SMTL ID : 6qr3.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

2 x JE8: 5-azanyl-3-[1-[[(3~{S})-1-methylpiperidin-3-yl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile(Non-covalent)

JE8.1: 20 residues within 4Å: Chain A: P.85, T.86, P.87, G.111, R.112, Y.113, E.114, V.133, S.134, I.135, G.136, Y.138, V.139, L.140, N.141, G.142, G.143, A.146 Chain B: R.156, E.182 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.139, A:L.140 Hydrogen bonds: A:T.86, A:I.135, A:G.136, A:G.136, A:Y.138, A:L.140 Salt bridges: A:E.114, B:E.182 JE8.2: 20 residues within 4Å: Chain A: R.156 Chain B: P.85, T.86, P.87, G.111, R.112, Y.113, E.114, G.115, V.133, S.134, I.135, G.136, Y.138, V.139, L.140, N.141, G.142, G.143, A.146 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain B Water bridges: A:R.156 Hydrophobic interactions: B:P.87, B:L.140 Hydrogen bonds: B:T.86, B:I.135, B:G.136, B:G.136, B:Y.138, B:L.140 Salt bridges: B:E.114

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

SO4.3: 6 residues within 4Å: Chain A: T.187, R.188 Chain B: D.52, S.53, P.54, Y.55 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.53, B:Y.55, A:R.188 SO4.4: 2 residues within 4Å: Chain B: R.129, R.131 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.130 Water bridges: 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 againstMycobacterium abscessustRNA (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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