SMTL ID : 8apu.1

Crystal Structure of H. influenzae TrmD in complex with Compound 14

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x NMV: 6-[[4-(aminomethyl)phenyl]methylamino]pyridine-3-carboxamide(Non-covalent)

NMV.1: 22 residues within 4Å: Chain A: Y.106, L.107, S.108, P.109, Q.110, G.133, R.134, Y.135, E.136, G.137, S.152, I.153, G.154, Y.156, V.157, L.158, T.159, G.160, G.161, P.164 Chain B: D.197, H.200 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.164 Hydrogen bonds: A:I.153, A:G.154, A:Y.156, A:L.158, A:L.158, B:D.197, B:D.197 NMV.3: 22 residues within 4Å: Chain A: D.197, H.200 Chain B: Y.106, L.107, S.108, P.109, Q.110, G.133, R.134, Y.135, E.136, G.137, S.152, I.153, G.154, Y.156, V.157, L.158, T.159, G.160, G.161, P.164 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.164 Hydrogen bonds: B:I.153, B:G.154, B:Y.156, B:L.158, B:L.158, A:D.197

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 3 residues within 4Å: Chain A: T.250, D.251, R.254 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.251 Water bridges: A:D.251, A:E.252, A:R.254 Salt bridges: A:R.254 CIT.4: 3 residues within 4Å: Chain B: T.250, D.251, R.254 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.251 Water bridges: B:D.251, B:D.251, B:E.252, B:R.254 Salt bridges: B:R.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilkinson, A.J. et al., Evaluating the druggability of TrmD, a potential antibacterial target, through design and microbiological profiling of a series of potent TrmD inhibitors. Bioorg.Med.Chem.Lett. (2023)

Release Date

2023-06-14

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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