SMTL ID : 6jof.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x BWR: ~{N}-[[4-[(4-azanylpiperidin-1-yl)methyl]phenyl]methyl]-4-oxidanylidene-3~{H}-thieno[2,3-d]pyrimidine-5-carboxamide(Non-covalent)

BWR.1: 18 residues within 4Å: Chain A: P.83, T.84, P.85, G.109, Y.111, E.112, V.131, S.132, I.133, G.134, Y.136, V.137, L.138, G.140, G.141, A.144 Chain B: R.154, E.180 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.85, A:V.137, A:L.138 Hydrogen bonds: A:I.133, A:Y.136, A:L.138 Water bridges: A:T.84, A:T.84 Salt bridges: A:E.112, B:E.180 BWR.2: 18 residues within 4Å: Chain A: R.154, E.180 Chain B: P.83, T.84, P.85, G.109, Y.111, E.112, V.131, S.132, I.133, G.134, Y.136, V.137, L.138, G.140, G.141, A.144 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Salt bridges: A:E.180, B:E.112 Hydrophobic interactions: B:P.85, B:V.137, B:L.138 Hydrogen bonds: B:I.133, B:Y.136, B:L.138

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

2019-09-04

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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