Magnesium in PDB 5uy8: Crystal Structure of Aicarft Bound to An Antifolate
Enzymatic activity of Crystal Structure of Aicarft Bound to An Antifolate
All present enzymatic activity of Crystal Structure of Aicarft Bound to An Antifolate:
2.1.2.3;
3.5.4.10;
Protein crystallography data
The structure of Crystal Structure of Aicarft Bound to An Antifolate, PDB code: 5uy8
was solved by
J.Wang,
Y.Wang,
K.R.Fales,
S.Atwell,
D.Clawson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.98 /
2.39
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.575,
104.226,
105.473,
113.16,
99.39,
95.50
|
R / Rfree (%)
|
20.5 /
24.5
|
Other elements in 5uy8:
The structure of Crystal Structure of Aicarft Bound to An Antifolate also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Aicarft Bound to An Antifolate
(pdb code 5uy8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Aicarft Bound to An Antifolate, PDB code: 5uy8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5uy8
Go back to
Magnesium Binding Sites List in 5uy8
Magnesium binding site 1 out
of 4 in the Crystal Structure of Aicarft Bound to An Antifolate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Aicarft Bound to An Antifolate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg604
b:20.8
occ:1.00
|
O
|
A:VAL425
|
2.2
|
13.9
|
1.0
|
OD1
|
A:ASP539
|
2.3
|
21.3
|
1.0
|
O
|
A:THR428
|
2.4
|
12.8
|
1.0
|
O
|
A:LEU589
|
2.6
|
17.6
|
1.0
|
OG
|
A:SER432
|
3.2
|
32.4
|
1.0
|
CG
|
A:ASP539
|
3.3
|
20.6
|
1.0
|
OG
|
A:SER430
|
3.3
|
26.4
|
1.0
|
C
|
A:VAL425
|
3.4
|
14.5
|
1.0
|
CB
|
A:ASP539
|
3.5
|
14.3
|
1.0
|
C
|
A:THR428
|
3.6
|
12.2
|
1.0
|
CB
|
A:HIS591
|
3.7
|
21.9
|
1.0
|
N
|
A:HIS591
|
3.7
|
22.3
|
1.0
|
C
|
A:LEU589
|
3.8
|
16.8
|
1.0
|
N
|
A:THR428
|
4.0
|
8.8
|
1.0
|
C
|
A:PHE590
|
4.1
|
22.8
|
1.0
|
CB
|
A:SER432
|
4.2
|
20.6
|
1.0
|
CA
|
A:PHE590
|
4.2
|
13.0
|
1.0
|
CA
|
A:THR428
|
4.2
|
7.8
|
1.0
|
CA
|
A:VAL425
|
4.2
|
14.0
|
1.0
|
O
|
A:LYS426
|
4.2
|
13.3
|
1.0
|
C
|
A:LYS426
|
4.3
|
14.0
|
1.0
|
N
|
A:LYS426
|
4.3
|
9.6
|
1.0
|
CA
|
A:HIS591
|
4.3
|
21.6
|
1.0
|
CB
|
A:THR428
|
4.4
|
12.7
|
1.0
|
OD2
|
A:ASP539
|
4.4
|
22.7
|
1.0
|
N
|
A:PHE590
