UniProt Q8E378
Peptide deformylase (Q8E378)
Peptide deformylase (UniProt Q8E378), EC 3.5.1.88: 24 experimental structures and 1 predicted model on GenesisL1, 10 ligands bound, 5 pockets. Binding sites, druggability and experiment against prediction (TM-score) in GL1X.
- UniProt
- Q8E378
- Protein
- Peptide deformylase
- EC
- 3.5.1.88
- Experimental structures
- 24
- Predicted models
- 1
- Ligands
- 10
- Pockets
- 5 · 4 records with a druggable one
Structures
25 records of Q8E378 in the MolNFT archive: 24 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 5JEX | Crystal structure of type 2 PDF from Streptococcus agalactiae, crystallized in imidazole buffer | x-ray diffraction | A | ZN | — |
| 5JEX | Crystal structure of type 2 pdf from streptococcus agalactiae, crystallized in imidazole buffer | x-ray diffraction | A | — | — |
| 5JEY | Crystal structure of type 2 PDF from Streptococcus agalactiae, crystallized in cacodylate buffer | x-ray diffraction | A | NI | — |
| 5JEY | Crystal structure of type 2 pdf from streptococcus agalactiae, crystallized in cacodylate buffer | x-ray diffraction | A | — | — |
| 5JEZ | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Ser | x-ray diffraction | A | ZN | — |
| 5JEZ | Crystal structure of type 2 pdf from streptococcus agalactiae in complex with tripeptide met-ala-ser | x-ray diffraction | A | — | — |
| 5JF0 | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Arg | x-ray diffraction | A | NI | — |
| 5JF0 | Crystal structure of type 2 pdf from streptococcus agalactiae in complex with tripeptide met-ala-arg | x-ray diffraction | A | — | — |
| 5JF1 | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with actinonin | x-ray diffraction | A | BB2, ZN | 1 (best 0.51) |
| 5JF1 | Crystal structure of type 2 pdf from streptococcus agalactiae in complex with actinonin | x-ray diffraction | A | — | — |
| 5JF2 | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT002 | x-ray diffraction | A | SF7, ZN | 1 (best 0.53) |
| 5JF2 | Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor AT002 | x-ray diffraction | A | — | — |
| 5JF3 | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT018 | x-ray diffraction | A | SF5, ZN | — |
| 5JF3 | Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor AT018 | x-ray diffraction | A | — | — |
| 5JF4 | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT019 | x-ray diffraction | A | 6JT, ZN | 1 (best 0.52) |
| 5JF4 | Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor AT019 | x-ray diffraction | A | — | — |
| 5JF5 | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT020 | x-ray diffraction | A | 7JT, ZN | 1 (best 0.51) |
| 5JF5 | Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor AT020 | x-ray diffraction | A | — | — |
| 5JF6 | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor 6b (AB47) | x-ray diffraction | A | BB4, ZN | 1 (best 0.48) |
| 5JF6 | Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor 6B (AB47) | x-ray diffraction | A | — | — |
| 5JF7 | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor SMP289 | x-ray diffraction | A | 6JU, ZN | — |
| 5JF7 | Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor SMP289 | x-ray diffraction | A | — | — |
| 5JF8 | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor RAS358 (21) | x-ray diffraction | A | PN3, ZN | — |
| 5JF8 | Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor RAS358 (21) | x-ray diffraction | A | — | — |
| Q8E378 | AlphaFold monomer V2.0 prediction for peptide deformylase (Q8E378) | predicted | A | — | — |
Ligands
- ZN · Zinc ion · in 10 records
- NI · Nickel (II) ion · in 2 records
- 6JT · (3R)-3-{3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl}-4-cyclopentyl-N-hydroxybutanamide · in 1 record
- 6JU · 2-(3-benzyl-5-bromo-1H-indol-1-yl)-N-hydroxyacetamide · in 1 record
- 7JT · (3R)-3-{3-[(2H-1,3-benzodioxol-5-yl)methyl]-1,2,4-oxadiazol-5-yl}-4-cyclopentyl-N-hydroxybutanamide · in 1 record
- BB2 · Actinonin · in 1 record
- BB4 · 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide · in 1 record
- PN3 · tert-butyl {(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl}carbamate · in 1 record
- SF5 · methyl 4-({5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl}methyl)benzoate · in 1 record
- SF7 · (3R)-3-{3-[(4-fluorophenyl)methyl]-1,2,4-oxadiazol-5-yl}-N-hydroxyheptanamide · in 1 record
Experiment against prediction
- 5JF1 chain A against the predicted model Q8E378: TM-score 0.99, RMSD 0.41 Å
- 5JF1 chain A against the predicted model Q8E378: TM-score 0.99, RMSD 0.41 Å
- 5JF3 chain A against the predicted model Q8E378: TM-score 0.99, RMSD 0.43 Å
- 5JF3 chain A against the predicted model Q8E378: TM-score 0.99, RMSD 0.43 Å
- 5JF5 chain A against the predicted model Q8E378: TM-score 0.99, RMSD 0.43 Å
- 5JF5 chain A against the predicted model Q8E378: TM-score 0.99, RMSD 0.43 Å
- 5JF4 chain A against the predicted model Q8E378: TM-score 0.99, RMSD 0.44 Å
- 5JF4 chain A against the predicted model Q8E378: TM-score 0.99, RMSD 0.44 Å
- 5JEZ chain A against the predicted model Q8E378: TM-score 0.99, RMSD 0.45 Å
- 5JEZ chain A against the predicted model Q8E378: TM-score 0.99, RMSD 0.45 Å
Elsewhere
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