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SMTL ID : 7jr6.1
H-PDGS complexed with a 2-phenylimidazo[1,2-a]pyridine-6-carboxamide inhibitors
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.88 Å
Oligo State
homo-dimer
Ligands
2 x
GSH
:
GLUTATHIONE
(Non-covalent)
GSH.1:
15 residues within 4Å:
Chain A:
Y.9
,
F.10
,
R.15
,
W.40
,
K.44
,
G.50
,
K.51
,
I.52
,
P.53
,
Q.64
,
S.65
,
L.66
Chain B:
D.94
,
D.98
Ligands:
VH4.2
18
PLIP interactions
:
18 interactions with chain A
Hydrophobic interactions:
A:K.51
Hydrogen bonds:
A:R.15
,
A:W.40
,
A:I.52
,
A:I.52
,
A:Q.64
,
A:Q.64
,
A:S.65
,
A:S.65
Water bridges:
A:R.15
,
A:R.15
,
A:Q.64
,
A:Q.64
,
A:L.66
,
A:D.97
,
A:D.97
Salt bridges:
A:R.15
,
A:K.44
GSH.6:
16 residues within 4Å:
Chain A:
D.94
,
D.98
Chain B:
Y.9
,
F.10
,
M.12
,
R.15
,
W.40
,
K.44
,
G.50
,
K.51
,
I.52
,
P.53
,
Q.64
,
S.65
,
L.66
Ligands:
VH4.7
18
PLIP interactions
:
15 interactions with chain B
,
3 interactions with chain A
Hydrogen bonds:
B:R.15
,
B:W.40
,
B:K.51
,
B:I.52
,
B:I.52
,
B:Q.64
,
B:S.65
,
B:S.65
,
A:D.98
Water bridges:
B:R.15
,
B:R.15
,
B:R.15
,
B:Q.64
,
B:L.66
,
A:D.94
,
A:D.94
Salt bridges:
B:R.15
,
B:K.51
2 x
VH4
:
1-(3-fluorophenyl)-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide
(Non-covalent)
VH4.2:
15 residues within 4Å:
Chain A:
Y.9
,
F.10
,
M.12
,
G.14
,
R.15
,
Q.37
,
D.97
,
M.100
,
S.101
,
W.105
,
A.106
,
Y.153
,
T.160
,
L.200
Ligands:
GSH.1
9
PLIP interactions
:
9 interactions with chain A
Hydrophobic interactions:
A:R.15
,
A:W.105
,
A:W.105
,
A:A.106
Hydrogen bonds:
A:Q.37
,
A:T.160
Water bridges:
A:L.200
pi-Stacking:
A:W.105
Halogen bonds:
A:S.101
VH4.7:
16 residues within 4Å:
Chain B:
Y.9
,
F.10
,
M.12
,
G.14
,
R.15
,
Q.37
,
W.40
,
D.97
,
M.100
,
S.101
,
W.105
,
A.106
,
Y.153
,
T.160
,
L.200
Ligands:
GSH.6
5
PLIP interactions
:
5 interactions with chain B
Hydrophobic interactions:
B:R.15
,
B:Q.37
,
B:W.105
pi-Stacking:
B:W.105
Halogen bonds:
B:S.101
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.3:
1 residues within 4Å:
Chain A:
D.97
No protein-ligand interaction detected (PLIP)
MG.8:
2 residues within 4Å:
Chain A:
E.83
Chain B:
Y.71
No protein-ligand interaction detected (PLIP)
2 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.4:
6 residues within 4Å:
Chain A:
D.77
,
G.80
,
N.81
,
S.146
,
V.147
,
T.148
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:N.81
,
A:V.147
Water bridges:
A:S.146
NA.5:
4 residues within 4Å:
Chain A:
K.165
,
D.167
,
D.170
,
N.171
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:D.167
Water bridges:
A:K.165
,
A:N.171
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Schulte, C.A. et al., A knowledge-based, structural-aided discovery of a novel class of 2-phenylimidazo[1,2-a]pyridine-6-carboxamide H-PGDS inhibitors. Bioorg.Med.Chem.Lett. (2021)
Release Date
2021-05-26
Peptides
Hematopoietic prostaglandin D synthase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Secondary Structure
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2° Structure
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Hematopoietic prostaglandin D synthase
Toggle Identical (AB)
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6n4e.1
|
6ztc.1
|
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