SMTL ID : 6qrc.1

Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x JFE: 3-[1-[(3-methoxyphenyl)methyl]indol-6-yl]-1~{H}-pyrazol-5-amine(Non-covalent)

JFE.1: 18 residues within 4Å: Chain A: P.85, T.86, P.87, G.111, R.112, Y.113, E.114, G.115, S.134, I.135, G.136, Y.138, V.139, L.140, N.141, G.142, G.143 Chain B: E.182 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.85, A:P.87, A:V.139 Hydrogen bonds: A:I.135, A:G.136, A:G.136, A:Y.138, A:L.140 JFE.3: 18 residues within 4Å: Chain A: E.182 Chain B: P.85, T.86, P.87, G.111, R.112, Y.113, E.114, G.115, S.134, I.135, G.136, Y.138, V.139, L.140, N.141, G.142, G.143 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.85, B:P.87, B:V.139 Hydrogen bonds: B:I.135, B:G.136, B:G.136, B:Y.138, B:L.140

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain B: R.129, R.131 3 PLIP interactions: 3 interactions with chain B Water bridges: B:V.130, B:R.131 Salt bridges: B:R.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whitehouse, A.J. et al., Development of Inhibitors against Mycobacterium abscessus tRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches. J.Med.Chem. (2019)

Release Date

2019-09-18

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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