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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
3had NAD Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 1.022
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.906
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.864
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.853
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.850
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.808
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.808
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.802
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.784
3hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.769
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.764
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.763
3f3s NADLambda-crystallin homolog / 0.757
3zw9 NADPeroxisomal bifunctional enzyme 1.1.1.35 0.754
3ggp NADPrephenate dehydrogenase / 0.745
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.736
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.735
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.735
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.733
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.732
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.731
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.725
1lsj NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.724
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.724
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.724
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.719
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.714
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.712
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.712
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.712
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.711
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.711
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.709
3q3c NADNAD-dependent L-serine dehydrogenase / 0.708
4dyd NADDiketoreductase / 0.708
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.707
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.705
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.704
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.704
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.703
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.701
4c4o NADSADH / 0.701
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.700
3adp NAILambda-crystallin 1.1.1.45 0.700
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.698
2voj NADAlanine dehydrogenase 1.4.1.1 0.697
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.695
1pjc NADAlanine dehydrogenase / 0.694
3w6u NAP6-phosphogluconate dehydrogenase, NAD-binding protein / 0.694
1ur5 NADMalate dehydrogenase / 0.693
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.692
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.690
3wsw NADL-lactate dehydrogenase / 0.689
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.687
3cgd NADCoenzyme A disulfide reductase / 0.686
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.685
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.684
3ikt NADRedox-sensing transcriptional repressor Rex / 0.682
5lc1 NADL-threonine 3-dehydrogenase / 0.681
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.679
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.679
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.678
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.678
2vhx NADAlanine dehydrogenase 1.4.1.1 0.678
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.677
3ggg NADPrephenate dehydrogenase / 0.677
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.676
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.676
4tvb NADHomospermidine synthase 2.5.1.44 0.676
4xgi NADGlutamate dehydrogenase / 0.676
1c1d NAIPhenylalanine dehydrogenase / 0.675
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.675
1zh8 NAPUncharacterized protein / 0.673
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.673
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.672
1zmd NAIDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.672
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.672
4pzd NAD3-Hydroxyacyl-CoA dehydrogenase / 0.672
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.671
2dc1 NADProbable L-aspartate dehydrogenase / 0.671
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.671
1uxj NADMalate dehydrogenase / 0.670
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.669
3hwr NDP2-dehydropantoate 2-reductase / 0.669
1ky4 NADAdenosylhomocysteinase 3.3.1.1 0.668
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.668
2qg4 NADUDP-glucose 6-dehydrogenase 1.1.1.22 0.668
2yy7 NADL-threonine dehydrogenase / 0.668
4xqc NADHomospermidine synthase 2.5.1.44 0.668
2hu2 NADC-terminal binding protein 1 / 0.666
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.666
3x2f NAIAdenosylhomocysteinase / 0.666
1guy NADMalate dehydrogenase / 0.665
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.665
4dpl NAPMalonyl-CoA reductase 1.2.1.75 0.665
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.664
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.664
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.664
4k28 NADShikimate dehydrogenase family protein / 0.664
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.664
3ec7 NADInositol 2-dehydrogenase / 0.662
1h6a NDPGlucose--fructose oxidoreductase 1.1.99.28 0.661
1i36 NAPConserved protein / 0.661
3oet NADErythronate-4-phosphate dehydrogenase / 0.661
4dl9 NADS-(hydroxymethyl)glutathione dehydrogenase / 0.661
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.661
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.660
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.660
3uko NADAlcohol dehydrogenase class-3 / 0.660
1mp0 NADAlcohol dehydrogenase class-3 1.1.1.1 0.659
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.659
2x0r NADMalate dehydrogenase / 0.659
3wmx NADNAD dependent epimerase/dehydratase / 0.659
5a02 NAPGlucose-fructose oxidoreductase / 0.659
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.658
5a06 NDPGlucose-fructose oxidoreductase / 0.658
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.657
4gae NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.657
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.656
1yjq NAP2-dehydropantoate 2-reductase 1.1.1.169 0.656
3cea NADMyo-inositol 2-dehydrogenase-like (Promiscuous) / 0.656
1pdh FASp-hydroxybenzoate hydroxylase / 0.654
2ph5 NADHomospermidine synthase / 0.654
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.654
5a05 NDPGlucose-fructose oxidoreductase / 0.654
2vq3 NAPMetalloreductase STEAP3 / 0.653
2ahr NAPPyrroline-5-carboxylate reductase / 0.652
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.652
5a03 NDPGlucose-fructose oxidoreductase / 0.652
1e6e FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.651
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.651
1u28 NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.651
2fsv NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.651
2npx NADNADH peroxidase 1.11.1.1 0.651
2o4c NADErythronate-4-phosphate dehydrogenase / 0.651
2oor NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.651
2rcy NAPPyrroline-5-carboxylate reductase / 0.651
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.651
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.650