SMTL ID : 9drv.1

Crystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-004

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

hetero-2-2-mer

Ligands

2 x 2AQ: QUINOLIN-2-AMINE(Non-covalent)

2AQ.1: 13 residues within 4Å: Chain A: H.184, T.185, S.186, Q.224, E.226, F.264, F.266, T.267, G.291, C.292, A.314, F.315, G.316 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.267, A:A.314 Hydrogen bonds: A:T.185, A:T.185, A:E.226 pi-Stacking: A:F.264, A:F.264, A:F.266 2AQ.18: 13 residues within 4Å: Chain D: T.185, S.186, Q.189, Q.224, E.226, F.264, F.266, T.267, G.291, C.292, A.314, F.315, G.316 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:T.267, D:A.314 Hydrogen bonds: D:T.185, D:E.226 pi-Stacking: D:F.264, D:F.264, D:F.266

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

MG.2: 3 residues within 4Å: Chain A: E.268 Chain B: D.176, E.480 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:E.268, B:E.480, H2O.2, H2O.4, H2O.7, H2O.7 MG.17: 2 residues within 4Å: Chain C: U.8, A.9 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain D: E.268 Chain E: D.176, D.471, E.480, E.481 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: D:E.268, E:E.480, H2O.18, H2O.20, H2O.21

10 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 9 residues within 4Å: Chain A: T.111, V.113, P.114, A.115, G.116, V.348 Chain B: A.519, L.520 Chain E: R.668 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A, 1 interactions with chain B Water bridges: E:R.668 Salt bridges: E:R.668 Hydrogen bonds: A:G.116, A:G.116 Hydrophobic interactions: B:L.520 ACT.5: 5 residues within 4Å: Chain B: A.381, D.416, D.417, W.418, S.419 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.417, B:W.418 ACT.6: 3 residues within 4Å: Chain B: R.82, Q.83, Y.84 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.84 Hydrogen bonds: B:Y.84 Salt bridges: B:R.82 ACT.14: 6 residues within 4Å: Chain B: G.541, L.682, H.706, R.712 Chain D: D.95 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.682 Salt bridges: B:H.706, B:R.712 ACT.15: 6 residues within 4Å: Chain B: R.36, A.193, R.484, L.485, G.487, E.489 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.193 Salt bridges: B:R.36 ACT.19: 7 residues within 4Å: Chain B: R.668 Chain D: P.114, A.115, G.116, V.348 Chain E: A.519, L.520 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: E:L.520, D:V.348 Hydrogen bonds: D:G.116, D:G.116 Salt bridges: B:R.668 ACT.20: 5 residues within 4Å: Chain D: G.233, L.234, S.311 Chain E: R.432, I.433 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.311 ACT.23: 4 residues within 4Å: Chain E: A.381, D.417, W.418, S.467 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.417, E:W.418, E:S.467 Water bridges: E:S.467 ACT.24: 5 residues within 4Å: Chain E: Q.440, G.441, T.442, R.445 Ligands: EDO.25 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.445 ACT.26: 10 residues within 4Å: Chain E: H.279, A.326, I.327, G.328, G.329, V.330, M.331, G.332, E.348, W.352 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:H.279, E:A.326 Hydrogen bonds: E:G.329, E:V.330

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: G.233, L.234 Chain B: R.432, I.433 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.233, A:S.311 PEG.7: 6 residues within 4Å: Chain B: E.655, A.656, A.657 Chain D: I.104, L.108, P.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.656, B:A.657 PEG.21: 5 residues within 4Å: Chain B: F.781, D.782, V.783 Chain E: G.646, P.647 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Water bridges: E:G.646, E:G.649 Hydrogen bonds: B:V.783

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 11 residues within 4Å: Chain B: H.279, I.318, A.326, I.327, G.328, G.329, V.330, G.332, E.348, W.352, A.370 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.279, B:I.327, B:G.329 GOL.9: 5 residues within 4Å: Chain B: D.431, G.435, V.436, A.437 Ligands: PEG.4 No protein-ligand interaction detected (PLIP) GOL.16: 7 residues within 4Å: Chain B: A.500, G.501, R.502 Chain D: M.135, A.245, R.248 Chain E: L.495 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.248 GOL.27: 2 residues within 4Å: Chain E: D.431, R.432 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.431

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.10: 5 residues within 4Å: Chain B: L.520, S.521 Chain D: V.113 Chain E: L.520, S.521 No protein-ligand interaction detected (PLIP)

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 8 residues within 4Å: Chain B: P.49, V.50, D.51, G.52, D.157, A.159, L.164, D.165 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.50, B:G.52 Salt bridges: B:D.51, B:D.157 EPE.12: 5 residues within 4Å: Chain B: E.14, W.247, R.251, R.389, L.393 8 PLIP interactions: 8 interactions with chain B Water bridges: B:W.247, B:R.250, B:R.251, B:Y.269, B:R.389 Salt bridges: B:E.14, B:E.14, B:R.389

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 2 residues within 4Å: Chain B: R.712 Ligands: ACT.14 No protein-ligand interaction detected (PLIP) EDO.25: 2 residues within 4Å: Chain E: Q.440 Ligands: ACT.24 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gade, P. et al., Different chemical scaffolds bind to L-phe site in Mycobacterium tuberculosis Phe-tRNA synthetase. Eur.J.Med.Chem. (2025)

Release Date

2025-02-12

Peptides

Phenylalanine--tRNA ligase alpha subunit: AD
Phenylalanine--tRNA ligase beta subunit: BE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

Phenylalanine--tRNA ligase alpha subunit

Phenylalanine--tRNA ligase beta subunit

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