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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
1nqo NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.998
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.959
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.953
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.948
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.946
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.940
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.939
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.938
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.928
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.921
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.918
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.917
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.891
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.889
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.884
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.874
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.865
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.865
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.864
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.862
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.861
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.860
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.858
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.853
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.853
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.848
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.847
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.846
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.845
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.840
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.837
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.834
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.820
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.820
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.820
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.817
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.816
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.809
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.807
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.804
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.802
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.801
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.791
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.787
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.784
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.783
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.781
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.778
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.776
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.768
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.766
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.764
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.757
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.756
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.754
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.753
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.742
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.741
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.734
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.721
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.720
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.718
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.712
3keo NADRedox-sensing transcriptional repressor Rex / 0.709
3ggp NADPrephenate dehydrogenase / 0.708
1o6z NADMalate dehydrogenase / 0.707
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.706
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.700
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.692
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.691
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.689
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.684
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.683
2o4c NADErythronate-4-phosphate dehydrogenase / 0.682
2pv7 NADT-protein 1.3.1.12 0.680
3ikt NADRedox-sensing transcriptional repressor Rex / 0.680
1c1d NAIPhenylalanine dehydrogenase / 0.679
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.679
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.677
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.677
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.677
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.675
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.675
1lsj NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.674
3ish FADThioredoxin reductase 1.8.1.9 0.672
2g5c NADPrephenate dehydrogenase / 0.671
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.670
4plp NADHomospermidine synthase 2.5.1.44 0.670
2eq7 NADDihydrolipoyl dehydrogenase / 0.669
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.667
3hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.667
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.666
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.665
2yy7 NADL-threonine dehydrogenase / 0.665
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.662
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.661
4xr9 NADCalS8 / 0.661
4xqc NADHomospermidine synthase 2.5.1.44 0.659
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.658
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.658
2yyy NAPGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.657
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.657
4kug NAD3-hydroxybutyryl-CoA dehydrogenase / 0.657
3zdn FADMonoamine oxidase N 1.4.3.4 0.655
4k28 NADShikimate dehydrogenase family protein / 0.655
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.654
4ywj NAD4-hydroxy-tetrahydrodipicolinate reductase / 0.654
1f17 NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.653
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.653
1guy NADMalate dehydrogenase / 0.651
4dpl NAPMalonyl-CoA reductase 1.2.1.75 0.651
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.651
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.650
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.650
3ggo NAIPrephenate dehydrogenase / 0.650
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.650