|
4.4
|
13.0
|
1.0
|
CA
|
A:LYS426
|
4.4
|
9.7
|
1.0
|
N
|
A:SER430
|
4.5
|
13.8
|
1.0
|
CB
|
A:VAL425
|
4.5
|
18.3
|
1.0
|
CB
|
A:SER430
|
4.6
|
16.5
|
1.0
|
C
|
A:GLN429
|
4.6
|
17.6
|
1.0
|
N
|
A:GLN429
|
4.7
|
9.4
|
1.0
|
CA
|
A:SER430
|
4.7
|
13.6
|
1.0
|
CB
|
A:LEU589
|
4.8
|
9.6
|
1.0
|
N
|
A:TYR427
|
4.8
|
8.8
|
1.0
|
O
|
A:PHE590
|
4.8
|
22.0
|
1.0
|
CG
|
A:HIS591
|
4.9
|
25.8
|
1.0
|
CA
|
A:LEU589
|
4.9
|
10.8
|
1.0
|
O
|
A:GLN429
|
4.9
|
18.6
|
1.0
|
CA
|
A:GLN429
|
4.9
|
9.5
|
1.0
|
O
|
A:HIS591
|
5.0
|
27.2
|
1.0
|
CA
|
A:ASP539
|
5.0
|
13.1
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5uy8
Go back to
Magnesium Binding Sites List in 5uy8
Magnesium binding site 2 out
of 4 in the Crystal Structure of Aicarft Bound to An Antifolate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Aicarft Bound to An Antifolate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:16.4
occ:1.00
|
O
|
B:VAL425
|
2.1
|
7.2
|
1.0
|
O
|
B:THR428
|
2.3
|
20.9
|
1.0
|
OD1
|
B:ASP539
|
2.5
|
24.7
|
1.0
|
O
|
B:LEU589
|
2.7
|
8.3
|
1.0
|
OG
|
B:SER432
|
3.3
|
33.8
|
1.0
|
C
|
B:VAL425
|
3.3
|
10.6
|
1.0
|
CG
|
B:ASP539
|
3.4
|
22.9
|
1.0
|
C
|
B:THR428
|
3.5
|
18.4
|
1.0
|
OG
|
B:SER430
|
3.5
|
22.2
|
1.0
|
CB
|
B:ASP539
|
3.6
|
17.1
|
1.0
|
CB
|
B:HIS591
|
3.6
|
12.4
|
1.0
|
N
|
B:HIS591
|
3.8
|
13.2
|
1.0
|
N
|
B:THR428
|
3.8
|
10.3
|
1.0
|
C
|
B:LEU589
|
3.9
|
10.5
|
1.0
|
CA
|
B:THR428
|
4.0
|
11.1
|
1.0
|
O
|
B:LYS426
|
4.1
|
13.3
|
1.0
|
CA
|
B:VAL425
|
4.1
|
10.0
|
1.0
|
C
|
B:LYS426
|
4.2
|
12.4
|
1.0
|
CB
|
B:THR428
|
4.2
|
14.4
|
1.0
|
CB
|
B:SER432
|
4.2
|
26.4
|
1.0
|
N
|
B:LYS426
|
4.2
|
7.2
|
1.0
|
C
|
B:PHE590
|
4.3
|
14.7
|
1.0
|
CA
|
B:LYS426
|
4.4
|
7.4
|
1.0
|
CA
|
B:HIS591
|
4.4
|
12.3
|
1.0
|
CA
|
B:PHE590
|
4.4
|
10.1
|
1.0
|
CB
|
B:VAL425
|
4.4
|
15.3
|
1.0
|
N
|
B:SER430
|
4.5
|
11.8
|
1.0
|
OD2
|
B:ASP539
|
4.6
|
22.6
|
1.0
|
N
|
B:PHE590
|
4.6
|
10.1
|
1.0
|
N
|
B:GLN429
|
4.6
|
11.8
|
1.0
|
C
|
B:GLN429
|
4.6
|
17.6
|
1.0
|
N
|
B:TYR427
|
4.7
|
9.8
|
1.0
|
CB
|
B:SER430
|
4.7
|
17.4
|
1.0
|
CB
|
B:LEU589
|
4.8
|
5.9
|
1.0
|
CG
|
B:HIS591
|
4.8
|
15.9
|
1.0
|
CA
|
B:SER430
|
4.8
|
11.9
|
1.0
