SMTL ID : 7y28.1

Controlling fibrosis using compound with novel binding mode to prolyl-tRNA synthetase 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

2 x F96: 1-[6-(3-fluorophenyl)benzimidazol-1-yl]-3-[(2R,3S)-3-oxidanylpiperidin-2-yl]propan-2-one(Non-covalent)

F96.1: 20 residues within 4Å: Chain A: L.72, H.78, F.82, A.83, E.85, V.86, P.105, T.106, E.108, R.137, W.154, E.156, H.158, F.201, T.225, H.227, S.257, W.258, G.259 Ligands: ATP.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.72, A:F.82, A:V.86, A:P.105, A:P.105, A:W.154, A:E.156, A:F.201 Hydrogen bonds: A:T.106, A:E.108, A:R.137, A:S.257 pi-Stacking: A:H.78, A:F.82, A:F.82 F96.6: 21 residues within 4Å: Chain B: T.77, H.78, F.82, E.85, V.86, P.105, T.106, E.108, T.109, R.137, W.154, E.156, H.158, F.201, T.225, H.227, S.257, W.258, G.259 Ligands: ATP.7, MG.9 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:H.78, B:F.82, B:V.86, B:P.105, B:P.105, B:W.154, B:E.156 Hydrogen bonds: B:T.106, B:E.108, B:R.137 pi-Stacking: B:F.82, B:F.82 pi-Cation interactions: B:R.137

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 18 residues within 4Å: Chain A: R.137, E.139, F.146, L.147, R.148, T.149, F.152, W.154, Q.222, G.223, G.224, T.225, G.259, T.261, R.263 Ligands: F96.1, MG.4, MG.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.137, A:E.139, A:T.149, A:Q.222, A:Q.222, A:T.225, A:T.225, A:T.261, A:R.263 Salt bridges: A:R.137, A:R.137, A:R.148, A:R.263 pi-Stacking: A:F.152, A:F.152 pi-Cation interactions: A:R.263 ATP.7: 16 residues within 4Å: Chain B: R.137, E.139, F.146, L.147, R.148, T.149, F.152, Q.222, G.223, G.224, T.225, T.261, R.263 Ligands: F96.6, MG.9, MG.10 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.137, B:E.139, B:E.139, B:T.149, B:Q.222, B:Q.222, B:T.225, B:T.225, B:T.261, B:R.263 Salt bridges: B:R.137, B:R.148, B:R.263 pi-Stacking: B:F.152 pi-Cation interactions: B:R.263, B:R.263

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: F.432, C.433, C.438, C.480, C.482 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.433, A:C.438, A:C.480, A:C.482 ZN.8: 2 residues within 4Å: Chain B: C.433, C.438 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.433, B:C.438, H2O.5

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.4: 1 residues within 4Å: Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: E.199, Q.222 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: E.139 Ligands: F96.6, ATP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: E.199 Ligands: ATP.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoon, I. et al., Control of fibrosis with enhanced safety via asymmetric inhibition of prolyl-tRNA synthetase 1. Embo Mol Med (2023)

Release Date

2023-07-05

Peptides

Bifunctional glutamate/proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional glutamate/proline--tRNA ligase