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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
4xyb NDP Formate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4xyb NDPFormate dehydrogenase / 1.354
4xye NADFormate dehydrogenase / 1.111
2nad NADFormate dehydrogenase / 1.069
2gsd NADFormate dehydrogenase / 0.980
3baz NAPHydroxyphenylpyruvate reductase 1.1.1.237 0.906
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.875
5bqf NAPProbable hydroxyacid dehydrogenase protein / 0.764
4z0p NDPNAD-dependent dehydrogenase / 0.762
1o8c NDPProbable acrylyl-CoA reductase AcuI 1.3.1.84 0.756
3qrw NDPPutative ketoacyl reductase 1.3.1 0.746
4weq NAPNAD-dependent dehydrogenase / 0.745
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.736
3o4r NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.735
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.734
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 0.731
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.729
2dbr NAPGlyoxylate reductase 1.1.1.26 0.724
3rku NAPNADP-dependent 3-hydroxy acid dehydrogenase / 0.717
4nu6 NADPhosphonate dehydrogenase 1.20.1.1 0.716
2zat NAPDehydrogenase/reductase SDR family member 4 1.1.1.184 0.715
4b4o NDPEpimerase family protein SDR39U1 / 0.711
4ejm NAPPutative zinc-binding dehydrogenase / 0.711
4hwk NAPSepiapterin reductase 1.1.1.153 0.711
4j16 NAPNAD(P) transhydrogenase subunit beta / 0.704
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.701
3ai3 NDPNADPH-sorbose reductase / 0.701
3uce NDPDehydrogenase / 0.699
3ai2 NDPNADPH-sorbose reductase / 0.697
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.695
5d2e NAPMlnE / 0.695
4hxy NDPPlm1 / 0.694
4dbz NDPPutative ketoacyl reductase 1.3.1 0.693
5j23 A2RPutative 2-hydroxyacid dehydrogenase / 0.692
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.691
3tn7 NJPShort-chain alcohol dehydrogenase / 0.690
2yut NAPPutative short-chain oxidoreductase / 0.689
1w4z NAPPutative ketoacyl reductase 1.3.1 0.687
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.686
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.685
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.684
1oaa NAPSepiapterin reductase 1.1.1.153 0.684
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.684
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.684
2c29 NAPDihydroflavonol 4-reductase / 0.683
2gcg NDPGlyoxylate reductase/hydroxypyruvate reductase 1.1.1.79 0.683
4oaq NDPR-specific carbonyl reductase / 0.681
1o9b NAIQuinate/shikimate dehydrogenase / 0.680
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.680
4j4b NAIUncharacterized protein / 0.680
3l77 NJPShort-chain alcohol dehydrogenase / 0.679
4hfm NAP2-alkenal reductase (NADP(+)-dependent) / 0.679
4i5e NAPAlclohol dehydrogenase/short-chain dehydrogenase / 0.679
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.679
2voj NADAlanine dehydrogenase 1.4.1.1 0.677
4jk3 NADUncharacterized protein / 0.677
4gkv NADAlcohol dehydrogenase, propanol-preferring 1.1.1.1 0.672
4xq9 NADHomospermidine synthase 2.5.1.44 0.672
1x7d NADPutative ornithine cyclodeaminase / 0.670
2vq3 NAPMetalloreductase STEAP3 / 0.670
1ib6 NADMalate dehydrogenase / 0.669
2o4c NADErythronate-4-phosphate dehydrogenase / 0.669
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.669
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.667
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.667
2vhx NADAlanine dehydrogenase 1.4.1.1 0.666
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.665
3p19 NDPPutative blue fluorescent protein / 0.664
3wg6 NDPNADPH-dependent conjugated polyketone reductase C1 / 0.663
5env NADAlcohol dehydrogenase 1 1.1.1.1 0.663
4bv9 NDPKetimine reductase mu-crystallin 1.5.1.25 0.662
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.662
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.660
2c3c NAP2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.659
3t4e NADQuinate/shikimate dehydrogenase / 0.659
3wbf NAPMeso-diaminopimelate D-dehydrogenase / 0.659
4j49 NAIUncharacterized protein / 0.659
1npd NADQuinate/shikimate dehydrogenase / 0.658
1x7g NAPPutative ketoacyl reductase 1.3.1 0.658
3wsw NADL-lactate dehydrogenase / 0.658
4imp NDPPolyketide synthase extender modules 3-4 / 0.658
4j49 NADUncharacterized protein / 0.658
4y1b NAPAntE / 0.657
2p9c NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.656
3wle NAD(R)-specific carbonyl reductase / 0.656
4l4x NDPAmphI / 0.656
4o0l NDPNADPH-dependent 3-quinuclidinone reductase / 0.656
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.656
1zha PEP2-dehydro-3-deoxyphosphooctonate aldolase 2.5.1.55 0.655
2f1k NAPPrephenate dehydrogenase / 0.655
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.653
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.651
3tri NAPPyrroline-5-carboxylate reductase / 0.651
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.650