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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
2ph5 NAD Homospermidine synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ph5 NADHomospermidine synthase / 1.172
4plp NADHomospermidine synthase 2.5.1.44 0.759
1e5q NDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming] 1.5.1.10 0.752
4xrg NADHomospermidine synthase 2.5.1.44 0.747
4xq9 NADHomospermidine synthase 2.5.1.44 0.735
4xqc NADHomospermidine synthase 2.5.1.44 0.731
4tvb NADHomospermidine synthase 2.5.1.44 0.726
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.715
4b7x NAPProbable oxidoreductase / 0.714
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.714
4xcv NDPProbable hydroxyacid dehydrogenase protein / 0.713
1i36 NAPConserved protein / 0.710
1lso NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.710
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.710
4ebf NADPhosphonate dehydrogenase 1.20.1.1 0.710
2voj NADAlanine dehydrogenase 1.4.1.1 0.708
1nyt NAPShikimate dehydrogenase (NADP(+)) / 0.705
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.702
5bqf NAPProbable hydroxyacid dehydrogenase protein / 0.700
3ing NDPHomoserine dehydrogenase related protein / 0.698
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.697
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.688
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.684
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.682
1x7d NADPutative ornithine cyclodeaminase / 0.680
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.680
3wsw NADL-lactate dehydrogenase / 0.680
3cea NADMyo-inositol 2-dehydrogenase-like (Promiscuous) / 0.678
1adc PADAlcohol dehydrogenase E chain 1.1.1.1 0.677
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.677
1guy NADMalate dehydrogenase / 0.676
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.676
4nu6 NADPhosphonate dehydrogenase 1.20.1.1 0.676
2o4c NADErythronate-4-phosphate dehydrogenase / 0.675
3zw9 NADPeroxisomal bifunctional enzyme 1.1.1.35 0.675
1c1d NAIPhenylalanine dehydrogenase / 0.674
4y1b NAPAntE / 0.674
3abi NADUncharacterized protein / 0.672
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.669
2vhx NADAlanine dehydrogenase 1.4.1.1 0.668
1j49 NADD-lactate dehydrogenase 1.1.1.28 0.667
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.667
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.666
5dt9 NADErythronate-4-phosphate dehydrogenase / 0.665
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.664
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.663
1pj3 NADNAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.663
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.662
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.662
1pj2 NAINAD-dependent malic enzyme, mitochondrial 1.1.1.38 0.661
4z0p NDPNAD-dependent dehydrogenase / 0.661
1bws NDPGDP-L-fucose synthase / 0.660
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.660
1ur5 NADMalate dehydrogenase / 0.659
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.659
3toz NADShikimate dehydrogenase (NADP(+)) / 0.659
5ijz NAPNADP-specific glutamate dehydrogenase 1.4.1.4 0.659
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.658
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.658
4y0k NAPAntE / 0.658
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.657
3ggg NADPrephenate dehydrogenase / 0.657
4j49 NAIUncharacterized protein / 0.657
4j49 NADUncharacterized protein / 0.656
2jd0 NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.655
1axe NADAlcohol dehydrogenase E chain 1.1.1.1 0.654
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.654
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.654
3wle NAD(R)-specific carbonyl reductase / 0.654
4lcj NADC-terminal-binding protein 2 / 0.654
4oqy NDP(S)-imine reductase / 0.654
1q7g NHOHomoserine dehydrogenase 1.1.1.3 0.653
2vq3 NAPMetalloreductase STEAP3 / 0.653
3hwr NDP2-dehydropantoate 2-reductase / 0.653
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.653
2rab NADGlutathione amide reductase / 0.652
3ikt NADRedox-sensing transcriptional repressor Rex / 0.652
1e3l NADAlcohol dehydrogenase 4 1.1.1.1 0.651
1u7h NADPutative ornithine cyclodeaminase / 0.650
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.650
2jcv NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.650
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.650
3q3c NADNAD-dependent L-serine dehydrogenase / 0.650