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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
4prv ADP DNA gyrase subunit B

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4prv ADPDNA gyrase subunit B / 1.052
4prx ADPDNA gyrase subunit B / 0.986
4wuc ANPDNA gyrase subunit B / 0.953
4wud ANPDNA gyrase subunit B / 0.952
1z5c ADPType 2 DNA topoisomerase 6 subunit B / 0.839
3zkb ANPDNA gyrase subunit B / 0.833
3a0t ADPSensor histidine kinase / 0.808
3sl2 ATPSensor histidine kinase WalK / 0.772
1th8 ADPAnti-sigma F factor / 0.771
1z5a ADPType 2 DNA topoisomerase 6 subunit B / 0.771
1mx0 ANPType 2 DNA topoisomerase 6 subunit B / 0.762
2zkj ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.756
3d2r ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.755
1gjv AGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial 2.7.11.4 0.749
1nhh ANPDNA mismatch repair protein MutL / 0.747
1ei1 ANPDNA gyrase subunit B / 0.743
4ivg ANPTNF receptor-associated protein 1 / 0.741
2e0a ANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.735
2xcm ADPCytosolic heat shock protein 90 / 0.733
1i59 ANPChemotaxis protein CheA 2.7.13.3 0.730
1z59 ADPType 2 DNA topoisomerase 6 subunit B / 0.730
3t1k ANPHeat shock protein HSP 90-alpha / 0.727
1i5a ACPChemotaxis protein CheA 2.7.13.3 0.726
3t0z ATPHeat shock protein HSP 90-alpha / 0.723
3t10 ACPHeat shock protein HSP 90-alpha / 0.722
3t2s AGSHeat shock protein HSP 90-alpha / 0.716
1i5b ANPChemotaxis protein CheA 2.7.13.3 0.713
4gt8 ADPSensor protein VraS 2.7.13.3 0.713
2bu8 ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial 2.7.11.2 0.711
1pvg ANPDNA topoisomerase 2 5.99.1.3 0.710
3crl ANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial 2.7.11.2 0.707
1zxn ADPDNA topoisomerase 2-alpha 5.99.1.3 0.706
4gqt ADPHeat shock protein 90 / 0.700
1i58 ACPChemotaxis protein CheA 2.7.13.3 0.699
2yef ANPHeat shock protein HSP 90-alpha / 0.695
1jm6 ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial 2.7.11.2 0.691
4xcj ADPHeat shock cognate 90 kDa protein / 0.689
5f5r ANPHeat shock protein 75 kDa, mitochondrial / 0.685
1yt0 ADPEndoplasmin / 0.684
4bix ADPSensor histidine kinase CpxA / 0.683
4xc0 ACPHeat shock cognate 90 kDa protein / 0.683
1id0 ANPSensor protein PhoQ 2.7.13.3 0.680
4xcl AGSHeat shock cognate 90 kDa protein / 0.679
3h4l ANPDNA mismatch repair protein PMS1 / 0.677
4ipe ANPTNF receptor-associated protein 1 / 0.677
3ehj ACPSensor histidine kinase DesK 2.7.13.3 0.674
2p0a ANPSynapsin-3 / 0.672
2ior ADPChaperone protein HtpG / 0.671
2ido TMPDNA polymerase III subunit epsilon 2.7.7.7 0.670
1am1 ADPATP-dependent molecular chaperone HSP82 / 0.669
4r1f ADPDNA topoisomerase 2-alpha 5.99.1.3 0.669
2c2a ADPSensor histidine kinase / 0.664
1mjh ATPUniversal stress protein MJ0577 / 0.662
4r3a ANPBlue-light-activated histidine kinase 2 2.7.13.3 0.654
2ywv ADPPhosphoribosylaminoimidazole-succinocarboxamide synthase / 0.653
4riy ANPReceptor tyrosine-protein kinase erbB-3 2.7.10.1 0.653