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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
3zkd ANP DNA gyrase subunit B

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3zkd ANPDNA gyrase subunit B / 1.217
1s16 ANPDNA topoisomerase 4 subunit B / 0.945
4wuc ANPDNA gyrase subunit B / 0.916
4wud ANPDNA gyrase subunit B / 0.906
1ei1 ANPDNA gyrase subunit B / 0.854
1nhh ANPDNA mismatch repair protein MutL / 0.823
3zkb ANPDNA gyrase subunit B / 0.822
4prx ADPDNA gyrase subunit B / 0.796
1pvg ANPDNA topoisomerase 2 5.99.1.3 0.793
1mx0 ANPType 2 DNA topoisomerase 6 subunit B / 0.788
1z5a ADPType 2 DNA topoisomerase 6 subunit B / 0.734
4ipe ANPTNF receptor-associated protein 1 / 0.734
4ivg ANPTNF receptor-associated protein 1 / 0.709
1zxm ANPDNA topoisomerase 2-alpha 5.99.1.3 0.704
3h4l ANPDNA mismatch repair protein PMS1 / 0.691
3a0t ADPSensor histidine kinase / 0.689
3crl ANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial 2.7.11.2 0.687
1i59 ANPChemotaxis protein CheA 2.7.13.3 0.682
5f5r ANPHeat shock protein 75 kDa, mitochondrial / 0.678
1z5c ADPType 2 DNA topoisomerase 6 subunit B / 0.677
1th8 ADPAnti-sigma F factor / 0.674
3t10 ACPHeat shock protein HSP 90-alpha / 0.672
3t0z ATPHeat shock protein HSP 90-alpha / 0.671
4xc0 ACPHeat shock cognate 90 kDa protein / 0.669
1xje GDPVitamin B12-dependent ribonucleotide reductase / 0.665
2ydo ADNAdenosine receptor A2a / 0.664
1byq ADPHeat shock protein HSP 90-alpha / 0.663
4gqt ADPHeat shock protein 90 / 0.660
4m69 ANPReceptor-interacting serine/threonine-protein kinase 3 2.7.11.1 0.659
5bsm ATP4-coumarate--CoA ligase 2 6.2.1.12 0.655
3sl2 ATPSensor histidine kinase WalK / 0.652