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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
3nfa CBJ Gag-Pol polyprotein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3nfa CBJGag-Pol polyprotein / 0.893
4cjw CBJIntegrase / 0.821
4chz H75Integrase / 0.758
1drt PCVClavaminate synthase 1 1.14.11.21 0.744
1efz PRFQueuine tRNA-ribosyltransferase 2.4.2.29 0.744
1n35 CH1RNA-directed RNA polymerase lambda-3 2.7.7.48 0.744
1n38 U3HRNA-directed RNA polymerase lambda-3 2.7.7.48 0.744
1p0e PRFQueuine tRNA-ribosyltransferase 2.4.2.29 0.744
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.744
1y56 ATPUncharacterized protein / 0.744
2hs4 ACPPhosphoribosylformylglycinamidine synthase subunit PurL / 0.744
2xi3 GTPGenome polyprotein 2.7.7.48 0.744
3dm5 GDPSignal recognition particle 54 kDa protein / 0.744
3kjg ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.744
3rzp PRFNADPH-dependent 7-cyano-7-deazaguanine reductase / 0.744
3ty3 GGGHomoisocitrate dehydrogenase 1.1.1.87 0.744
3uxv GUNNADPH-dependent 7-cyano-7-deazaguanine reductase / 0.744
4a8m ATPRNA-directed RNA polymerase 2.7.7.48 0.744
4nau AGSPhosphopantetheine adenylyltransferase / 0.744
4y8v ADPAcyl-CoA synthetase (NDP forming) / 0.744
4yqf GDPSeptin-9 / 0.744
5cyp GSPSeptin-9 / 0.744
1wdt GTPElongation factor G (EF-G-2) / 0.660
1wet GUNHTH-type transcriptional repressor PurR / 0.660
1yra GDPGPN-loop GTPase PAB0955 / 0.660
2jey HLOAcetylcholinesterase 3.1.1.7 0.660
2puc GUNHTH-type transcriptional repressor PurR / 0.660
2puf GUNHTH-type transcriptional repressor PurR / 0.660
2xka GSPCell division protein FtsZ / 0.660
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.660
3ieu GDPGTPase Era / 0.660
4g01 GDPRas-related protein RABF2b / 0.660
4hi0 GDPUrease accessory protein UreG / 0.660
4hrq AZGCytidine and deoxycytidylate deaminase zinc-binding region / 0.660
4ldj GDPGTPase KRas / 0.660
4uxj TTPThymidine kinase / 0.660
5bnt NAPAspartate-semialdehyde dehydrogenase 1.2.1.11 0.660
5cyo GDPSeptin-9 / 0.660