SMTL ID : 7db8.1

Crystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA synthetase in complex with compound PF-3845

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

26 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: R.201, R.312 Ligands: H2R.4 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: R.231, R.247, R.249 Chain B: E.485 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: D.206, A.207, R.324 Ligand excluded by PLIP SO4.5: 8 residues within 4Å: Chain A: E.259 Chain B: D.172, R.173, R.465, D.467, D.473, E.476, E.477 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: N.289 Chain B: R.469, Q.470 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: E.132 Chain B: T.501, G.503, R.507 Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain B: M.1, L.167, A.168, I.169, M.177, R.368, R.372 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: R.9, A.13, S.17, G.18 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain B: T.296, A.297, V.298, A.319, T.320 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain B: R.575, R.579 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: Y.739, R.803, T.804 Ligand excluded by PLIP SO4.13: 10 residues within 4Å: Chain B: H.275, A.322, I.323, G.324, G.325, V.326, M.327, G.328, E.344, W.348 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain A: P.105 Chain B: G.518, D.583, A.585, L.637, R.638 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain C: R.201, R.312 Ligands: H2R.18 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain C: R.231, R.247, R.249 Chain D: E.485 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain C: D.206, A.207, R.324 Ligand excluded by PLIP SO4.19: 8 residues within 4Å: Chain C: E.259 Chain D: D.172, R.173, R.465, D.467, D.473, E.476, E.477 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain C: N.289 Chain D: R.469, Q.470 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain C: E.132 Chain D: T.501, G.503, R.507 Ligand excluded by PLIP SO4.22: 7 residues within 4Å: Chain D: M.1, L.167, A.168, I.169, M.177, R.368, R.372 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain D: R.9, A.13, S.17, G.18 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain D: T.296, A.297, V.298, A.319, T.320 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain D: R.575, R.579 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain D: Y.739, R.803, T.804 Ligand excluded by PLIP SO4.27: 10 residues within 4Å: Chain D: H.275, A.322, I.323, G.324, G.325, V.326, M.327, G.328, E.344, W.348 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain C: P.105 Chain D: G.518, D.583, A.585, L.637, R.638 Ligand excluded by PLIP

2 x H2R: N-pyridin-3-yl-4-[[3-[5-(trifluoromethyl)pyridin-2-yl]oxyphenyl]methyl]piperidine-1-carboxamide(Non-covalent)

H2R.4: 22 residues within 4Å: Chain A: L.146, S.177, Q.180, I.181, R.201, F.213, Q.215, E.217, G.218, L.219, F.255, F.257, G.282, C.283, V.290, A.305, F.306, G.307, M.308, G.309, R.312 Ligands: SO4.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.257, A:F.257 Hydrogen bonds: A:Q.215, A:E.217, A:F.306 Water bridges: A:G.309, A:R.312, A:R.312 pi-Stacking: A:F.213, A:F.255, A:F.257 pi-Cation interactions: A:R.312 Halogen bonds: A:S.177 H2R.18: 22 residues within 4Å: Chain C: L.146, S.177, Q.180, I.181, R.201, F.213, Q.215, E.217, G.218, L.219, F.255, F.257, G.282, C.283, V.290, A.305, F.306, G.307, M.308, G.309, R.312 Ligands: SO4.15 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.257, C:F.257 Hydrogen bonds: C:Q.215, C:F.306 Water bridges: C:G.309, C:R.312, C:R.312 pi-Stacking: C:F.213, C:F.255, C:F.257 pi-Cation interactions: C:R.312 Halogen bonds: C:S.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis . J.Biol.Chem. (2021)

Release Date

2021-01-13

Peptides

Phenylalanine--tRNA ligase alpha subunit: AC
Phenylalanine--tRNA ligase beta subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Phenylalanine--tRNA ligase alpha subunit

Phenylalanine--tRNA ligase beta subunit

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