SMTL ID : 7y1h.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

2 x F99: 1-(5-chloranyl-4-methyl-benzimidazol-1-yl)-3-[(2R,3S)-3-oxidanylpiperidin-2-yl]propan-2-one(Non-covalent)

F99.1: 17 residues within 4Å: Chain A: H.93, F.97, E.100, V.101, P.120, T.121, E.123, R.152, W.169, E.171, H.173, F.216, H.242, S.272, W.273, G.274 Ligands: ATP.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:H.93, A:F.97, A:E.100, A:P.120, A:T.121, A:W.169, A:E.171, A:F.216 Hydrogen bonds: A:T.121, A:T.121, A:R.152, A:S.272 Water bridges: A:R.152 pi-Stacking: A:F.97, A:F.97 F99.6: 17 residues within 4Å: Chain B: T.92, H.93, F.97, V.101, P.120, T.121, E.123, R.152, W.169, E.171, H.173, F.216, H.242, S.272, W.273, G.274 Ligands: ATP.7 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:H.93, B:F.97, B:F.97, B:P.120, B:T.121, B:W.169, B:E.171, B:F.216 Hydrogen bonds: B:T.121, B:T.121, B:R.152, B:S.272 Water bridges: B:R.152, B:H.242 pi-Stacking: B:F.97, B:F.97

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

ATP.2: 18 residues within 4Å: Chain A: R.152, E.154, F.161, L.162, R.163, T.164, F.167, W.169, Q.237, G.238, G.239, T.240, G.274, T.276, R.278 Ligands: F99.1, MG.4, MG.5 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.152, A:E.154, A:T.164, A:Q.237, A:Q.237, A:T.240, A:T.240, A:T.276, A:R.278 Water bridges: A:R.163, A:R.163, A:R.163, A:Y.197 Salt bridges: A:R.152, A:R.152, A:R.163, A:R.278 pi-Stacking: A:F.167, A:F.167 pi-Cation interactions: A:R.278 ATP.7: 18 residues within 4Å: Chain B: R.152, E.154, F.161, L.162, R.163, T.164, F.167, W.169, Q.237, G.238, G.239, T.240, G.274, T.276, R.278 Ligands: F99.6, MG.9, MG.10 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.152, B:E.154, B:E.154, B:R.163, B:T.164, B:Q.237, B:Q.237, B:T.240, B:T.240, B:T.276, B:R.278, B:R.278 Water bridges: B:H.242 Salt bridges: B:R.152, B:R.152, B:R.163, B:R.278 pi-Stacking: B:F.167 pi-Cation interactions: B:R.278

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.448, C.453, C.495, C.497 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.448, A:C.453, A:C.495, A:C.497, H2O.2 ZN.8: 4 residues within 4Å: Chain B: C.448, C.453, C.495, V.496 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.448, B:C.453, B:C.495

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

MG.4: 2 residues within 4Å: Chain A: R.163 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: Q.237 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: E.214, Q.237 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

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