.691
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.691
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.690
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.690
4lcj NADC-terminal-binding protein 2 / 0.690
1bdm NAXMalate dehydrogenase / 0.689
1h2h NADL-aspartate dehydrogenase 1.4.1.21 0.689
4oaq NDPR-specific carbonyl reductase / 0.689
1o6z NADMalate dehydrogenase / 0.688
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 0.688
4j49 NADUncharacterized protein / 0.688
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.687
2o23 NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.685
4k28 NADShikimate dehydrogenase family protein / 0.684
1hld NADAlcohol dehydrogenase E chain 1.1.1.1 0.682
1vjt NADAlpha-glucosidase, putative / 0.682
2x0i NAIMalate dehydrogenase / 0.682
1o8c NDPProbable acrylyl-CoA reductase AcuI 1.3.1.84 0.681
4jk3 NADUncharacterized protein / 0.681
4nfs NAJAlcohol dehydrogenase E chain 1.1.1.1 0.681
4ng5 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.681
1pl8 NADSorbitol dehydrogenase 1.1.1.14 0.680
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.680
6adh NADAlcohol dehydrogenase E chain 1.1.1.1 0.680
1hf3 NADAlcohol dehydrogenase E chain 1.1.1.1 0.679
4cpd NADAlcohol dehydrogenase / 0.679
1zem NADXylitol dehydrogenase / 0.678
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.678
1het NADAlcohol dehydrogenase E chain 1.1.1.1 0.677
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.677
2hu2 NADC-terminal binding protein 1 / 0.677
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.677
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.677
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.677
1pl6 NADSorbitol dehydrogenase 1.1.1.14 0.676
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.676
1heu NADAlcohol dehydrogenase E chain 1.1.1.1 0.675
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.675
1j49 NADD-lactate dehydrogenase 1.1.1.28 0.673
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.673
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.673
4nu6 NADPhosphonate dehydrogenase 1.20.1.1 0.671
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.670
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.670
4xd2 NAIAlcohol dehydrogenase E chain 1.1.1.1 0.670
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.670
1i3l NADUDP-glucose 4-epimerase / 0.669
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.669
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.669
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.669
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.668
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.668
1a71 NADAlcohol dehydrogenase E chain 1.1.1.1 0.667
2w2l NADD-mandelate dehydrogenase / 0.667
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.667
3q2k NAIProbable oxidoreductase / 0.665
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.663
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.663
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.661
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.661
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.661
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.660
3two NDPMannitol dehydrogenase / 0.660
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.659
3tqh NDPQuinone oxidoreductase / 0.659
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.658
1bxk NADdTDP-glucose 4,6-dehydratase 2 / 0.657
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.657
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.657
5dt9 NADErythronate-4-phosphate dehydrogenase / 0.657
1cdo NADAlcohol dehydrogenase 1 1.1.1.1 0.656
1kc1 NDPdTDP-4-dehydrorhamnose reductase 1.1.1.133 0.656
2jhf NADAlcohol dehydrogenase E chain 1.1.1.1 0.656
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.656
2hun NAD336aa long hypothetical dTDP-glucose 4,6-dehydratase / 0.655
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.655
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.655
4bv9 NDPKetimine reductase mu-crystallin 1.5.1.25 0.655
4ros APRMalate dehydrogenase / 0.655
1gq2 NAPNADP-dependent malic enzyme 1.1.1.40 0.654
2g5c NADPrephenate dehydrogenase / 0.654
3adp NAILambda-crystallin 1.1.1.45 0.654
4gae NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.654
2vhx NADAlanine dehydrogenase 1.4.1.1 0.653
4cr8 NADN-acylmannosamine 1-dehydrogenase 1.1.1.233 0.653
2fzw NADAlcohol dehydrogenase class-3 1.1.1.1 0.652
2rcy NAPPyrroline-5-carboxylate reductase / 0.652
3d64 NADAdenosylhomocysteinase / 0.652
1wze NADMalate dehydrogenase / 0.651
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.651
2yy7 NADL-threonine dehydrogenase / 0.651
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.651
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.651
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.650
1q7g NHOHomoserine dehydrogenase 1.1.1.3 0.650
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.650