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SMTL ID : 4pvx.1
Crystal structure of human FPPS in complex with [({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.18 Å
Oligo State
homo-dimer
Ligands
6 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.1:
4 residues within 4Å:
Chain A:
D.125
,
D.129
Ligands:
MG.2
,
YS1.4
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.2:
4 residues within 4Å:
Chain A:
D.125
,
D.129
Ligands:
MG.1
,
YS1.4
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:
2 residues within 4Å:
Chain A:
D.265
Ligands:
YS1.4
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.1
MG.6:
4 residues within 4Å:
Chain B:
D.125
,
D.129
Ligands:
MG.7
,
YS1.9
5
PLIP interactions
:
2 interactions with chain B
,
3 Ligand-Water interactions
Metal complexes:
B:D.125
,
B:D.129
,
H
2
O.6
,
H
2
O.6
,
H
2
O.6
MG.7:
4 residues within 4Å:
Chain B:
D.125
,
D.129
Ligands:
MG.6
,
YS1.9
4
PLIP interactions
:
2 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:D.125
,
B:D.129
,
H
2
O.6
,
H
2
O.6
MG.8:
2 residues within 4Å:
Chain B:
D.265
Ligands:
YS1.9
4
PLIP interactions
:
1 interactions with chain B
,
3 Ligand-Water interactions
Metal complexes:
B:D.265
,
H
2
O.7
,
H
2
O.7
,
H
2
O.7
2 x
YS1
:
[({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)
(Non-covalent)
YS1.4:
20 residues within 4Å:
Chain A:
F.121
,
A.124
,
D.125
,
M.128
,
D.129
,
R.134
,
T.189
,
E.190
,
Q.193
,
K.222
,
T.223
,
Y.226
,
Q.262
,
D.265
,
K.279
Chain B:
N.152
,
N.155
Ligands:
MG.1
,
MG.2
,
MG.3
22
PLIP interactions
:
21 interactions with chain A
,
1 interactions with chain B
Hydrophobic interactions:
A:F.121
,
A:F.121
,
A:F.121
,
A:A.124
,
A:D.125
,
A:T.189
,
A:Q.193
,
B:N.155
Hydrogen bonds:
A:R.134
,
A:R.134
,
A:Q.262
Water bridges:
A:D.129
,
A:D.129
,
A:D.129
,
A:S.131
,
A:K.222
,
A:K.222
,
A:K.222
,
A:K.222
,
A:T.223
,
A:D.269
,
A:D.269
YS1.9:
20 residues within 4Å:
Chain A:
N.152
,
N.155
Chain B:
F.121
,
A.124
,
D.125
,
M.128
,
D.129
,
R.134
,
T.189
,
E.190
,
Q.193
,
K.222
,
T.223
,
Y.226
,
Q.262
,
D.265
,
K.279
Ligands:
MG.6
,
MG.7
,
MG.8
17
PLIP interactions
:
16 interactions with chain B
,
1 interactions with chain A
Hydrophobic interactions:
B:F.121
,
B:F.121
,
B:F.121
,
B:A.124
,
B:D.125
,
B:T.189
,
B:Q.193
,
A:N.155
Hydrogen bonds:
B:R.134
,
B:R.134
,
B:Q.262
Water bridges:
B:S.131
,
B:K.222
,
B:K.222
,
B:K.222
,
B:K.222
,
B:K.279
2 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.5:
6 residues within 4Å:
Chain A:
Y.162
,
R.163
,
K.166
Chain B:
E.180
,
L.183
,
Q.184
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:R.163
Water bridges:
A:R.163
,
A:Y.175
GOL.10:
6 residues within 4Å:
Chain A:
E.180
,
L.183
,
Q.184
Chain B:
Y.162
,
R.163
,
K.166
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:R.163
Water bridges:
B:R.163
,
B:Y.175
,
B:Y.175
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Park, J. et al., Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase. PLoS ONE (2017)
Release Date
2015-04-15
Peptides
Farnesyl pyrophosphate synthase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
F
B
F
Export Alignment
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Secondary Structure
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Fade Mismatches
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2° Structure
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Farnesyl pyrophosphate synthase
Toggle Identical (AB)
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