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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
3zkb ANP DNA gyrase subunit B

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3zkb ANPDNA gyrase subunit B / 1.156
4wud ANPDNA gyrase subunit B / 1.010
4wuc ANPDNA gyrase subunit B / 1.004
1mx0 ANPType 2 DNA topoisomerase 6 subunit B / 0.898
4prx ADPDNA gyrase subunit B / 0.864
1pvg ANPDNA topoisomerase 2 5.99.1.3 0.846
1nhh ANPDNA mismatch repair protein MutL / 0.834
4prv ADPDNA gyrase subunit B / 0.833
3zkd ANPDNA gyrase subunit B / 0.822
4ipe ANPTNF receptor-associated protein 1 / 0.789
4ivg ANPTNF receptor-associated protein 1 / 0.785
1zxm ANPDNA topoisomerase 2-alpha 5.99.1.3 0.771
1z5a ADPType 2 DNA topoisomerase 6 subunit B / 0.769
1s16 ANPDNA topoisomerase 4 subunit B / 0.765
1z5c ADPType 2 DNA topoisomerase 6 subunit B / 0.763
1ei1 ANPDNA gyrase subunit B / 0.735
1i58 ACPChemotaxis protein CheA 2.7.13.3 0.718
3t1k ANPHeat shock protein HSP 90-alpha / 0.712
1z59 ADPType 2 DNA topoisomerase 6 subunit B / 0.703
3crl ANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial 2.7.11.2 0.701
1i59 ANPChemotaxis protein CheA 2.7.13.3 0.689
2bu2 ATP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial 2.7.11.2 0.688
2e0a ANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.688
1byq ADPHeat shock protein HSP 90-alpha / 0.686
3h4l ANPDNA mismatch repair protein PMS1 / 0.686
3sl2 ATPSensor histidine kinase WalK / 0.686
2xk2 ADPHeat shock protein HSP 90-alpha / 0.678
3a0t ADPSensor histidine kinase / 0.677
3t10 ACPHeat shock protein HSP 90-alpha / 0.677
4xc0 ACPHeat shock cognate 90 kDa protein / 0.676
3d2r ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.669
2z4w 749Geranylgeranyl pyrophosphate synthase / 0.666
5f5r ANPHeat shock protein 75 kDa, mitochondrial / 0.666
3t0z ATPHeat shock protein HSP 90-alpha / 0.657
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.655
4gqt ADPHeat shock protein 90 / 0.654
4gt8 ADPSensor protein VraS 2.7.13.3 0.654
4h5d YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.653
4iij GTPTubulin alpha-1B chain / 0.653
2yef ANPHeat shock protein HSP 90-alpha / 0.652
3s3t ATPUniversal stress protein / 0.652