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SMTL ID : 5zhn.1
Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.65 Å
Oligo State
homo-dimer
Ligands
2 x
9D0
:
N-({4-[(octylamino)methyl]phenyl}methyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide
(Non-covalent)
9D0.1:
22 residues within 4Å:
Chain A:
L.111
,
S.112
,
P.113
,
R.138
,
Y.139
,
W.155
,
S.156
,
I.157
,
G.158
,
Y.160
,
V.161
,
L.162
,
G.164
,
G.165
,
P.168
Chain B:
D.197
,
L.199
,
L.200
,
D.201
,
C.202
,
R.232
,
A.236
14
PLIP interactions
:
5 interactions with chain B
,
9 interactions with chain A
Hydrophobic interactions:
B:L.199
,
B:D.201
,
B:R.232
,
B:A.236
,
A:P.113
,
A:P.113
,
A:Y.139
,
A:Y.139
,
A:V.161
Hydrogen bonds:
B:D.201
,
A:I.157
,
A:Y.160
,
A:L.162
,
A:L.162
9D0.2:
19 residues within 4Å:
Chain A:
L.199
,
D.201
Chain B:
L.111
,
S.112
,
P.113
,
Q.114
,
E.140
,
W.155
,
S.156
,
I.157
,
G.158
,
D.159
,
Y.160
,
V.161
,
L.162
,
S.163
,
G.164
,
G.165
,
P.168
14
PLIP interactions
:
11 interactions with chain B
,
3 interactions with chain A
Hydrophobic interactions:
B:P.113
,
B:P.113
,
B:D.159
,
B:V.161
,
B:V.161
,
B:P.168
,
A:D.201
Hydrogen bonds:
B:I.157
,
B:Y.160
,
B:L.162
,
B:L.162
,
A:D.201
,
A:D.201
Water bridges:
B:G.137
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Zhong, W. et al., Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism. J.Med.Chem. (2019)
Release Date
2019-03-27
Peptides
tRNA (guanine-N(1)-)-methyltransferase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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tRNA (guanine-N(1)-)-methyltransferase
Related Entries With Identical Sequence
5zhm.1
|
6afk.1
|
6joe.1
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
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