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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
3zcx NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 1.058
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 1.001
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.952
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.943
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.930
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.920
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.918
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.915
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.901
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.899
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.895
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.892
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.885
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.884
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.884
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.883
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.882
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.882
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.880
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.878
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.870
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.869
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.868
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.864
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.859
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.858
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.853
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.851
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.848
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.848
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.848
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.847
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.845
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.842
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.839
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.827
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.819
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.819
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.817
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.816
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.812
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.807
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.805
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.795
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.795
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.793
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.786
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.780
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.766
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.765
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.762
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.759
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.758
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.757
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.744
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.739
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.734
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.733
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.733
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.732
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.709
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.708
3ggp NADPrephenate dehydrogenase / 0.707
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.706
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.699
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.695
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.695
2g5c NADPrephenate dehydrogenase / 0.690
3adp NAILambda-crystallin 1.1.1.45 0.689
1guy NADMalate dehydrogenase / 0.686
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.685
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.681
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.680
3hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.677
4k28 NADShikimate dehydrogenase family protein / 0.676
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.675
3w6u NAP6-phosphogluconate dehydrogenase, NAD-binding protein / 0.675
4jji NADAlcohol dehydrogenase class-3 / 0.675
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.671
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.671
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.670
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.669
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.669
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.669
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.667
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.666
3t4e NADQuinate/shikimate dehydrogenase / 0.666
4j4b NAIUncharacterized protein / 0.666
3uko NADAlcohol dehydrogenase class-3 / 0.662
3hwr NDP2-dehydropantoate 2-reductase / 0.661
3oet NADErythronate-4-phosphate dehydrogenase / 0.661
2o4c NADErythronate-4-phosphate dehydrogenase / 0.659
2vhx NADAlanine dehydrogenase 1.4.1.1 0.658
3tri NAPPyrroline-5-carboxylate reductase / 0.657
4dlb NADS-(hydroxymethyl)glutathione dehydrogenase / 0.657
4j49 NADUncharacterized protein / 0.657
5bsg NAPPyrroline-5-carboxylate reductase / 0.657
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.656
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.656
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.656
5ijz NAPNADP-specific glutamate dehydrogenase 1.4.1.4 0.656
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.655
1lsj NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.654
2rcy NAPPyrroline-5-carboxylate reductase / 0.653
4xb1 NDP319aa long hypothetical homoserine dehydrogenase / 0.653
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.653
2yy7 NADL-threonine dehydrogenase / 0.651
4pzd NAD3-Hydroxyacyl-CoA dehydrogenase / 0.651