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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
4bub ADP UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4bub ADPUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase / 0.970
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.702
3kuc GDPRas-related protein Rap-1A / 0.700
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.696
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.691
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.688
3kko GNPRas-related protein M-Ras / 0.686
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.676
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.672
3pit GNPRas-related protein M-Ras / 0.671
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.668
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.668
1l8q ADPChromosomal replication initiator protein DnaA / 0.667
1tu3 GNPRas-related protein Rab-5A / 0.667
3kji ADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC / 0.666
3lbh GNPGTPase HRas / 0.666
4ike ADPAdenylate kinase / 0.666
4jl5 ADPAdenylate kinase / 0.666
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.664
4cf7 ADPAdenylate kinase / 0.661
5bn3 ADPV-type ATP synthase alpha chain / 0.661
5bn3 ADPNEQ263 / 0.661
2vor ACPFolylpolyglutamate synthase / 0.660
1ank ANPAdenylate kinase / 0.657
4ap0 ADPKinesin-like protein KIF11 / 0.656
4dxa GSPRas-related protein Rap-1b / 0.656
4qos ADPPsp operon transcriptional activator / 0.656
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.655
3kud GDPGTPase HRas / 0.655
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.654
3tqc ADPPantothenate kinase / 0.654
3lbn GNPGTPase HRas / 0.653
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.651
3tlx ADPAdenylate kinase 2 / 0.651
1jx2 ADPMyosin-2 heavy chain / 0.650
5d3q GDPDynamin-1 3.6.5.5 0.650