SMTL ID : 8ytk.1

Crystal structure of human prolyl-tRNA synthetase in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 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: 22 residues within 4Å: Chain A: T.133, E.135, R.164, E.166, F.173, L.174, R.175, T.176, F.179, W.181, E.183, H.185, F.228, Q.249, T.252, H.254, S.284, W.285, G.286, T.288, R.290 Ligands: EDO.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.183 Hydrogen bonds: A:T.133, A:T.133, A:R.164, A:R.164, A:E.166, A:R.175, A:T.176, A:T.252, A:H.254, A:S.284 pi-Stacking: A:F.179, A:F.179 pi-Cation interactions: A:R.290, A:R.290 W2H.4: 21 residues within 4Å: Chain B: F.109, T.133, E.135, R.164, F.173, L.174, R.175, T.176, F.179, W.181, E.183, H.185, F.228, Q.249, T.252, H.254, S.284, W.285, G.286, T.288, R.290 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.181, B:E.183 Hydrogen bonds: B:T.133, B:R.164, B:R.164, B:T.176, B:T.176, B:Q.249, B:H.254, B:S.284, B:R.290 pi-Stacking: B:F.179, B:F.179, B:W.181 pi-Cation interactions: B:R.290, B:R.290

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

EDO.2: 8 residues within 4Å: Chain A: Y.66, W.69, K.73, W.159, C.160, L.180, W.181 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.66, A:C.160, A:W.181, A:W.181 EDO.3: 5 residues within 4Å: Chain A: D.108, F.109, F.228, A.229 Ligands: W2H.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.229 EDO.5: 9 residues within 4Å: Chain A: Y.89, W.159, C.160 Chain B: Y.89, W.159, C.160, N.161, L.180 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, Z. et al., Development of potent inhibitors targeting bacterial prolyl-tRNA synthetase through fluorine scanning-directed activity tuning. Eur.J.Med.Chem. (2025)

Release Date

2025-04-02

Peptides

Bifunctional glutamate/proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional glutamate/proline--tRNA ligase