SMTL ID : 7y3s.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x F9C: 1-(6-bromanyl-7-methyl-imidazo[4,5-b]pyridin-3-yl)-3-[(2R,3S)-3-oxidanylpiperidin-2-yl]propan-2-one(Non-covalent)

F9C.1: 17 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, H.228, S.258, W.259, G.260 Ligands: ATP.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.83, A:F.83, A:P.106, A:W.155, A:E.157, A:F.202 Hydrogen bonds: A:T.107, A:E.109, A:R.138, A:S.258 pi-Stacking: A:F.83, A:F.83 F9C.5: 17 residues within 4Å: Chain B: H.79, 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 Ligands: ATP.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.83, B:P.106, B:E.157, B:F.202 Hydrogen bonds: B:T.107, B:E.109, B:R.138, B:S.258 Water bridges: B:R.138 pi-Stacking: B:F.83, B:F.83

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

ATP.2: 18 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, H.228, G.260, T.262, R.264 Ligands: F9C.1, MG.3, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.138, A:E.140, A:T.150, A:Q.223, A:T.226, A:T.226, A:H.228, 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, A:F.153 pi-Cation interactions: A:R.264 ATP.6: 16 residues within 4Å: Chain B: 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: F9C.5, MG.8, MG.9 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.138, B:E.140, B:E.140, B:R.149, B:T.150, B:Q.223, B:Q.223, B:T.226, B:T.226, B:T.262, B:R.264, B:R.264 Salt bridges: B:R.138, B:K.142, B:R.149, B:R.264 pi-Cation interactions: B:R.264

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

MG.3: 3 residues within 4Å: Chain A: R.138, E.140 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: Q.223 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain B: K.196, E.200, Q.223 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.200

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain B: C.434, C.439, C.481, C.483 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.434, B:C.439, B:C.481, B:C.483

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

Related Entries With Identical Sequence