SMTL ID : 8w8l.1

Crystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-38

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x W20: (2~{S})-~{N}-[5-(4-azanyl-8-fluoranyl-quinazolin-7-yl)-2-fluoranyl-phenyl]sulfonylpyrrolidine-2-carboxamide(Non-covalent)

W20.1: 20 residues within 4Å: Chain A: T.117, E.119, R.148, E.150, L.157, M.158, R.159, G.160, F.163, M.165, D.167, Y.169, I.210, H.419, F.421, C.449, Y.450, G.451, G.453, R.456 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.167, A:F.421 Hydrogen bonds: A:E.119, A:R.148, A:R.148, A:G.160, A:G.160, A:H.419, A:R.456 Water bridges: A:Y.97 pi-Stacking: A:F.163, A:F.163 pi-Cation interactions: A:R.456, A:R.456 Halogen bonds: A:H.419 W20.16: 19 residues within 4Å: Chain B: T.117, E.119, R.148, E.150, L.157, M.158, R.159, G.160, F.163, M.165, D.167, Y.169, H.419, F.421, C.449, Y.450, G.451, G.453, R.456 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:D.167 Hydrogen bonds: B:E.119, B:R.148, B:R.148, B:E.150, B:G.160, B:G.160, B:H.419, B:R.456 pi-Stacking: B:F.163, B:F.163 pi-Cation interactions: B:R.456, B:R.456 Halogen bonds: B:H.419

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

SO4.2: 4 residues within 4Å: Chain A: R.42, A.44, S.45 Chain B: R.110 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.45 Salt bridges: A:R.42, B:R.110 Water bridges: B:R.110, B:R.110 SO4.3: 3 residues within 4Å: Chain A: R.152, R.154, F.155 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.152, A:R.154 SO4.17: 3 residues within 4Å: Chain B: R.152, R.154, F.155 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.154, B:R.154 Salt bridges: B:R.152, B:R.154

9 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: V.291, H.292, V.321, A.322, L.325, V.326 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.292, A:A.322 MG.5: 7 residues within 4Å: Chain A: S.30, H.31, F.155, G.156, L.157, M.158, A.459 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.30, A:F.155 MG.6: 7 residues within 4Å: Chain A: V.304, R.305, H.308, D.356, S.358, V.359, R.394 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.308, A:D.356 MG.7: 7 residues within 4Å: Chain A: Q.83, W.88, T.117, H.118, E.119, E.120, V.121 No protein-ligand interaction detected (PLIP) MG.8: 6 residues within 4Å: Chain A: G.424, T.425, K.426, Y.427, S.428, M.447 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.424 MG.9: 4 residues within 4Å: Chain A: A.316, N.317, Q.318, V.321 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.316, A:Q.318, A:V.321, H2O.4 MG.10: 4 residues within 4Å: Chain A: E.150, I.151, R.152, R.154 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.150 MG.18: 7 residues within 4Å: Chain B: S.30, H.31, F.155, G.156, L.157, M.158, A.459 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.30, B:F.155 MG.19: 5 residues within 4Å: Chain B: A.316, N.317, Q.318, V.321, S.323 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.316, B:Q.318, B:V.321

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 3 residues within 4Å: Chain A: R.59, E.62, T.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.59, A:E.62 Water bridges: A:T.145 EDO.12: 5 residues within 4Å: Chain A: M.158, E.226, E.416, R.456 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.226, A:D.227, A:E.416 Water bridges: A:E.226 EDO.13: 6 residues within 4Å: Chain A: V.28, F.155, S.224, E.226, I.415 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.463 EDO.14: 7 residues within 4Å: Chain A: Y.48, W.50, L.157, E.162, F.163, I.164, S.455 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.48 Water bridges: A:Y.48, A:T.145 EDO.15: 3 residues within 4Å: Chain A: T.270, I.271, A.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.271, A:A.272 EDO.20: 3 residues within 4Å: Chain B: T.270, I.271, K.287 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.271 EDO.21: 5 residues within 4Å: Chain B: V.28, F.155, M.158, S.224, I.415 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.226 EDO.22: 4 residues within 4Å: Chain B: L.349, I.351, A.352, C.353 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.349, B:C.353, B:C.353 EDO.23: 4 residues within 4Å: Chain B: M.260, N.348, Y.376 Ligands: EDO.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.348, B:Y.376, B:Y.376 EDO.24: 5 residues within 4Å: Chain B: T.270, I.271, I.286, G.342, H.375 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.286, B:G.342, B:G.368 Water bridges: B:T.288, B:G.342 EDO.25: 7 residues within 4Å: Chain B: M.530, E.531, I.535, R.538, K.554, G.555, R.556 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.530, B:R.538, B:G.555 EDO.26: 4 residues within 4Å: Chain B: M.260, L.262, Y.376 Ligands: EDO.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.260 Water bridges: B:L.262, B:L.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, Z. et al., Structure-Guided Fluorine Scanning Accelerates the Discovery of Potent and Selective Inhibitors Against Bacterial Prolyl-tRNA Synthetase. To Be Published

Release Date

2024-09-04

Peptides

Proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proline--tRNA ligase

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