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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
1you PFD Collagenase 3 3.4.24

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1you PFDCollagenase 3 3.4.24 0.984
3kry 3KRCollagenase 3 3.4.24 0.770
4a7b 3W5Collagenase 3 3.4.24 0.752
2yig 5ELCollagenase 3 3.4.24 0.721
4dpe NGHStromelysin-1 3.4.24.17 0.711
2ow1 7MRMatrix metalloproteinase-9 3.4.24.35 0.707
2ovx 4MRMatrix metalloproteinase-9 3.4.24.35 0.700
4g9l NGHStromelysin-1 3.4.24.17 0.683
1zs0 EINNeutrophil collagenase 3.4.24.34 0.679
2x23 TCUEnoyl-[acyl-carrier-protein] reductase [NADH] 1.3.1.9 0.679
1g4k HQQStromelysin-1 3.4.24.17 0.672
3oho Z79Stromelysin-1 3.4.24.17 0.667
1d8f SPIStromelysin-1 3.4.24.17 0.665
1efz PRFQueuine tRNA-ribosyltransferase 2.4.2.29 0.660
1g7u PEP2-dehydro-3-deoxyphosphooctonate aldolase 2.5.1.55 0.660
1m3q ANGN-glycosylase/DNA lyase 3.2.2 0.660
1v2h GUNPurine nucleoside phosphorylase 2.4.2.1 0.660
2puc GUNHTH-type transcriptional repressor PurR / 0.660
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.660
1d7x SPCStromelysin-1 3.4.24.17 0.658
1d5j MM3Stromelysin-1 3.4.24.17 0.656
1hy7 MBSStromelysin-1 3.4.24.17 0.656
3cy3 JN5Serine/threonine-protein kinase pim-1 2.7.11.1 0.654
3vs2 VSBTyrosine-protein kinase HCK 2.7.10.2 0.653
1d8m BBHStromelysin-1 3.4.24.17 0.650
4rw6 494Gag-Pol polyprotein 2.7.7.49 0.650