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SMTL ID : 4qpf.1
New lower bone affinity bisphosphonate drug design for effective use in diseases characterized by abnormal bone resorption
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.59 Å
Oligo State
homo-dimer
Ligands
2 x
39L
:
[1-fluoro-2-(imidazo[1,2-a]pyridin-3-yl)ethane-1,1-diyl]bis(phosphonic acid)
(Non-covalent)
39L.1:
16 residues within 4Å:
Chain A:
F.121
,
L.122
,
D.125
,
D.129
,
R.134
,
T.189
,
Q.193
,
K.222
,
T.223
,
Y.226
,
Q.262
,
D.265
,
K.279
Ligands:
MG.2
,
MG.3
,
MG.4
20
PLIP interactions
:
20 interactions with chain A
Hydrophobic interactions:
A:F.121
,
A:L.122
,
A:D.125
,
A:T.189
,
A:Q.193
,
A:Y.226
Hydrogen bonds:
A:R.134
,
A:R.134
,
A:Q.262
Water bridges:
A:R.82
,
A:S.131
,
A:S.131
,
A:S.131
,
A:Q.193
,
A:K.222
,
A:K.222
,
A:D.265
,
A:D.265
,
A:K.279
Halogen bonds:
A:Q.262
39L.5:
16 residues within 4Å:
Chain B:
F.121
,
L.122
,
D.125
,
D.129
,
R.134
,
T.189
,
Q.193
,
K.222
,
T.223
,
Y.226
,
Q.262
,
D.265
,
K.279
Ligands:
MG.6
,
MG.7
,
MG.8
22
PLIP interactions
:
22 interactions with chain B
Hydrophobic interactions:
B:F.121
,
B:L.122
,
B:D.125
,
B:T.189
,
B:Q.193
,
B:Y.226
Hydrogen bonds:
B:R.134
,
B:R.134
,
B:Y.226
,
B:Q.262
Water bridges:
B:R.82
,
B:D.129
,
B:S.131
,
B:S.131
,
B:S.131
,
B:Q.193
,
B:K.222
,
B:K.222
,
B:D.269
,
B:D.269
,
B:K.279
Halogen bonds:
B:Q.262
6 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.2:
4 residues within 4Å:
Chain A:
D.125
,
D.129
Ligands:
39L.1
,
MG.3
4
PLIP interactions
:
2 interactions with chain A
,
2 Ligand-Water interactions
Metal complexes:
A:D.125
,
A:D.129
,
H
2
O.1
,
H
2
O.1
MG.3:
5 residues within 4Å:
Chain A:
D.125
,
D.129
,
D.196
Ligands:
39L.1
,
MG.2
5
PLIP interactions
:
2 interactions with chain A
,
3 Ligand-Water interactions
Metal complexes:
A:D.125
,
A:D.129
,
H
2
O.1
,
H
2
O.1
,
H
2
O.1
MG.4:
3 residues within 4Å:
Chain A:
D.265
,
D.269
Ligands:
39L.1
4
PLIP interactions
:
1 interactions with chain A
,
3 Ligand-Water interactions
Metal complexes:
A:D.265
,
H
2
O.1
,
H
2
O.1
,
H
2
O.2
MG.6:
4 residues within 4Å:
Chain B:
D.125
,
D.129
Ligands:
39L.5
,
MG.7
4
PLIP interactions
:
2 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:D.125
,
B:D.129
,
H
2
O.18
,
H
2
O.18
MG.7:
5 residues within 4Å:
Chain B:
D.125
,
D.129
,
D.196
Ligands:
39L.5
,
MG.6
5
PLIP interactions
:
2 interactions with chain B
,
3 Ligand-Water interactions
Metal complexes:
B:D.125
,
B:D.129
,
H
2
O.18
,
H
2
O.18
,
H
2
O.19
MG.8:
3 residues within 4Å:
Chain B:
D.265
,
D.269
Ligands:
39L.5
4
PLIP interactions
:
1 interactions with chain B
,
3 Ligand-Water interactions
Metal complexes:
B:D.265
,
H
2
O.18
,
H
2
O.18
,
H
2
O.19
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Ebetino, F.H. et al., New lower bone affinity bisphosphonate drug design for effective use in diseases characterized by abnormal bone resorption. To be Published
Release Date
2015-06-24
Peptides
Farnesyl pyrophosphate synthase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
Export Alignment
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Secondary Structure
None
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Farnesyl pyrophosphate synthase
Toggle Identical (AB)
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