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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
4jwr 1MY E3 ubiquitin-protein ligase Mdm2 6.3.2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4jwr 1MYE3 ubiquitin-protein ligase Mdm2 6.3.2 1.007
4erf 0R3E3 ubiquitin-protein ligase Mdm2 6.3.2 0.814
4hbm 0Y7E3 ubiquitin-protein ligase Mdm2 6.3.2 0.771
1efz PRFQueuine tRNA-ribosyltransferase 2.4.2.29 0.744
1g7u PEP2-dehydro-3-deoxyphosphooctonate aldolase 2.5.1.55 0.744
1m3q ANGN-glycosylase/DNA lyase 3.2.2 0.744
1v2h GUNPurine nucleoside phosphorylase 2.4.2.1 0.744
4e5i 0N9Polymerase acidic protein / 0.744
4e5l DBHPolymerase acidic protein / 0.744
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.744
4dij BLFE3 ubiquitin-protein ligase Mdm2 6.3.2 0.705
4jrg I09E3 ubiquitin-protein ligase Mdm2 6.3.2 0.703
4jsc 1OYE3 ubiquitin-protein ligase Mdm2 6.3.2 0.700
4ere 0R2E3 ubiquitin-protein ligase Mdm2 6.3.2 0.693
4jvr 1MTE3 ubiquitin-protein ligase Mdm2 6.3.2 0.686
2lzg 13QE3 ubiquitin-protein ligase Mdm2 6.3.2 0.673
1ozq PRFQueuine tRNA-ribosyltransferase 2.4.2.29 0.660
1p0e PRFQueuine tRNA-ribosyltransferase 2.4.2.29 0.660
1ulb GUNPurine nucleoside phosphorylase 2.4.2.1 0.660
2pot GUNQueuine tRNA-ribosyltransferase 2.4.2.29 0.660
2pwu GUNQueuine tRNA-ribosyltransferase 2.4.2.29 0.660
3bld PRFQueuine tRNA-ribosyltransferase 2.4.2.29 0.660
4gcx PRFQueuine tRNA-ribosyltransferase 2.4.2.29 0.660
4h7z GUNQueuine tRNA-ribosyltransferase 2.4.2.29 0.660
4hqv QEIQueuine tRNA-ribosyltransferase 2.4.2.29 0.660
4hvx QEIQueuine tRNA-ribosyltransferase 2.4.2.29 0.660