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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
1v3s ATP Signaling protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1v3s ATPSignaling protein / 1.132
4co4 ATPNitrogen regulatory protein P-II 1 / 0.858
1v9o ADPSignaling protein / 0.791
4rx6 ATPNitrogen regulatory PII-like protein / 0.740
4ozn ATPAmmonium transporter / 0.715
3ncq ATPNitrogen regulatory protein P-II (GlnB-2) / 0.702
4aff ATPNitrogen regulatory protein P-II / 0.698
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.688
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.677
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.675
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.673
3hyo ADPPyridoxal kinase / 0.670
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.668
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.668
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.668
3ta1 ADPNitrogen regulatory protein P-II (GlnB-3) / 0.666
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.664
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.661
2xul ATPNitrogen regulatory protein P-II / 0.660
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.660
3tw6 ADPPyruvate carboxylase / 0.660
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.658
5ah5 LSSLeucine--tRNA ligase / 0.657
4cnf MTASpoU rRNA methylase / 0.656
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.654
4cng SAHSpoU rRNA methylase / 0.654
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.651
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.651
4ffm ADPUncharacterized protein / 0.651
4ffl ADPUncharacterized protein / 0.650
4ffr ATPUncharacterized protein / 0.650