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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
1dap NDP Meso-diaminopimelate D-dehydrogenase 1.4.1.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1dap NDPMeso-diaminopimelate D-dehydrogenase 1.4.1.16 1.390
1f06 NDPMeso-diaminopimelate D-dehydrogenase 1.4.1.16 1.067
3wyc NAPMeso-diaminopimelate D-dehydrogenase 1.4.1.16 0.872
3wbf NAPMeso-diaminopimelate D-dehydrogenase / 0.814
3wbb NAPMeso-diaminopimelate D-dehydrogenase / 0.789
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.724
2vhx NADAlanine dehydrogenase 1.4.1.1 0.723
2zat NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.690
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.680
4gcm NAPThioredoxin reductase 1.8.1.9 0.678
1p0f NAPNADP-dependent alcohol dehydrogenase 1.1.1.2 0.666
4xcv NDPProbable hydroxyacid dehydrogenase protein / 0.666
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.665
4a5l NDPThioredoxin reductase / 0.665
1b5d DCMDeoxycytidylate 5-hydroxymethyltransferase 2.1.2.8 0.664
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.664
3two NDPMannitol dehydrogenase / 0.661
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.660
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.659
5aq1 NDPGlucose-6-phosphate 1-dehydrogenase / 0.658
3l77 NJPShort-chain alcohol dehydrogenase / 0.656
3dk4 NDPGlutathione reductase, mitochondrial 1.8.1.7 0.655
2qx7 NAPEugenol synthase 1 1.1.1.318 0.654
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.653
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.653
3jv7 NADSecondary alcohol dehydrogenase / 0.652
3uko NADAlcohol dehydrogenase class-3 / 0.652
3krf DSTGeranyl diphosphate synthase large subunit / 0.651
3tc5 3T5Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 5.2.1.8 0.651
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.650
5a04 NDPGlucose-fructose oxidoreductase / 0.650