SMTL ID : 9drs.1

Crystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-116

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-2-2-mer

Ligands

2 x AX7: 1H-benzimidazol-2-amine(Non-covalent)

AX7.1: 12 residues within 4Å: Chain A: H.175, S.177, Q.215, E.217, F.255, F.257, T.258, G.282, C.283, A.305, F.306, G.307 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.258, A:A.305 Hydrogen bonds: A:Q.215 Salt bridges: A:E.217 pi-Stacking: A:F.255, A:F.255, A:F.257, A:F.257 AX7.27: 10 residues within 4Å: Chain D: Q.215, E.217, F.255, F.257, T.258, G.282, C.283, A.305, F.306, G.307 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:T.258, D:A.305 Hydrogen bonds: D:Q.215, D:Q.215 Salt bridges: D:E.217 pi-Stacking: D:F.255, D:F.255, D:F.257, D:F.257

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

MG.2: 3 residues within 4Å: Chain A: E.259 Chain B: D.176, E.480 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.480, A:E.259, H2O.5, H2O.7, H2O.9 MG.23: 3 residues within 4Å: Chain C: U.8, A.9, U.12 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain C: G.46 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain C: A.38 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain C: C.30, G.42, G.43 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain D: E.259 Chain E: D.176, D.471, E.480 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: D:E.259, E:E.480, H2O.19, H2O.21, H2O.21, H2O.23 MG.39: 1 residues within 4Å: Chain F: G.31 No protein-ligand interaction detected (PLIP)

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

ACT.3: 8 residues within 4Å: Chain A: P.105, A.106, G.107, V.339 Chain B: A.519, L.520, G.522 Chain E: R.668 Ligand excluded by PLIP ACT.4: 4 residues within 4Å: Chain A: A.236, R.239 Chain E: A.500, G.501 Ligand excluded by PLIP ACT.5: 3 residues within 4Å: Chain B: R.82, Q.83, Y.84 Ligand excluded by PLIP ACT.7: 6 residues within 4Å: Chain B: R.36, I.37, A.193, R.484, L.485, G.487 Ligand excluded by PLIP ACT.8: 4 residues within 4Å: Chain A: V.104 Chain B: L.520 Chain D: V.104 Chain E: L.520 Ligand excluded by PLIP ACT.11: 5 residues within 4Å: Chain B: I.45, L.47, N.136, L.137, G.138 Ligand excluded by PLIP ACT.12: 6 residues within 4Å: Chain B: G.160, V.161, G.163, W.246, R.250 Ligands: EPE.19 Ligand excluded by PLIP ACT.13: 5 residues within 4Å: Chain B: W.540, L.682, A.708, R.712 Chain D: D.86 Ligand excluded by PLIP ACT.14: 4 residues within 4Å: Chain B: L.196, D.197, F.198, Q.449 Ligand excluded by PLIP ACT.15: 5 residues within 4Å: Chain B: P.215, A.216, W.217, P.218 Ligands: ACT.16 Ligand excluded by PLIP ACT.16: 4 residues within 4Å: Chain B: W.217, P.218, G.288 Ligands: ACT.15 Ligand excluded by PLIP ACT.22: 3 residues within 4Å: Chain C: C.26, G.27, U.28 Ligand excluded by PLIP ACT.29: 7 residues within 4Å: Chain B: R.668 Chain D: T.102, V.104, P.105, A.106, G.107, V.339 Ligand excluded by PLIP ACT.33: 4 residues within 4Å: Chain E: Q.440, G.441, T.442, R.445 Ligand excluded by PLIP ACT.34: 3 residues within 4Å: Chain E: L.196, F.198, Q.449 Ligand excluded by PLIP ACT.35: 4 residues within 4Å: Chain E: Q.788, L.833, R.834, G.835 Ligand excluded by PLIP

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

EDO.6: 4 residues within 4Å: Chain B: D.431, G.435, V.436, A.437 No protein-ligand interaction detected (PLIP) EDO.17: 4 residues within 4Å: Chain B: V.753, Q.788, R.834, G.835 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.835, B:G.835 EDO.18: 5 residues within 4Å: Chain B: G.22, W.23, D.24, V.25, Y.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.22, B:D.24 EDO.21: 3 residues within 4Å: Chain C: A.14, G.23, A.24 No protein-ligand interaction detected (PLIP) EDO.31: 4 residues within 4Å: Chain E: D.431, G.435, V.436, A.437 No protein-ligand interaction detected (PLIP) EDO.36: 5 residues within 4Å: Chain A: T.98 Chain E: T.675, L.676, Q.761, A.762 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.676 Water bridges: E:V.674 EDO.37: 4 residues within 4Å: Chain E: R.739, Y.743, P.805, D.806 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.743 EDO.38: 3 residues within 4Å: Chain E: V.672, D.673, V.694 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.673, E:D.673

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

PEG.9: 9 residues within 4Å: Chain B: M.278, H.279, A.326, I.327, G.328, G.329, E.348, W.352, A.370 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.327, B:G.329 Water bridges: B:M.278, B:M.278, B:A.370 PEG.10: 3 residues within 4Å: Chain B: D.538, G.541, R.712 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.538 PEG.20: 6 residues within 4Å: Chain B: A.500, G.501, R.502 Chain D: A.236, R.239 Chain E: L.495 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.239 PEG.32: 5 residues within 4Å: Chain D: P.105 Chain E: D.587, L.641, P.644, R.645 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.641, E:R.645

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

EPE.19: 6 residues within 4Å: Chain B: E.14, W.247, R.251, R.389, L.393 Ligands: ACT.12 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.389 Salt bridges: B:E.14, B:R.389 pi-Cation interactions: B:W.247

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

DMS.30: 4 residues within 4Å: Chain A: D.121, I.124 Chain D: D.121 Chain E: L.504 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Salt bridges: A:D.121, D:D.121

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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