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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
4dbv NDP Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 1.043
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.917
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.912
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.885
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.882
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.880
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.876
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.871
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.871
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.869
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.868
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.868
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.866
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.865
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.864
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.863
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.860
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.858
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.855
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.852
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.850
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.847
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.845
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.843
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.842
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.841
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.834
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.832
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.832
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.829
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.828
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.827
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.824
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.822
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.820
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.817
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.808
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.805
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.799
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.797
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.797
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.794
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.788
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.785
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.785
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.783
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.780
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.779
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.771
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.767
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.765
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.762
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.759
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.757
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.747
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.742
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.738
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.736
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.736
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.732
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.732
3f3s NADLambda-crystallin homolog / 0.724
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.717
3ikt NADRedox-sensing transcriptional repressor Rex / 0.716
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.715
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.713
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.712
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.709
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.707
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.707
3tri NAPPyrroline-5-carboxylate reductase / 0.707
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.702
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.694
2vhx NADAlanine dehydrogenase 1.4.1.1 0.693
3q3c NADNAD-dependent L-serine dehydrogenase / 0.692
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.689
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.689
2g5c NADPrephenate dehydrogenase / 0.688
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.685
3l0d NADGlyceraldehyde-3-phosphate dehydrogenase / 0.679
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.675
3hwr NDP2-dehydropantoate 2-reductase / 0.671
3keo NADRedox-sensing transcriptional repressor Rex / 0.670
1ihx SNDGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.666
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.665
2czc NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.662
1gae NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.661
3wv7 ADPHmd co-occurring protein HcgE / 0.659
1zh8 NAPUncharacterized protein / 0.658
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.656
3wmx NADNAD dependent epimerase/dehydratase / 0.655
1o6z NADMalate dehydrogenase / 0.654
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.654
4k28 NADShikimate dehydrogenase family protein / 0.654
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.652
2o4c NADErythronate-4-phosphate dehydrogenase / 0.652
3ggp NADPrephenate dehydrogenase / 0.652