Fluorine in PDB 7c04: Crystal Structure of Human TRAP1 with DN203492
Protein crystallography data
The structure of Crystal Structure of Human TRAP1 with DN203492, PDB code: 7c04
was solved by
D.Kim,
D.Kim,
S.Y.Kim,
J.H.Lee,
B.H.Kang,
S.Kang,
C.Lee,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.21 /
1.70
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
110.405,
110.405,
59.445,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.9 /
23.4
|
Other elements in 7c04:
The structure of Crystal Structure of Human TRAP1 with DN203492 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Human TRAP1 with DN203492
(pdb code 7c04). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Crystal Structure of Human TRAP1 with DN203492, PDB code: 7c04:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 7c04
Go back to
Fluorine Binding Sites List in 7c04
Fluorine binding site 1 out
of 3 in the Crystal Structure of Human TRAP1 with DN203492
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Human TRAP1 with DN203492 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:32.3
occ:1.00
|
F20
|
A:FEU301
|
0.0
|
32.3
|
1.0
|
C19
|
A:FEU301
|
1.3
|
37.6
|
1.0
|
F21
|
A:FEU301
|
2.2
|
32.7
|
1.0
|
F22
|
A:FEU301
|
2.2
|
39.8
|
1.0
|
C16
|
A:FEU301
|
2.3
|
24.9
|
1.0
|
H1
|
A:FEU301
|
2.8
|
32.7
|
1.0
|
C15
|
A:FEU301
|
2.9
|
27.3
|
1.0
|
CD1
|
A:LEU172
|
3.3
|
37.8
|
1.0
|
CZ2
|
A:TRP231
|
3.3
|
26.7
|
1.0
|
C17
|
A:FEU301
|
3.4
|
22.4
|
1.0
|
CB
|
A:LEU172
|
3.5
|
37.9
|
1.0
|
CE2
|
A:PHE205
|
3.5
|
31.5
|
1.0
|
H2
|
A:FEU301
|
3.7
|
26.9
|
1.0
|
CE2
|
A:TRP231
|
3.8
|
22.9
|
1.0
|
CG
|
A:LEU172
|
3.8
|
45.6
|
1.0
|
O
|
A:HOH479
|
3.8
|
40.0
|
1.0
|
CH2
|
A:TRP231
|
3.9
|
27.0
|
1.0
|
CD2
|
A:PHE205
|
3.9
|
29.6
|
1.0
|
CA
|
A:LEU172
|
4.0
|
42.7
|
1.0
|
NE1
|
A:TRP231
|
4.1
|
29.3
|
1.0
|
N
|
A:LEU172
|
4.1
|
38.2
|
1.0
|
C14
|
A:FEU301
|
4.3
|
23.7
|
1.0
|
CD2
|
A:LEU172
|
4.4
|
48.8
|
1.0
|
CZ
|
A:PHE205
|
4.4
|
25.7
|
1.0
|
C18
|
A:FEU301
|
4.6
|
21.3
|
1.0
|
CD2
|
A:TRP231
|
4.6
|
24.2
|
1.0
|
CZ3
|
A:TRP231
|
4.7
|
27.8
|
1.0
|
O
|
A:LEU168
|
4.8
|
28.3
|
1.0
|
H11
|
A:FEU301
|
4.9
|
28.4
|
1.0
|
C13
|
A:FEU301
|
5.0
|
23.2
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 7c04
Go back to
Fluorine Binding Sites List in 7c04
Fluorine binding site 2 out
of 3 in the Crystal Structure of Human TRAP1 with DN203492
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Human TRAP1 with DN203492 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:32.7
occ:1.00
|
F21
|
A:FEU301
|
0.0
|
32.7
|
1.0
|
C19
|
A:FEU301
|
1.3
|
37.6
|
1.0
|
F20
|
A:FEU301
|
2.2
|
32.3
|
1.0
|
F22
|
A:FEU301
|
2.2
|
39.8
|
1.0
|
H2
|
A:FEU301
|
2.3
|
26.9
|
1.0
|
C16
|
A:FEU301
|
2.3
|
24.9
|
1.0
|
C17
|
A:FEU301
|
2.7
|
22.4
|
1.0
|
CE2
|
A:TRP231
|
3.1
|
22.9
|
1.0
|
NE1
|
A:TRP231
|
3.4
|
29.3
|
1.0
|
CD2
|
A:TRP231
|
3.5
|
24.2
|
1.0
|
CZ2
|
A:TRP231
|
3.5
|
26.7
