SMTL ID : 8qic.1

Structure-based identification of salicylic acid derivatives as malarial threonyl tRNA-synthetase inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x VL0: 2-oxidanyl-5-[[4-(phenylmethyl)phenyl]sulfamoyl]benzoic acid(Non-covalent)

VL0.1: 22 residues within 4Å: Chain A: M.90, C.92, R.121, E.123, M.132, V.134, F.137, Q.139, D.141, H.143, Y.220, K.223, Q.237, C.238, T.240, Q.242, H.269, R.270, A.271, S.275, R.278 Ligands: ZN.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.134, A:F.137, A:T.240 Hydrogen bonds: A:R.121, A:R.121, A:Q.139, A:K.223, A:Q.237, A:T.240, A:Q.242 Water bridges: A:N.91 Salt bridges: A:H.143, A:H.269 pi-Stacking: A:F.137 pi-Cation interactions: A:R.278 VL0.4: 21 residues within 4Å: Chain B: M.90, C.92, R.121, E.123, M.132, R.133, V.134, F.137, Q.139, D.141, H.143, Y.220, K.223, Q.237, T.240, Q.242, H.269, G.274, S.275, R.278 Ligands: ZN.8 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:V.134, B:F.137, B:Q.139, B:Q.237, B:T.240 Hydrogen bonds: B:R.121, B:R.121, B:Q.139, B:K.223, B:Q.237, B:T.240, B:T.240, B:Q.242 Water bridges: B:N.91, B:N.91 Salt bridges: B:H.143, B:H.269 pi-Stacking: B:F.137 pi-Cation interactions: B:R.278

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: V.39, L.43, A.114, E.115, F.116, D.140, D.141, A.142, R.270, I.272 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.115, A:D.140, A:D.141, A:D.141, A:R.270, A:R.270, A:I.272 GOL.5: 3 residues within 4Å: Chain B: E.286, F.287, R.370 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.370 GOL.6: 5 residues within 4Å: Chain B: Y.71, G.217, A.218, F.219, K.223 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.219, B:K.223, B:K.223 GOL.7: 10 residues within 4Å: Chain B: V.39, L.43, A.114, E.115, F.116, D.140, D.141, A.142, R.270, I.272 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.115, B:D.140, B:D.140, B:R.270, B:R.270

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.92, H.143, H.269 Ligands: VL0.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.92, A:H.143, A:H.269 ZN.8: 4 residues within 4Å: Chain B: C.92, H.143, H.269 Ligands: VL0.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.92, B:H.143, B:H.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bobrovs, R. et al., Structure-based identification of salicylic acid derivatives as malarial threonyl tRNA-synthetase inhibitors. Plos One (2024)

Release Date

2024-04-10

Peptides

Threonine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Threonine--tRNA ligase