SMTL ID : 4mcb.1

H.influenzae TrmD in complex with N-(4-{[(1H-IMIDAZOL-2-YLMETHYL)AMINO]METHYL}BENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-5-CARBOXAMIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: A.103, Q.104, N.105, Q.106, F.155, I.156, P.157 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.104, A:F.155 Water bridges: A:Q.106, A:F.155

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

SO4.2: 4 residues within 4Å: Chain A: V.186, L.187, E.188 Chain B: R.68 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.188 Water bridges: A:V.186, A:G.189, B:R.68, B:R.68 Salt bridges: B:R.68 SO4.5: 6 residues within 4Å: Chain B: A.103, N.105, Q.106, F.155, I.156, P.157 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.106, B:F.155 Water bridges: B:Q.106, B:Q.106, B:Q.106, B:Q.106

2 x 21W: N-(4-{[(1H-imidazol-2-ylmethyl)amino]methyl}benzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide(Non-covalent)

21W.3: 19 residues within 4Å: Chain A: L.87, S.88, P.89, Y.115, E.116, W.131, S.132, I.133, G.134, Y.136, V.137, L.138, G.140, G.141, P.144 Chain B: D.169, A.172, D.173, D.177 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:D.169, B:D.173, A:E.116, A:I.133, A:Y.136, A:L.138, A:L.138 Hydrophobic interactions: A:P.89, A:P.89, A:V.137 Water bridges: A:S.132, A:S.132 21W.6: 16 residues within 4Å: Chain B: L.87, S.88, P.89, G.113, Y.115, E.116, W.131, S.132, I.133, G.134, Y.136, V.137, L.138, G.140, G.141, P.144 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.89, B:V.137 Hydrogen bonds: B:E.116, B:I.133, B:Y.136, B:L.138, B:L.138 Water bridges: B:S.132, B:S.132, A:R.154, A:R.154

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 4 residues within 4Å: Chain B: W.2, A.77, A.78, K.107 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hill, P.J. et al., Selective Inhibitors of Bacterial t-RNA-(N(1)G37) Methyltransferase (TrmD) That Demonstrate Novel Ordering of the Lid Domain. J.Med.Chem. (2013)

Release Date

2013-09-04

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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