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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
2pkr NDP Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2pkr NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.957
1rm3 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.764
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.728
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.727
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.719
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.716
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.714
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.714
2dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.711
1rm4 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.710
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.707
3zcx NADGlyceraldehyde-3-phosphate dehydrogenase / 0.706
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.702
1j0x NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.700
1vc2 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.699
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.694
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.694
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.692
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.690
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.690
3zdf NADGlyceraldehyde-3-phosphate dehydrogenase / 0.690
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.688
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.688
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.687
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.684
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.683
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.680
3ksd NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.679
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.678
1cer NADGlyceraldehyde-3-phosphate dehydrogenase / 0.676
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.675
1gyp NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.674
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.672
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.670
3lvf NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.670
1nq5 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.669
3dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.667
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.665
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.665
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.664
3v1y NADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic 1.2.1.12 0.662
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.661
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.659
1znq NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.657
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.657
4z0h NADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 1.2.1.12 0.657
1gd1 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.656
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.653
1f0y NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.651
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.650
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.650