SMTL ID : 8w9i.1

Crystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x W2H: (2~{S})-~{N}-[3-(4-azanylquinazolin-7-yl)phenyl]sulfonylpyrrolidine-2-carboxamide(Non-covalent)

W2H.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, I.210, H.419, F.421, C.449, Y.450, G.451, G.453, R.456 Ligands: EDO.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.167 Hydrogen bonds: A:T.117, A:R.148, A:R.148, A:G.160, A:G.160, A:H.419 pi-Stacking: A:F.163, A:F.163 pi-Cation interactions: A:R.456 W2H.6: 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 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:D.167 Hydrogen bonds: B:T.117, B:R.148, B:R.148, B:E.150, B:G.160, B:G.160, B:H.419 pi-Stacking: B:F.163, B:F.163

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: A.316, Q.318, V.321, S.323 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.316, A:Q.318, A:V.321 MG.7: 6 residues within 4Å: Chain B: A.316, N.317, Q.318, P.319, V.321, S.323 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.316, B:Q.318, B:V.321 MG.8: 6 residues within 4Å: Chain B: K.269, G.340, P.341, G.342, S.343, E.372 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:P.341, B:S.343, B:E.372

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

EDO.3: 6 residues within 4Å: Chain A: M.9, Y.502, T.506, F.510, E.511, V.512 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.512, A:V.512 EDO.4: 3 residues within 4Å: Chain A: E.330, A.331, R.334 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: E.150, M.158, R.159, R.456 Ligands: W2H.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.150 EDO.9: 5 residues within 4Å: Chain A: R.110 Chain B: R.42, A.44, S.45 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.45 EDO.10: 3 residues within 4Å: Chain A: R.110 Chain B: R.42 Ligands: EDO.9 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.42, B:R.42, A:R.110, A:R.110 EDO.11: 7 residues within 4Å: Chain B: F.155, M.158, S.224, G.225, E.226, I.415, R.456 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.226, B:R.456

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

2024-09-11

Peptides

Proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proline--tRNA ligase

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