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SMTL ID : 4edy.1
Crystal structure of hH-PGDS with water displacing inhibitor
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.72 Å
Oligo State
homo-dimer
Ligands
1 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.1:
2 residues within 4Å:
Chain A:
D.96
Chain B:
D.96
No protein-ligand interaction detected (PLIP)
2 x
GSH
:
GLUTATHIONE
(Non-covalent)
GSH.2:
12 residues within 4Å:
Chain A:
Y.8
,
F.9
,
R.14
,
W.39
,
K.43
,
K.50
,
I.51
,
P.52
,
Q.63
,
S.64
Chain B:
D.97
Ligands:
9PQ.3
16
PLIP interactions
:
15 interactions with chain A
,
1 interactions with chain B
Hydrophobic interactions:
A:K.50
Hydrogen bonds:
A:R.14
,
A:W.39
,
A:I.51
,
A:I.51
,
A:Q.63
,
A:S.64
,
B:D.97
Water bridges:
A:K.50
,
A:I.51
,
A:Q.63
,
A:S.64
,
A:S.64
,
A:L.65
Salt bridges:
A:K.43
,
A:K.50
GSH.5:
10 residues within 4Å:
Chain A:
D.97
Chain B:
Y.8
,
R.14
,
W.39
,
K.43
,
K.50
,
I.51
,
P.52
,
Q.63
,
S.64
15
PLIP interactions
:
14 interactions with chain B
,
1 interactions with chain A
Hydrogen bonds:
B:R.14
,
B:I.51
,
B:I.51
,
B:Q.63
,
B:S.64
,
A:D.97
Water bridges:
B:Q.63
,
B:Q.63
,
B:S.64
,
B:S.64
,
B:L.65
,
B:D.96
Salt bridges:
B:R.14
,
B:K.43
,
B:K.50
1 x
9PQ
:
4-[2-(hydroxymethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide
(Non-covalent)
9PQ.3:
14 residues within 4Å:
Chain A:
Y.8
,
F.9
,
M.11
,
R.12
,
G.13
,
R.14
,
Q.36
,
D.96
,
M.99
,
W.104
,
Y.152
,
T.159
,
L.199
Ligands:
GSH.2
8
PLIP interactions
:
8 interactions with chain A
Hydrophobic interactions:
A:R.14
,
A:M.99
,
A:W.104
,
A:L.199
Hydrogen bonds:
A:R.12
,
A:G.13
,
A:T.159
,
A:L.199
1 x
DMS
:
DIMETHYL SULFOXIDE
(Non-functional Binders)
DMS.4:
4 residues within 4Å:
Chain B:
G.13
,
M.99
,
Y.152
,
T.159
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:T.159
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Trujillo, J.I. et al., Investigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): a tale of two waters. Bioorg.Med.Chem.Lett. (2012)
Release Date
2012-10-03
Peptides
Hematopoietic prostaglandin D synthase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
Export Alignment
FASTA format
Clustal Format
PNG Image
Secondary Structure
None
DSSP
PSIPRED
SSpro
Colour Scheme
Fade Mismatches
Enhance Mismatches
Chain
Unique Chain
Rainbow
2° Structure
Bfactor
Bfactor Range
SOA
Entropy
Clustal
Hydrophobic
Size
Charged
Polar
Proline
Ser/Thr
Cysteine
Aliphatic
Aromatic
No Colour
Background
3D Viewer
NGL
PV
2D
FASTA
Multi FASTA
ClustalW
PNG
Hematopoietic prostaglandin D synthase
Related Entries With Identical Sequence
4ee0.1
|
5ais.1
|
5ais.2
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
Resolution
Low
Medium
High
Extreme