SMTL ID : 7y1w.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.434, C.439, C.481, V.482 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.434, A:C.439, A:C.481 ZN.6: 4 residues within 4Å: Chain B: C.434, C.439, C.481, C.483 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.434, B:C.439, B:C.481

2 x F9O: (2R,3S)-2-[3-[4,5-bis(chloranyl)benzimidazol-1-yl]propyl]piperidin-3-ol(Non-covalent)

F9O.2: 18 residues within 4Å: Chain A: H.79, F.83, E.86, V.87, P.106, T.107, E.109, R.138, W.155, E.157, H.159, F.202, T.226, H.228, S.258, W.259, G.260 Ligands: ATP.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.79, A:T.107, A:W.155, A:E.157 Hydrogen bonds: A:T.107, A:T.107, A:E.157, A:T.226 pi-Stacking: A:F.83, A:F.83 Halogen bonds: A:E.86 F9O.7: 15 residues within 4Å: Chain B: F.83, E.86, V.87, P.106, T.107, E.109, R.138, E.157, H.159, F.202, T.226, H.228, S.258, W.259, G.260 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.157 Hydrogen bonds: B:T.107, B:T.107, B:S.258 pi-Stacking: B:F.83

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

ATP.3: 16 residues within 4Å: Chain A: R.138, E.140, F.147, L.148, R.149, T.150, F.153, Q.223, G.224, G.225, T.226, T.262, R.264 Ligands: F9O.2, MG.4, MG.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.138, A:E.140, A:R.149, A:T.150, A:Q.223, A:G.225, A:T.226, A:T.262, A:R.264 Salt bridges: A:R.138, A:R.138, A:R.149, A:R.264 pi-Stacking: A:F.153 pi-Cation interactions: A:R.264

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: E.140 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: K.196, E.200, Q.223 Ligands: ATP.3 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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