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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
3d2r ADP [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3d2r ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.995
2zkj ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.984
3a0t ADPSensor histidine kinase / 0.884
2e0a ANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.869
1gjv AGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial 2.7.11.4 0.839
1z5c ADPType 2 DNA topoisomerase 6 subunit B / 0.814
4prx ADPDNA gyrase subunit B / 0.802
3sl2 ATPSensor histidine kinase WalK / 0.791
1nhh ANPDNA mismatch repair protein MutL / 0.770
1jm6 ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial 2.7.11.2 0.761
4prv ADPDNA gyrase subunit B / 0.755
2bu8 ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial 2.7.11.2 0.744
4wuc ANPDNA gyrase subunit B / 0.744
4ivg ANPTNF receptor-associated protein 1 / 0.743
1z5a ADPType 2 DNA topoisomerase 6 subunit B / 0.742
2zdy ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.740
5f5r ANPHeat shock protein 75 kDa, mitochondrial / 0.738
4wud ANPDNA gyrase subunit B / 0.737
4ipe ANPTNF receptor-associated protein 1 / 0.724
3t2s AGSHeat shock protein HSP 90-alpha / 0.721
1thn ADPAnti-sigma F factor / 0.714
4xcj ADPHeat shock cognate 90 kDa protein / 0.712
4xcl AGSHeat shock cognate 90 kDa protein / 0.711
2ior ADPChaperone protein HtpG / 0.695
4bix ADPSensor histidine kinase CpxA / 0.693
3crl ANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial 2.7.11.2 0.692
3h4l ANPDNA mismatch repair protein PMS1 / 0.681
4xc0 ACPHeat shock cognate 90 kDa protein / 0.681
3t1k ANPHeat shock protein HSP 90-alpha / 0.677
1l0o ADPAnti-sigma F factor / 0.674
2xcm ADPCytosolic heat shock protein 90 / 0.670
2xk2 ADPHeat shock protein HSP 90-alpha / 0.670
3zkb ANPDNA gyrase subunit B / 0.669
1id0 ANPSensor protein PhoQ 2.7.13.3 0.668
2o1u ANPEndoplasmin / 0.664
3t10 ACPHeat shock protein HSP 90-alpha / 0.664
1y4s ADPChaperone protein HtpG / 0.663
1byq ADPHeat shock protein HSP 90-alpha / 0.662
4r3a ANPBlue-light-activated histidine kinase 2 2.7.13.3 0.661
1i58 ACPChemotaxis protein CheA 2.7.13.3 0.660
3tr0 5GPGuanylate kinase / 0.659
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.659
1m8g NADNicotinamide-nucleotide adenylyltransferase 2.7.7.1 0.657
1z59 ADPType 2 DNA topoisomerase 6 subunit B / 0.654
3dge ADPSensor histidine kinase / 0.654
1ei1 ANPDNA gyrase subunit B / 0.653
1zxn ADPDNA topoisomerase 2-alpha 5.99.1.3 0.652
3kmw ATPIntegrin-linked protein kinase 2.7.11.1 0.652
3ehj ACPSensor histidine kinase DesK 2.7.13.3 0.651
3iae D7KBenzaldehyde lyase / 0.651
3t0z ATPHeat shock protein HSP 90-alpha / 0.651
5c93 ACPTwo-component system histidine protein kinase / 0.650