SMTL ID : 8apv.1

Crystal Structure of H. influenzae TrmD in complex with Compound 27

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x NLL: 1-[[4-(aminomethyl)phenyl]methyl]pyrrolo[2,3-b]pyridine-5-carboxamide(Non-covalent)

NLL.1: 24 residues within 4Å: Chain A: Y.106, L.107, S.108, P.109, Q.110, G.133, R.134, Y.135, E.136, S.152, I.153, G.154, Y.156, V.157, L.158, T.159, G.160, G.161, P.164 Chain B: R.174, D.189, S.190, D.197, H.200 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.109, A:V.157, A:P.164 Hydrogen bonds: A:E.136, A:I.153, A:G.154, A:Y.156, A:L.158, B:H.200 NLL.3: 24 residues within 4Å: Chain A: R.174, D.189, S.190, D.197, H.200 Chain B: Y.106, L.107, S.108, P.109, Q.110, G.133, R.134, Y.135, E.136, S.152, I.153, G.154, Y.156, V.157, L.158, T.159, G.160, G.161, P.164 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.109, B:V.157, B:P.164 Hydrogen bonds: B:E.136, B:E.136, B:I.153, B:G.154, B:Y.156, B:L.158, A:H.200

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

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