|
1.0
|
C15
|
A:FEU301
|
3.6
|
27.3
|
1.0
|
CD1
|
A:TRP231
|
3.8
|
25.3
|
1.0
|
CE2
|
A:PHE205
|
3.9
|
31.5
|
1.0
|
CG
|
A:TRP231
|
3.9
|
23.3
|
1.0
|
H1
|
A:FEU301
|
4.0
|
32.7
|
1.0
|
CH2
|
A:TRP231
|
4.0
|
27.0
|
1.0
|
CD2
|
A:LEU168
|
4.0
|
26.7
|
1.0
|
CE3
|
A:TRP231
|
4.0
|
22.3
|
1.0
|
C18
|
A:FEU301
|
4.1
|
21.3
|
1.0
|
H5
|
A:FEU301
|
4.1
|
33.2
|
1.0
|
CZ
|
A:PHE205
|
4.1
|
25.7
|
1.0
|
CZ3
|
A:TRP231
|
4.3
|
27.8
|
1.0
|
O
|
A:LEU168
|
4.5
|
28.3
|
1.0
|
CD2
|
A:PHE205
|
4.6
|
29.6
|
1.0
|
C14
|
A:FEU301
|
4.8
|
23.7
|
1.0
|
C24
|
A:FEU301
|
4.8
|
27.6
|
1.0
|
CG2
|
A:VAL217
|
4.8
|
22.7
|
1.0
|
CE
|
A:MET163
|
4.8
|
26.3
|
1.0
|
H3
|
A:FEU301
|
4.8
|
33.2
|
1.0
|
CA
|
A:LEU168
|
4.9
|
23.1
|
1.0
|
CB
|
A:TRP231
|
4.9
|
22.8
|
1.0
|
O
|
A:HOH479
|
4.9
|
40.0
|
1.0
|
C13
|
A:FEU301
|
4.9
|
23.2
|
1.0
|
O23
|
A:FEU301
|
5.0
|
22.9
|
1.0
|
CE1
|
A:PHE205
|
5.0
|
23.2
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 7c04
Go back to
Fluorine Binding Sites List in 7c04
Fluorine binding site 3 out
of 3 in the Crystal Structure of Human TRAP1 with DN203492
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Human TRAP1 with DN203492 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:39.8
occ:1.00
|
F22
|
A:FEU301
|
0.0
|
39.8
|
1.0
|
C19
|
A:FEU301
|
1.3
|
37.6
|
1.0
|
F21
|
A:FEU301
|
2.2
|
32.7
|
1.0
|
F20
|
A:FEU301
|
2.2
|
32.3
|
1.0
|
C16
|
A:FEU301
|
2.3
|
24.9
|
1.0
|
H1
|
A:FEU301
|
2.9
|
32.7
|
1.0
|
C15
|
A:FEU301
|
2.9
|
27.3
|
1.0
|
O
|
A:HOH479
|
3.3
|
40.0
|
1.0
|
C17
|
A:FEU301
|
3.3
|
22.4
|
1.0
|
O
|
A:LEU168
|
3.4
|
28.3
|
1.0
|
H2
|
A:FEU301
|
3.6
|
26.9
|
1.0
|
O
|
A:GLU167
|
3.6
|
29.0
|
1.0
|
CA
|
A:LEU168
|
3.7
|
23.1
|
1.0
|
C
|
A:LEU168
|
3.8
|
30.2
|
1.0
|
NE1
|
A:TRP231
|
3.9
|
29.3
|
1.0
|
CE
|
A:MET163
|
4.0
|
26.3
|
1.0
|
N
|
A:LEU172
|
4.0
|
38.2
|
1.0
|
CB
|
A:ASN171
|
4.1
|
28.7
|
1.0
|
CE2
|
A:TRP231
|
4.2
|
22.9
|
1.0
|
C14
|
A:FEU301
|
4.2
|
23.7
|
1.0
|
CD2
|
A:LEU168
|
4.3
|
26.7
|
1.0
|
CB
|
A:LEU172
|
4.4
|
37.9
|
1.0
|
CZ2
|
A:TRP231
|
4.4
|
26.7
|
1.0
|
C
|
A:GLU167
|
4.5
|
27.6
|
1.0
|
C18
|
A:FEU301
|
4.5
|
21.3
|
1.0
|
CD1
|
A:TRP231
|
4.5
|
25.3
|
1.0
|
N
|
A:LEU168
|
4.6
|
24.6
|
1.0
|
N
|
A:ASN171
|
4.6
|
36.5
|
1.0
|
CA
|
A:LEU172
|
4.6
|
42.7
|
1.0
|
C
|
A:ASN171
|
4.6
|
35.0
|
1.0
|
CA
|
A:ASN171
|
4.7
|
34.6
|
1.0
|
CB
|
A:LEU168
|
4.7
|
23.8
|
1.0
|
C13
|
A:FEU301
|
4.9
|
23.2
|
1.0
|
H11
|
A:FEU301
|
4.9
|
28.4
|
1.0
|
SD
|
A:MET163
|
4.9
|
24.9
|
1.0
|
N
|
A:VAL169
|
5.0
|
31.7
|
1.0
|
|
Reference:
D.Kim,
S.Y.Kim,
D.Kim,
N.G.Yoon,
J.Yun,
K.B.Hong,
C.Lee,
J.H.Lee,
B.H.Kang,
S.Kang.
Development of Pyrazolo[3,4-D]Pyrimidine-6-Amine-Based TRAP1 Inhibitors That Demonstrate in Vivo Anticancer Activity in Mouse Xenograft Models. Bioorg.Chem. V. 101 03901 2020.
ISSN: ISSN 0045-2068
PubMed: 32590225
DOI: 10.1016/J.BIOORG.2020.103901
Page generated: Fri Aug 2 06:06:29 2024
|