SMTL ID : 5zhl.1

Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x 9D0: N-({4-[(octylamino)methyl]phenyl}methyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide(Non-covalent)

9D0.1: 16 residues within 4Å: Chain A: P.57, P.83, T.84, P.85, E.112, V.131, S.132, I.133, G.134, Y.136, V.137, L.138, G.140, G.141, A.144 Chain B: E.180 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.57, A:P.85, A:V.137, A:L.138 Hydrogen bonds: A:E.112, A:I.133, A:Y.136, A:L.138 Water bridges: A:Y.136 9D0.2: 16 residues within 4Å: Chain A: E.180 Chain B: P.57, P.83, T.84, P.85, E.112, V.131, S.132, I.133, G.134, Y.136, V.137, L.138, G.140, G.141, A.144 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.57, B:P.85, B:V.137, B:L.138 Hydrogen bonds: B:E.112, B:I.133, B:Y.136, B:L.138 Water bridges: B:E.112, B:Y.136, A:E.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, W. et al., Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism. J.Med.Chem. (2019)

Release Date

2019-03-06

Peptides

tRNA (guanine-N(1)-)-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

tRNA (guanine-N(1)-)-methyltransferase

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