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SMTL ID : 8aze.1
Small molecule stabilizer for ERalpha and 14-3-3 (1075306)
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.60 Å
Oligo State
homo-dimer
Ligands
2 x
PHE
-
PRO
-
ALA
-
TPO
-
VAL
:
ERalpha peptide
(Non-covalent)
PHE-PRO-ALA-TPO-VAL.1:
15 residues within 4Å:
Chain A:
K.54
,
R.61
,
R.65
,
K.127
,
R.134
,
Y.135
,
G.176
,
L.179
,
N.180
,
V.183
,
E.187
,
L.227
,
N.231
,
W.235
Ligands:
O5I.5
26
PLIP interactions
:
26 interactions with chain A
Hydrophobic interactions:
A:L.179
,
A:V.183
,
A:E.187
,
A:L.227
,
A:L.227
,
A:W.235
Hydrogen bonds:
A:K.54
,
A:N.180
,
A:N.180
,
A:N.180
,
A:N.231
,
A:N.231
Water bridges:
A:R.61
,
A:R.61
,
A:R.61
,
A:R.61
,
A:R.65
,
A:Y.135
,
A:Y.135
,
A:Y.135
Salt bridges:
A:K.54
,
A:K.54
,
A:R.61
,
A:K.127
,
A:R.134
pi-Cation interactions:
A:R.65
PHE-PRO-ALA-TPO-VAL.6:
15 residues within 4Å:
Chain B:
K.54
,
R.61
,
R.65
,
K.127
,
R.134
,
Y.135
,
G.176
,
L.179
,
N.180
,
V.183
,
E.187
,
L.227
,
N.231
,
W.235
Ligands:
O5I.10
26
PLIP interactions
:
26 interactions with chain B
Hydrophobic interactions:
B:L.179
,
B:V.183
,
B:E.187
,
B:L.227
,
B:L.227
,
B:W.235
Hydrogen bonds:
B:K.54
,
B:Y.135
,
B:N.180
,
B:N.180
,
B:N.231
,
B:N.231
Water bridges:
B:K.54
,
B:R.61
,
B:R.61
,
B:R.61
,
B:R.61
,
B:R.65
,
B:K.127
,
B:Y.135
Salt bridges:
B:K.54
,
B:K.54
,
B:R.61
,
B:K.127
,
B:R.134
pi-Cation interactions:
B:R.65
6 x
MG
:
MAGNESIUM ION
(Non-functional Binders)
(Non-covalent)
MG.2:
0 residues within 4Å:
(No contacts)
No protein-ligand interaction detected (PLIP)
MG.3:
1 residues within 4Å:
Chain A:
E.7
4
PLIP interactions
:
1 interactions with chain A
,
3 Ligand-Water interactions
Metal complexes:
A:E.7
,
H
2
O.2
,
H
2
O.5
,
H
2
O.10
MG.4:
1 residues within 4Å:
Chain A:
E.94
4
PLIP interactions
:
1 interactions with chain A
,
3 Ligand-Water interactions
Metal complexes:
A:E.94
,
H
2
O.4
,
H
2
O.8
,
H
2
O.8
MG.7:
0 residues within 4Å:
(No contacts)
No protein-ligand interaction detected (PLIP)
MG.8:
1 residues within 4Å:
Chain B:
E.7
4
PLIP interactions
:
1 interactions with chain B
,
3 Ligand-Water interactions
Metal complexes:
B:E.7
,
H
2
O.13
,
H
2
O.17
,
H
2
O.21
MG.9:
1 residues within 4Å:
Chain B:
E.94
4
PLIP interactions
:
1 interactions with chain B
,
3 Ligand-Water interactions
Metal complexes:
B:E.94
,
H
2
O.15
,
H
2
O.19
,
H
2
O.19
2 x
O5I
:
2-chloranyl-~{N}-[[1-[1-[(4-chlorophenyl)amino]cyclopentyl]carbonylpiperidin-4-yl]methyl]ethanamide
(Covalent)
O5I.5:
9 residues within 4Å:
Chain A:
C.43
,
R.46
,
N.47
,
F.124
,
K.127
,
P.172
,
I.173
,
I.224
Ligands:
PHE-PRO-ALA-TPO-VAL.1
7
PLIP interactions
:
7 interactions with chain A
Hydrophobic interactions:
A:F.124
,
A:P.172
,
A:I.224
Hydrogen bonds:
A:N.47
,
A:N.47
Water bridges:
A:R.46
,
A:R.46
O5I.10:
9 residues within 4Å:
Chain B:
C.43
,
R.46
,
N.47
,
F.124
,
K.127
,
P.172
,
I.173
,
I.224
Ligands:
PHE-PRO-ALA-TPO-VAL.6
7
PLIP interactions
:
7 interactions with chain B
Hydrophobic interactions:
B:F.124
,
B:P.172
,
B:I.224
Hydrogen bonds:
B:N.47
,
B:N.47
Water bridges:
B:R.46
,
B:R.46
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Konstantinidou, M. et al., Structure-Based Optimization of Covalent, Small-Molecule Stabilizers of the 14-3-3 sigma /ER alpha Protein-Protein Interaction from Nonselective Fragments. J.Am.Chem.Soc. (2023)
Release Date
2023-09-20
Peptides
14-3-3 protein sigma:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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Secondary Structure
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14-3-3 protein sigma
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