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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
5k8b PDG 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5k8b PDG8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase / 1.260
1b9i PXG3-amino-5-hydroxybenzoate synthase 4.2.1.144 0.723
4zm3 PLPAminotransferase / 0.713
1mlz PLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase 2.6.1.62 0.699
2hp2 KE4Glutamate-1-semialdehyde 2,1-aminomutase 5.4.3.8 0.695
3tfu PL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase 2.6.1.62 0.692
2gmu PDGPutative pyridoxamine 5-phosphate-dependent dehydrase / 0.684
1x28 PGUAspartate aminotransferase 2.6.1.1 0.682
4jf1 PLPAcetylornithine/succinyldiaminopimelate aminotransferase 2.6.1.11 0.682
2po3 T4K4-dehydrase / 0.678
1o69 X04Aminotransferase DegT / 0.675
2gms P0PPutative pyridoxamine 5-phosphate-dependent dehydrase / 0.665
1map KETAspartate aminotransferase, mitochondrial 2.6.1.1 0.663
1akb PPDAspartate aminotransferase, mitochondrial 2.6.1.1 0.658
3vax PLPUncharacterized protein / 0.656
1u08 PLPMethionine aminotransferase / 0.654
1arg PPDAspartate aminotransferase 2.6.1.1 0.653
2bwp PLG5-aminolevulinate synthase 2.3.1.37 0.653
1arh PPDAspartate aminotransferase 2.6.1.1 0.651
2ycn P61Tyrosine phenol-lyase 4.1.99.2 0.651