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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
1ywg NAD Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 1.003
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.910
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.892
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.881
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.878
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.875
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.858
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.854
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.844
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.842
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.837
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.833
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.829
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.828
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.815
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.811
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.809
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.807
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.806
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.804
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.801
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.800
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.799
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.798
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.798
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.798
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.797
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.796
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.794
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.793
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.790
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.789
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.786
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.785
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.782
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.781
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.779
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.779
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.779
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.773
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.772
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.771
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.770
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.767
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.767
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.763
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.754
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.746
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.743
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.733
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.730
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.730
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.728
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.714
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.712
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.711
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.708
3adp NAILambda-crystallin 1.1.1.45 0.706
3f3s NADLambda-crystallin homolog / 0.705
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.703
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.697
3keo NADRedox-sensing transcriptional repressor Rex / 0.696
3ec7 NADInositol 2-dehydrogenase / 0.695
3gvi ADPMalate dehydrogenase / 0.694
3hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.693
2hu2 NADC-terminal binding protein 1 / 0.691
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.688
2qg4 NADUDP-glucose 6-dehydrogenase 1.1.1.22 0.686
2vhw NAIAlanine dehydrogenase 1.4.1.1 0.686
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.686
2hdh NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.685
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.684
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.683
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.682
3d64 NADAdenosylhomocysteinase / 0.682
1guy NADMalate dehydrogenase / 0.681
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.678
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.678
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.672
2o4c NADErythronate-4-phosphate dehydrogenase / 0.672
1o6z NADMalate dehydrogenase / 0.671
3gnq NADGlyceraldehyde-3-phosphate dehydrogenase / 0.671
2ome NADC-terminal-binding protein 2 / 0.670
1c1d NAIPhenylalanine dehydrogenase / 0.669
4j36 FADKynurenine 3-monooxygenase / 0.669
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.668
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.667
3pqf NADL-lactate dehydrogenase 1.1.1.27 0.667
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.666
3wmx NADNAD dependent epimerase/dehydratase / 0.666
2x0r NADMalate dehydrogenase / 0.665
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.659
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.658
2rcy NAPPyrroline-5-carboxylate reductase / 0.658
3wv8 ATPHmd co-occurring protein HcgE / 0.658
3q3c NADNAD-dependent L-serine dehydrogenase / 0.657
2ldb NADL-lactate dehydrogenase 1.1.1.27 0.656
3tri NAPPyrroline-5-carboxylate reductase / 0.656
1hku NADC-terminal-binding protein 1 1.1.1 0.655
1ur5 NADMalate dehydrogenase / 0.655
2vhx NADAlanine dehydrogenase 1.4.1.1 0.655
3wv7 ADPHmd co-occurring protein HcgE / 0.655
4lcj NADC-terminal-binding protein 2 / 0.655
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.653
4xq9 NADHomospermidine synthase 2.5.1.44 0.652
1zem NADXylitol dehydrogenase / 0.651
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.650
3q9t FAYUncharacterized protein / 0.650