SMTL ID : 8w8j.1

Crystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-19

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

2 x W1Q: (2~{S})-~{N}-[3-(4-azanyl-5-fluoranyl-quinazolin-7-yl)phenyl]sulfonylpyrrolidine-2-carboxamide(Non-covalent)

W1Q.1: 21 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, E.416, H.419, F.421, C.449, Y.450, G.451, I.452, G.453, R.456 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.167 Hydrogen bonds: A:T.117, A:E.119, A:R.148, A:R.148, A:E.150, A:G.160, A:G.160 pi-Stacking: A:F.163, A:F.163 pi-Cation interactions: A:R.456, A:R.456 W1Q.9: 20 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, E.416, H.419, F.421, C.449, Y.450, G.451, G.453, R.456 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:D.167 Hydrogen bonds: B:T.117, B:E.119, B:R.148, B:R.148, B:G.160, B:G.160 Water bridges: B:R.93 pi-Stacking: B:F.163, B:F.163 pi-Cation interactions: B:R.456, B:R.456

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

EDO.2: 8 residues within 4Å: Chain A: M.530, E.531, I.535, H.537, R.538, K.554, G.555, R.556 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: Q.175, L.178, Q.422, G.424 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: M.158, E.226, D.227, E.416, R.456 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: T.268, K.269, T.270, I.271, G.342, H.375 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: R.357, V.390, A.391 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: A.81, V.114, Q.144, T.145, K.146, F.147, E.162 Chain B: V.82 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: V.28, F.155, M.158, S.224, E.226, I.415 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: Q.175, L.178, Q.422, G.424, I.446 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: S.12, D.516 Chain B: K.134 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain B: Y.48, W.50, L.157, E.162, F.163, I.164, S.455 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain B: S.91, K.426, Y.427, A.430 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain B: R.107, H.108, E.109 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: F.155, M.158, S.224, I.415 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: M.158, E.226, D.227, R.456 Ligands: EDO.15 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: I.210, G.211, E.245, D.392 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: M.260, Y.376 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: M.260, N.348, Y.376 Ligand excluded by PLIP

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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