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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
3m6r BB2 Peptide deformylase 1B, chloroplastic/mitochondrial 3.5.1.88

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3m6r BB2Peptide deformylase 1B, chloroplastic/mitochondrial 3.5.1.88 1.142
3pn4 BB2Peptide deformylase 1B, chloroplastic/mitochondrial 3.5.1.88 0.965
3uwb BB2RIIA-RIIB membrane-associated protein / 0.894
3m6q BB2Peptide deformylase 1B, chloroplastic/mitochondrial 3.5.1.88 0.886
3m6p BB2Peptide deformylase 1B, chloroplastic/mitochondrial 3.5.1.88 0.885
4e9b BB2Peptide deformylase / 0.846
1lru BB2Peptide deformylase 3.5.1.88 0.829
2okl BB2Peptide deformylase 2 / 0.827
3u04 BB2Peptide deformylase / 0.820
4je7 BB2Peptide deformylase 1A, chloroplastic/mitochondrial 3.5.1.88 0.808
1g2a BB2Peptide deformylase 3.5.1.88 0.802
1lry BB2Peptide deformylase / 0.783
1ix1 BB2Peptide deformylase / 0.772
1ws1 BB2Peptide deformylase 1 / 0.741
2os1 BB2Peptide deformylase / 0.739
1lqy BB2Peptide deformylase 2 3.5.1.88 0.735
2os3 BB2Peptide deformylase / 0.691
1mnc PLHNeutrophil collagenase 3.4.24.34 0.675
2w14 WR2Snake venom metalloproteinase BaP1 3.4.24 0.663
3k6l 2BBPeptide deformylase 3.5.1.88 0.661
3g5k BB2Peptide deformylase, mitochondrial 3.5.1.88 0.659
3e3u NVCPeptide deformylase 3.5.1.88 0.657