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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
3lvf NAD Glyceraldehyde-3-phosphate dehydrogenase 1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 1.030
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.964
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.956
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.927
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.923
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.921
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.920
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.912
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.905
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.905
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.901
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.899
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.897
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.894
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.891
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.886
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.885
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.885
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.885
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.884
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.882
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.880
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.873
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.873
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.871
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.871
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.871
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.865
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.860
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.859
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.849
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.836
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.832
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.826
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.826
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.824
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.817
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.817
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.808
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.806
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.798
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.797
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.797
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.796
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.790
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.789
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.788
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.777
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.771
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.765
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.758
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.757
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.754
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.748
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.742
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.737
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.728
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.721
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.721
3keo NADRedox-sensing transcriptional repressor Rex / 0.718
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.715
3ikt NADRedox-sensing transcriptional repressor Rex / 0.714
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.709
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.708
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.707
4yag NAIC alpha-dehydrogenase / 0.704
1o6z NADMalate dehydrogenase / 0.698
3ntr NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.694
3keq NADRedox-sensing transcriptional repressor Rex / 0.691
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.689
4yac NAIC alpha-dehydrogenase / 0.689
2pv7 NADT-protein 1.3.1.12 0.687
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.686
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.686
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.683
2g5c NADPrephenate dehydrogenase / 0.681
2ixa NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.679
2o4c NADErythronate-4-phosphate dehydrogenase / 0.679
4xr9 NADCalS8 / 0.678
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.677
2vhx NADAlanine dehydrogenase 1.4.1.1 0.675
3ket NADRedox-sensing transcriptional repressor Rex / 0.675
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.674
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.674
1c1d NAIPhenylalanine dehydrogenase / 0.673
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.673
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.673
3f3s NADLambda-crystallin homolog / 0.673
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.671
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.670
3nt2 NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.670
4hb9 FADUncharacterized protein / 0.670
2vhz NAIAlanine dehydrogenase 1.4.1.1 0.669
4xrg NADHomospermidine synthase 2.5.1.44 0.668
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.667
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.665
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.664
1pjc NADAlanine dehydrogenase / 0.662
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.660
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.660
2yyy NAPGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.659
1bw9 NADPhenylalanine dehydrogenase / 0.658
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.657
3cgb FADCoenzyme A disulfide reductase / 0.657
3fpz AHZThiamine thiazole synthase / 0.657
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.657
4xq9 NADHomospermidine synthase 2.5.1.44 0.657
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.656
3ggp NADPrephenate dehydrogenase / 0.656
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.655
3cgd FADCoenzyme A disulfide reductase / 0.655
5jla NADPutative short-chain dehydrogenase/reductase / 0.655
1i36 NAPConserved protein / 0.654
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.653
4wct FADFructosyl amine:oxygen oxidoreductase / 0.653
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.652
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.652
5lc1 NADL-threonine 3-dehydrogenase / 0.652
3k30 ADPHistamine dehydrogenase / 0.651
4wji NAPPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase / 0.650