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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
2dbv NDP Glyceraldehyde-3-phosphate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 1.040
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.888
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.874
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.874
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.860
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.849
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.842
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.839
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.836
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.830
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.822
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.820
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.817
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.813
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.810
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.806
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.805
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.801
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.801
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.799
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.796
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.794
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.792
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.792
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.791
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.788
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.785
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.784
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.779
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.772
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.771
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.770
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.768
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.767
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.766
3dmt NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.766
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.765
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.765
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.764
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.763
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.763
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.759
3b1j NADGlyceraldehyde-3-phosphate dehydrogenase / 0.756
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.752
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.752
2b4r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.747
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.736
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.734
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.728
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.727
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.726
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.711
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.711
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.711
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.710
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.710
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.705
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.704
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.700
3e5r NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.697
1ml3 NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.696
1rm5 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.696
3doc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.695
1qxs NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.694
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.682
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.678
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.676
3ikt NADRedox-sensing transcriptional repressor Rex / 0.674
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.674
3tri NAPPyrroline-5-carboxylate reductase / 0.672
4om8 NAD3-hydroxybutyryl-coA dehydrogenase / 0.663
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.660
2yyy NAPGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 0.656
1gl3 NDPAspartate-semialdehyde dehydrogenase / 0.654