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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
1psd NAD D-3-phosphoglycerate dehydrogenase 1.1.1.95

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 1.082
1wwk NAD307aa long hypothetical phosphoglycerate dehydrogenase / 0.837
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.829
1yba NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.799
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.776
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.765
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.765
3oet NADErythronate-4-phosphate dehydrogenase / 0.762
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.757
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.752
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.751
2p9g NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.746
2p9c NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.744
2aa3 AP0L-lactate dehydrogenase / 0.741
2hu2 NADC-terminal binding protein 1 / 0.739
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.739
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.733
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.727
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.727
3kb6 NADD-lactate dehydrogenase / 0.724
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.723
2p9e NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.721
1t2c NAIL-lactate dehydrogenase 1.1.1.27 0.719
1pzh NADLactate dehydrogenase / 0.715
2vhx NADAlanine dehydrogenase 1.4.1.1 0.715
3ikt NADRedox-sensing transcriptional repressor Rex / 0.715
1hku NADC-terminal-binding protein 1 1.1.1 0.713
2o4c NADErythronate-4-phosphate dehydrogenase / 0.713
1j49 NADD-lactate dehydrogenase 1.1.1.28 0.712
4weq NAPNAD-dependent dehydrogenase / 0.712
4xcv NDPProbable hydroxyacid dehydrogenase protein / 0.703
1dxy NADD-2-hydroxyisocaproate dehydrogenase 1.1.1 0.701
1pjc NADAlanine dehydrogenase / 0.701
4xyb NDPFormate dehydrogenase / 0.701
2x0i NAIMalate dehydrogenase / 0.698
3adp NAILambda-crystallin 1.1.1.45 0.698
3uko NADAlcohol dehydrogenase class-3 / 0.697
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.696
1uxk NADMalate dehydrogenase / 0.696
2voj NADAlanine dehydrogenase 1.4.1.1 0.694
2g5c NADPrephenate dehydrogenase / 0.690
3jv7 NADSecondary alcohol dehydrogenase / 0.690
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.688
4z0p NDPNAD-dependent dehydrogenase / 0.688
1sow NADL-lactate dehydrogenase 1.1.1.27 0.685
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.685
5bqf NAPProbable hydroxyacid dehydrogenase protein / 0.685
1pzg A3DLactate dehydrogenase / 0.684
4lcj NADC-terminal-binding protein 2 / 0.684
2dbr NAPGlyoxylate reductase 1.1.1.26 0.681
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.680
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.678
1f8f NADBenzyl alcohol dehydrogenase / 0.677
2ome NADC-terminal-binding protein 2 / 0.677
3ggg NADPrephenate dehydrogenase / 0.677
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.676
5kje NAJAlcohol dehydrogenase E chain 1.1.1.1 0.676
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.675
4xqc NADHomospermidine synthase 2.5.1.44 0.675
5kjc NAJAlcohol dehydrogenase E chain 1.1.1.1 0.675
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.673
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.673
1uxj NADMalate dehydrogenase / 0.673
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.673
3wle NAD(R)-specific carbonyl reductase / 0.673
4id9 NADPutative UDP-glucose 4-epimerase / 0.673
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.672
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.672
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.671
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.671
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.671
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.671
2a92 NAIL-lactate dehydrogenase / 0.670
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.669
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.669
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.669
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.668
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.667
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.667
1lde NADAlcohol dehydrogenase E chain 1.1.1.1 0.666
2gr0 ADPFerredoxin reductase / 0.666
3kbo NDPGlyoxylate/hydroxypyruvate reductase A / 0.666
3keo NADRedox-sensing transcriptional repressor Rex / 0.666
2wsb NADGalactitol dehydrogenase / 0.665
4c4o NADSADH / 0.665
1ur5 NADMalate dehydrogenase / 0.664
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.664
4xye NADFormate dehydrogenase / 0.664
1wze NADMalate dehydrogenase / 0.663
4xq9 NADHomospermidine synthase 2.5.1.44 0.663
1u3v NADAlcohol dehydrogenase 1B 1.1.1.1 0.662
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.662
1zmd NAIDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.661
4jji NADAlcohol dehydrogenase class-3 / 0.661
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.660
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.659
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.658
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.658
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.658
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.658
2nad NADFormate dehydrogenase / 0.657
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.656
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.656
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.655
4wlv NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.655
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.654
3baz NAPHydroxyphenylpyruvate reductase 1.1.1.237 0.654
3ggp NADPrephenate dehydrogenase / 0.654
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 0.654
1hsz NADAlcohol dehydrogenase 1B 1.1.1.1 0.653
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.653
3wsw NADL-lactate dehydrogenase / 0.653
5bsg NAPPyrroline-5-carboxylate reductase / 0.653
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.653
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.652
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.652
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.652
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.652
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.652
5jla NADPutative short-chain dehydrogenase/reductase / 0.651
1bw9 NADPhenylalanine dehydrogenase / 0.650
1e3l NADAlcohol dehydrogenase 4 1.1.1.1 0.650
1f8g NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.650
2dc1 NADProbable L-aspartate dehydrogenase / 0.650
4nbt NAD3-oxoacyl-[acyl-carrier-protein] reductase / 0.650