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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
1nhh ANP DNA mismatch repair protein MutL

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1nhh ANPDNA mismatch repair protein MutL / 1.126
4wud ANPDNA gyrase subunit B / 0.943
1pvg ANPDNA topoisomerase 2 5.99.1.3 0.907
1mx0 ANPType 2 DNA topoisomerase 6 subunit B / 0.902
4wuc ANPDNA gyrase subunit B / 0.901
3zkb ANPDNA gyrase subunit B / 0.834
3zkd ANPDNA gyrase subunit B / 0.823
4ivg ANPTNF receptor-associated protein 1 / 0.799
3d2r ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.770
3a0t ADPSensor histidine kinase / 0.769
1z5a ADPType 2 DNA topoisomerase 6 subunit B / 0.765
4ipe ANPTNF receptor-associated protein 1 / 0.762
1zxm ANPDNA topoisomerase 2-alpha 5.99.1.3 0.761
1gjv AGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial 2.7.11.4 0.759
2e0a ANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.759
2zkj ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.753
3sl2 ATPSensor histidine kinase WalK / 0.747
4prv ADPDNA gyrase subunit B / 0.747
1i58 ACPChemotaxis protein CheA 2.7.13.3 0.730
4prx ADPDNA gyrase subunit B / 0.727
3kmw ATPIntegrin-linked protein kinase 2.7.11.1 0.717
1i59 ANPChemotaxis protein CheA 2.7.13.3 0.712
4xc0 ACPHeat shock cognate 90 kDa protein / 0.710
1th8 ADPAnti-sigma F factor / 0.707
3crl ANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial 2.7.11.2 0.703
4biw ANPSensor histidine kinase CpxA / 0.703
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.692
1s16 ANPDNA topoisomerase 4 subunit B / 0.688
2idx ATPCob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial 2.5.1.17 0.688
2c2a ADPSensor histidine kinase / 0.687
1i5b ANPChemotaxis protein CheA 2.7.13.3 0.686
3t1k ANPHeat shock protein HSP 90-alpha / 0.685
3t0z ATPHeat shock protein HSP 90-alpha / 0.684
3t10 ACPHeat shock protein HSP 90-alpha / 0.679
1til ATPAnti-sigma F factor / 0.675
4r39 ANPBlue-light-activated histidine kinase 2 2.7.13.3 0.674
1z5c ADPType 2 DNA topoisomerase 6 subunit B / 0.673
2pz8 APCNH(3)-dependent NAD(+) synthetase / 0.673
1z59 ADPType 2 DNA topoisomerase 6 subunit B / 0.672
2xk2 ADPHeat shock protein HSP 90-alpha / 0.672
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.671
3rep ATPIntegrin-linked protein kinase 2.7.11.1 0.671
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.669
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.669
2zdy ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.666
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.666
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.666
3umo ATPATP-dependent 6-phosphofructokinase isozyme 2 2.7.1.11 0.665
3v2u ATPProtein GAL3 / 0.665
3vth APCCarbamoyltransferase / 0.665
4a62 ANPPlasmid segregation protein ParM / 0.665
4biz ADPSensor histidine kinase CpxA / 0.664
3orl AGSSerine/threonine protein kinase / 0.663
3ump ATPATP-dependent 6-phosphofructokinase isozyme 2 2.7.1.11 0.663
4gqt ADPHeat shock protein 90 / 0.663
5i4n ATPTyrosine-protein kinase JAK2 / 0.662
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.660
1i5a ACPChemotaxis protein CheA 2.7.13.3 0.659
3n0z 3ATAdenylate cyclase 2 / 0.659
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.659
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.658
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.658
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.658
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.658
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.657
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.657
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.657
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.656
4col DTPUncharacterized protein / 0.655
1ozh HE3Acetolactate synthase, catabolic 2.2.1.6 0.652
4gt8 ADPSensor protein VraS 2.7.13.3 0.652
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.651
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.651
3law GNPRas-related protein Rab-7a / 0.651
1i58 ADPChemotaxis protein CheA 2.7.13.3 0.650
1qsy DDSDNA polymerase I, thermostable 2.7.7.7 0.650
3ahe THDProbable phosphoketolase / 0.650
4fvq ATPTyrosine-protein kinase JAK2 / 0.650
4qbg AP5Adenylate kinase / 0.650
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.650