Chlorine in PDB 6v2f: Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207
Protein crystallography data
The structure of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207, PDB code: 6v2f
was solved by
T.C.Appleby,
J.O.Link,
S.R.Yant,
A.G.Villasenor,
J.R.Somoza,
E.Y.Hu,
S.D.Schroeder,
T.Cihlar,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.92 /
2.00
|
Space group
|
P 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
158.301,
158.301,
55.648,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.9 /
25.1
|
Other elements in 6v2f:
The structure of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207
(pdb code 6v2f). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207, PDB code: 6v2f:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 6v2f
Go back to
Chlorine Binding Sites List in 6v2f
Chlorine binding site 1 out
of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl300
b:29.1
occ:1.00
|
CL47
|
A:QNG300
|
0.0
|
29.1
|
1.0
|
C10
|
A:QNG300
|
1.7
|
24.9
|
1.0
|
C09
|
A:QNG300
|
2.7
|
24.5
|
1.0
|
C11
|
A:QNG300
|
2.7
|
22.2
|
1.0
|
N17
|
A:QNG300
|
3.1
|
28.6
|
1.0
|
C16
|
A:QNG300
|
3.3
|
25.1
|
1.0
|
CG2
|
A:ILE73
|
3.6
|
20.3
|
1.0
|
CG
|
A:LYS70
|
3.7
|
34.2
|
1.0
|
OD1
|
A:ASN74
|
3.7
|
34.3
|
1.0
|
O
|
A:LYS70
|
3.9
|
25.2
|
1.0
|
CB
|
A:ILE73
|
3.9
|
21.1
|
1.0
|
ND2
|
A:ASN74
|
4.0
|
36.1
|
1.0
|
C12
|
A:QNG300
|
4.0
|
22.0
|
1.0
|
CG
|
A:ASN74
|
4.0
|
30.1
|
1.0
|
C08
|
A:QNG300
|
4.0
|
22.9
|
1.0
|
N
|
A:ASN74
|
4.4
|
21.3
|
1.0
|
CA
|
A:LYS70
|
4.5
|
23.4
|
1.0
|
CD1
|
A:ILE73
|
4.5
|
19.9
|
1.0
|
C07
|
A:QNG300
|
4.5
|
19.6
|
1.0
|
N15
|
A:QNG300
|
4.6
|
24.3
|
1.0
|
C
|
A:LYS70
|
4.6
|
26.7
|
1.0
|
S48
|
A:QNG300
|
4.7
|
36.0
|
1.0
|
CD
|
A:LYS70
|
4.7
|
30.0
|
1.0
|
CB
|
A:ALA105
|
4.7
|
23.0
|
1.0
|
CB
|
A:LYS70
|
4.7
|
24.0
|
1.0
|
C
|
A:ILE73
|
4.8
|
20.6
|
1.0
|
CG1
|
A:ILE73
|
4.8
|
20.1
|
1.0
|
CG2
|
A:THR107
|
4.9
|
24.5
|
1.0
|
N14
|
A:QNG300
|
4.9
|
23.6
|
1.0
|
O51
|
A:QNG300
|
4.9
|
38.9
|
1.0
|
CA
|
A:ILE73
|
4.9
|
22.6
|
1.0
|
CA
|
A:ASN74
|
4.9
|
25.1
|
1.0
|
CB
|
A:ASN74
|
5.0
|
28.4
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 6v2f
Go back to
Chlorine Binding Sites List in 6v2f
Chlorine binding site 2 out
of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl300
b:25.4
occ:1.00
|
CL47
|
B:QNG300
|
0.0
|
25.4
|
1.0
|
C10
|
B:QNG300
|
1.7
|
21.3
|
1.0
|
C09
|
B:QNG300
|
2.7
|
24.8
|
1.0
|
C11
|
B:QNG300
|
2.7
|
19.3
|
1.0
|
N17
|
B:QNG300
|
3.2
|
25.6
|
1.0
|
C16
|
B:QNG300
|
3.3
|
23.8
|
1.0
|
CG2
|
B:ILE73
|
3.5
|
19.8
|
1.0
|
OD1
|
B:ASN74
|
3.7
|
36.0
|
1.0
|
ND2
|
B:ASN74
|
3.8
|
31.2
|
1.0
|
O
|
B:LYS70
|
3.8
|
19.6
|
1.0
|
CG
|
B:LYS70
|
3.9
|
30.1
|
1.0
|
CB
|
B:ILE73
|
3.9
|
20.8
|
1.0
|
CG
|
B:ASN74
|
3.9
|
30.5
|
1.0
|
C12
|
B:QNG300
|
4.0
|
19.6
|
1.0
|
C08
|
B:QNG300
|
4.0
|
20.9
|
1.0
|
O
|
B:HOH492
|
4.1
|
35.6
|
1.0
|
O
|
B:HOH407
