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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
3m6p 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
3m6p BB2Peptide deformylase 1B, chloroplastic/mitochondrial 3.5.1.88 1.153
3pn4 BB2Peptide deformylase 1B, chloroplastic/mitochondrial 3.5.1.88 1.003
3uwb BB2RIIA-RIIB membrane-associated protein / 0.973
3u04 BB2Peptide deformylase / 0.906
3m6r BB2Peptide deformylase 1B, chloroplastic/mitochondrial 3.5.1.88 0.885
4e9b BB2Peptide deformylase / 0.865
1lru BB2Peptide deformylase 3.5.1.88 0.861
2okl BB2Peptide deformylase 2 / 0.861
1ws1 BB2Peptide deformylase 1 / 0.845
1g2a BB2Peptide deformylase 3.5.1.88 0.819
3m6q BB2Peptide deformylase 1B, chloroplastic/mitochondrial 3.5.1.88 0.819
4je7 BB2Peptide deformylase 1A, chloroplastic/mitochondrial 3.5.1.88 0.803
1lqy BB2Peptide deformylase 2 3.5.1.88 0.774
2os3 BB2Peptide deformylase / 0.766
3g5k BB2Peptide deformylase, mitochondrial 3.5.1.88 0.756
1ix1 BB2Peptide deformylase / 0.715
2os1 BB2Peptide deformylase / 0.714
4q4e BB2Aminopeptidase N 3.4.11.2 0.714
4pkw GM6Lethal factor 3.4.24.83 0.710
4dd8 BATDisintegrin and metalloproteinase domain-containing protein 8 3.4.24 0.694
1lry BB2Peptide deformylase / 0.693
3l0t INNDisintegrin and metalloproteinase domain-containing protein 17 3.4.24.86 0.691
2w13 WR2Snake venom metalloproteinase BaP1 3.4.24 0.690
2w14 WR2Snake venom metalloproteinase BaP1 3.4.24 0.689
2aia SB8Peptide deformylase / 0.673
3e3u NVCPeptide deformylase 3.5.1.88 0.672
3hy7 097A disintegrin and metalloproteinase with thrombospondin motifs 5 3.4.24 0.668
4eox 0S5Peptide deformylase / 0.654
1rm8 BATMatrix metalloproteinase-16 3.4.24 0.653