|
CA
|
B:GLN429
|
4.9
|
12.3
|
1.0
|
C
|
B:TYR427
|
5.0
|
14.2
|
1.0
|
O
|
B:GLN429
|
5.0
|
17.3
|
1.0
|
CA
|
B:LEU589
|
5.0
|
5.9
|
1.0
|
O
|
B:PHE590
|
5.0
|
15.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5uy8
Go back to
Magnesium Binding Sites List in 5uy8
Magnesium binding site 3 out
of 4 in the Crystal Structure of Aicarft Bound to An Antifolate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Aicarft Bound to An Antifolate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg604
b:18.5
occ:1.00
|
O
|
C:VAL425
|
2.0
|
14.5
|
1.0
|
OD1
|
C:ASP539
|
2.3
|
25.4
|
1.0
|
O
|
C:LEU589
|
2.5
|
12.1
|
1.0
|
O
|
C:THR428
|
2.5
|
16.4
|
1.0
|
CG
|
C:ASP539
|
3.2
|
23.7
|
1.0
|
C
|
C:VAL425
|
3.2
|
15.6
|
1.0
|
OG
|
C:SER432
|
3.2
|
39.9
|
1.0
|
CB
|
C:ASP539
|
3.4
|
19.9
|
1.0
|
OG
|
C:SER430
|
3.5
|
31.4
|
1.0
|
C
|
C:THR428
|
3.7
|
16.6
|
1.0
|
C
|
C:LEU589
|
3.7
|
11.9
|
1.0
|
CB
|
C:HIS591
|
3.7
|
20.0
|
1.0
|
N
|
C:HIS591
|
3.8
|
18.7
|
1.0
|
N
|
C:THR428
|
4.0
|
11.5
|
1.0
|
CA
|
C:VAL425
|
4.1
|
15.1
|
1.0
|
O
|
C:LYS426
|
4.2
|
15.3
|
1.0
|
N
|
C:LYS426
|
4.2
|
10.6
|
1.0
|
C
|
C:PHE590
|
4.2
|
16.8
|
1.0
|
C
|
C:LYS426
|
4.2
|
16.7
|
1.0
|
CB
|
C:SER432
|
4.2
|
22.5
|
1.0
|
CA
|
C:THR428
|
4.2
|
12.0
|
1.0
|
CA
|
C:PHE590
|
4.3
|
9.1
|
1.0
|
CA
|
C:LYS426
|
4.3
|
11.0
|
1.0
|
CB
|
C:VAL425
|
4.3
|
21.0
|
1.0
|
CB
|
C:THR428
|
4.4
|
19.6
|
1.0
|
OD2
|
C:ASP539
|
4.4
|
16.8
|
1.0
|
CA
|
C:HIS591
|
4.4
|
19.2
|
1.0
|
N
|
C:PHE590
|
4.5
|
8.3
|
1.0
|
CB
|
C:LEU589
|
4.6
|
3.2
|
1.0
|
N
|
C:SER430
|
4.6
|
14.9
|
1.0
|
N
|
C:TYR427
|
4.7
|
13.0
|
1.0
|
CB
|
C:SER430
|
4.8
|
16.7
|
1.0
|
C
|
C:GLN429
|
4.8
|
18.6
|
1.0
|
N
|
C:GLN429
|
4.8
|
14.2
|
1.0
|
CA
|
C:LEU589
|
4.8
|
3.4
|
1.0
|
CA
|
C:SER430
|
4.9
|
14.5
|
1.0
|
CA
|
C:ASP539
|
4.9
|
17.4
|
1.0
|
O
|
C:PHE590
|
4.9
|
14.7
|
1.0
|
CG
|
C:HIS591
|
4.9
|
24.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5uy8
Go back to
Magnesium Binding Sites List in 5uy8
Magnesium binding site 4 out
of 4 in the Crystal Structure of Aicarft Bound to An Antifolate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Aicarft Bound to An Antifolate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg604
