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SMTL ID : 4htx.1
(1 other biounit)
Crystal structure of PDE2 catalytic domain in complex with BAY60-7550
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.90 Å
Oligo State
homo-dimer
Ligands
2 x
ZN
:
ZINC ION
(Non-covalent)
ZN.1:
5 residues within 4Å:
Chain A:
H.83
,
H.119
,
D.120
,
D.231
Ligands:
MG.2
6
PLIP interactions
:
4 interactions with chain A
,
2 Ligand-Water interactions
Metal complexes:
A:H.83
,
A:H.119
,
A:D.120
,
A:D.231
,
H
2
O.1
,
H
2
O.8
ZN.4:
5 residues within 4Å:
Chain B:
H.83
,
H.119
,
D.120
,
D.231
Ligands:
MG.5
6
PLIP interactions
:
4 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:H.83
,
B:H.119
,
B:D.120
,
B:D.231
,
H
2
O.9
,
H
2
O.10
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.2:
2 residues within 4Å:
Chain A:
D.120
Ligands:
ZN.1
6
PLIP interactions
:
1 interactions with chain A
,
5 Ligand-Water interactions
Metal complexes:
A:D.120
,
H
2
O.1
,
H
2
O.1
,
H
2
O.1
,
H
2
O.7
,
H
2
O.8
MG.5:
2 residues within 4Å:
Chain B:
D.120
Ligands:
ZN.4
6
PLIP interactions
:
1 interactions with chain B
,
5 Ligand-Water interactions
Metal complexes:
B:D.120
,
H
2
O.9
,
H
2
O.9
,
H
2
O.9
,
H
2
O.9
,
H
2
O.10
2 x
19F
:
2-(3,4-dimethoxybenzyl)-7-[(2R,3R)-2-hydroxy-6-phenylhexan-3-yl]-5-methylimidazo[5,1-f][1,2,4]triazin-4(3H)-one
(Non-covalent)
19F.3:
19 residues within 4Å:
Chain A:
Y.78
,
H.79
,
T.191
,
D.192
,
L.193
,
H.196
,
T.228
,
L.232
,
Q.235
,
I.249
,
Y.250
,
F.253
,
M.270
,
L.281
,
Q.282
,
S.284
,
F.285
,
I.289
,
I.293
19
PLIP interactions
:
19 interactions with chain A
Hydrophobic interactions:
A:Y.78
,
A:L.193
,
A:L.193
,
A:H.196
,
A:T.228
,
A:L.232
,
A:L.232
,
A:Q.235
,
A:I.249
,
A:F.253
,
A:F.285
,
A:F.285
,
A:I.289
,
A:I.293
Hydrogen bonds:
A:Q.235
,
A:Q.282
,
A:Q.282
Water bridges:
A:Y.78
pi-Stacking:
A:F.285
19F.6:
18 residues within 4Å:
Chain B:
Y.78
,
H.79
,
T.191
,
L.193
,
H.196
,
T.228
,
L.232
,
Q.235
,
I.249
,
Y.250
,
F.253
,
M.270
,
L.281
,
Q.282
,
S.284
,
F.285
,
I.289
,
I.293
16
PLIP interactions
:
16 interactions with chain B
Hydrophobic interactions:
B:Y.78
,
B:L.193
,
B:H.196
,
B:L.232
,
B:L.232
,
B:I.249
,
B:F.253
,
B:F.285
,
B:F.285
,
B:F.285
,
B:I.289
,
B:I.293
Hydrogen bonds:
B:Q.235
,
B:Q.282
,
B:Q.282
pi-Stacking:
B:F.285
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Zhu, J. et al., X-ray Crystal Structure of Phosphodiesterase 2 in Complex with a Highly Selective, Nanomolar Inhibitor Reveals a Binding-Induced Pocket Important for Selectivity. J.Am.Chem.Soc. (2013)
Release Date
2013-08-28
Peptides
cGMP-dependent 3',5'-cyclic phosphodiesterase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
C
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cGMP-dependent 3',5'-cyclic phosphodiesterase
Related Entries With Identical Sequence
4htx.2
|
4htz.1
|
4htz.2
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
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