b:24.5
occ:1.00
|
O
|
D:VAL425
|
2.1
|
10.6
|
1.0
|
OD1
|
D:ASP539
|
2.4
|
23.5
|
1.0
|
O
|
D:THR428
|
2.5
|
21.2
|
1.0
|
O
|
D:LEU589
|
2.6
|
12.9
|
1.0
|
OG
|
D:SER432
|
3.2
|
33.8
|
1.0
|
CG
|
D:ASP539
|
3.2
|
19.6
|
1.0
|
C
|
D:VAL425
|
3.3
|
11.3
|
1.0
|
CB
|
D:ASP539
|
3.4
|
11.5
|
1.0
|
OG
|
D:SER430
|
3.4
|
27.6
|
1.0
|
C
|
D:THR428
|
3.6
|
19.2
|
1.0
|
C
|
D:LEU589
|
3.8
|
12.8
|
1.0
|
CB
|
D:HIS591
|
3.8
|
12.0
|
1.0
|
N
|
D:HIS591
|
3.9
|
13.1
|
1.0
|
N
|
D:THR428
|
4.0
|
11.3
|
1.0
|
CA
|
D:VAL425
|
4.1
|
9.1
|
1.0
|
CB
|
D:SER432
|
4.1
|
22.2
|
1.0
|
CA
|
D:THR428
|
4.2
|
11.8
|
1.0
|
CA
|
D:PHE590
|
4.3
|
10.1
|
1.0
|
C
|
D:PHE590
|
4.3
|
14.8
|
1.0
|
O
|
D:LYS426
|
4.3
|
13.0
|
1.0
|
N
|
D:LYS426
|
4.3
|
6.9
|
1.0
|
CB
|
D:THR428
|
4.3
|
12.2
|
1.0
|
C
|
D:LYS426
|
4.3
|
12.3
|
1.0
|
CB
|
D:VAL425
|
4.4
|
12.2
|
1.0
|
OD2
|
D:ASP539
|
4.4
|
21.0
|
1.0
|
CA
|
D:LYS426
|
4.4
|
8.1
|
1.0
|
N
|
D:PHE590
|
4.5
|
9.8
|
1.0
|
CA
|
D:HIS591
|
4.5
|
12.4
|
1.0
|
N
|
D:SER430
|
4.5
|
12.9
|
1.0
|
CB
|
D:SER430
|
4.6
|
18.4
|
1.0
|
C
|
D:GLN429
|
4.7
|
18.0
|
1.0
|
CB
|
D:LEU589
|
4.7
|
9.8
|
1.0
|
N
|
D:GLN429
|
4.7
|
13.7
|
1.0
|
CA
|
D:SER430
|
4.7
|
13.3
|
1.0
|
N
|
D:TYR427
|
4.8
|
9.5
|
1.0
|
CA
|
D:LEU589
|
4.9
|
10.2
|
1.0
|
CA
|
D:ASP539
|
4.9
|
10.6
|
1.0
|
O
|
D:GLN429
|
5.0
|
19.7
|
1.0
|
CG
|
D:HIS591
|
5.0
|
14.9
|
1.0
|
|
Reference:
K.R.Fales,
F.G.Njoroge,
H.B.Brooks,
S.Thibodeaux,
A.Torrado,
C.Si,
J.L.Toth,
J.R.Mc Cowan,
K.D.Roth,
K.J.Thrasher,
K.Frimpong,
M.R.Lee,
R.D.Dally,
T.A.Shepherd,
T.B.Durham,
B.J.Margolis,
Z.Wu,
Y.Wang,
S.Atwell,
J.Wang,
Y.H.Hui,
T.I.Meier,
S.A.Konicek,
S.Geeganage.
Discovery of N-(6-Fluoro-1-Oxo-1,2-Dihydroisoquinolin-7-Yl)-5-[(3R) -3-Hydroxypyrrolidin-1-Yl]Thiophene-2-Sulfonamide (Lsn 3213128), A Potent and Selective Nonclassical Antifolate Aminoimidazole-4-Carboxamide Ribonucleotide Formyltransferase (Aicarft) Inhibitor Effective at Tumor Suppression in A Cancer Xenograft Model. J. Med. Chem. V. 60 9599 2017.
ISSN: ISSN 1520-4804
PubMed: 29072452
DOI: 10.1021/ACS.JMEDCHEM.7B01046
Page generated: Mon Sep 30 05:56:41 2024
|