|
4.4
|
33.7
|
1.0
|
N
|
B:ASN74
|
4.5
|
20.6
|
1.0
|
C07
|
B:QNG300
|
4.5
|
20.1
|
1.0
|
CA
|
B:LYS70
|
4.5
|
21.4
|
1.0
|
CD
|
B:LYS70
|
4.6
|
29.3
|
1.0
|
N15
|
B:QNG300
|
4.6
|
23.5
|
1.0
|
C
|
B:LYS70
|
4.6
|
23.8
|
1.0
|
CD1
|
B:ILE73
|
4.6
|
18.0
|
1.0
|
CB
|
B:ALA105
|
4.6
|
19.2
|
1.0
|
CB
|
B:LYS70
|
4.7
|
26.9
|
1.0
|
CG2
|
B:THR107
|
4.8
|
22.9
|
1.0
|
S48
|
B:QNG300
|
4.8
|
29.3
|
1.0
|
C
|
B:ILE73
|
4.8
|
21.5
|
1.0
|
CG1
|
B:ILE73
|
4.9
|
23.4
|
1.0
|
N14
|
B:QNG300
|
4.9
|
24.2
|
1.0
|
CA
|
B:ILE73
|
4.9
|
20.6
|
1.0
|
CB
|
B:ASN74
|
4.9
|
24.6
|
1.0
|
CA
|
B:ASN74
|
5.0
|
25.1
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 6v2f
Go back to
Chlorine Binding Sites List in 6v2f
Chlorine binding site 3 out
of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl300
b:26.2
occ:1.00
|
CL47
|
C:QNG300
|
0.0
|
26.2
|
1.0
|
C10
|
C:QNG300
|
1.7
|
18.6
|
1.0
|
C09
|
C:QNG300
|
2.7
|
24.9
|
1.0
|
C11
|
C:QNG300
|
2.7
|
18.9
|
1.0
|
N17
|
C:QNG300
|
3.2
|
23.9
|
1.0
|
C16
|
C:QNG300
|
3.3
|
23.3
|
1.0
|
CG2
|
C:ILE73
|
3.5
|
18.7
|
1.0
|
CG
|
C:LYS70
|
3.6
|
36.0
|
1.0
|
ND2
|
C:ASN74
|
3.6
|
31.5
|
1.0
|
OD1
|
C:ASN74
|
3.8
|
42.1
|
1.0
|
O
|
C:LYS70
|
3.8
|
22.1
|
1.0
|
CB
|
C:ILE73
|
3.9
|
19.2
|
1.0
|
CG
|
C:ASN74
|
3.9
|
34.8
|
1.0
|
C12
|
C:QNG300
|
4.0
|
19.5
|
1.0
|
C08
|
C:QNG300
|
4.0
|
20.2
|
1.0
|
O
|
C:HOH490
|
4.1
|
34.4
|
1.0
|
CD
|
C:LYS70
|
4.2
|
36.1
|
1.0
|
O
|
C:HOH437
|
4.4
|
34.4
|
1.0
|
CA
|
C:LYS70
|
4.5
|
22.0
|
1.0
|
N
|
C:ASN74
|
4.5
|
20.8
|
1.0
|
C07
|
C:QNG300
|
4.5
|
19.6
|
1.0
|
CD1
|
C:ILE73
|
4.6
|
19.8
|
1.0
|
C
|
C:LYS70
|
4.6
|
21.4
|
1.0
|
N15
|
C:QNG300
|
4.6
|
23.4
|
1.0
|
CB
|
C:ALA105
|
4.6
|
19.7
|
1.0
|
CB
|
C:LYS70
|
4.6
|
28.7
|
1.0
|
CG2
|
C:THR107
|
4.8
|
23.2
|
1.0
|
C
|
C:ILE73
|
4.8
|
21.4
|
1.0
|
S48
|
C:QNG300
|
4.8
|
26.9
|
1.0
|
CG1
|
C:ILE73
|
4.8
|
22.0
|
1.0
|
N14
|
C:QNG300
|
4.9
|
24.2
|
1.0
|
CA
|
C:ILE73
|
4.9
|
20.0
|
1.0
|
CA
|
C:ASN74
|
5.0
|
23.0
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 6v2f
Go back to
Chlorine Binding Sites List in 6v2f
Chlorine binding site 4 out
of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl300
b:30.5
occ:1.00
|
CL47
|
D:QNG300
|
0.0
|
30.5
|
1.0
|
C10
|
D:QNG300
|
1.7
|
24.9
|
1.0
|
C09
|
D:QNG300
|
2.7
|
23.7
|
1.0
|
C11
|
D:QNG300
|
2.7
|
22.5
|
1.0
|
N17
|
D:QNG300
|
3.1
|
28.4
|
1.0
|
C16
|
D:QNG300
|
3.3
|
26.6
|
1.0
|
CG2
|
D:ILE73
|
3.5
|
21.0
|
1.0
|
ND2
|
D:ASN74
|
3.7
|
31.0
|
1.0
|
OD1
|
D:ASN74
|
3.8
|
38.0
|
1.0
|
O
|
D:LYS70
|
3.9
|
25.2
|
1.0
|
CG
|
D:LYS70
|
3.9
|
34.5
|
1.0
|
CB
|
D:ILE73
|
3.9
|
21.4
|
1.0
|
CG
|
D:ASN74
|
3.9
|
31.6
|
1.0
|
C12
|
D:QNG300
|
4.0
|
23.0
|
1.0
|
C08
|
D:QNG300
|
4.0
|
24.3
|
1.0
|
O
|
D:HOH462
|
4.3
|
34.4
|
1.0
|
N
|
D:ASN74
|
4.4
|
23.8
|
1.0
|
CA
|
D:LYS70
|
4.5
|
26.8
|
1.0
|
C07
|
D:QNG300
|
4.5
|
21.2
|
1.0
|
N15
|
D:QNG300
|
4.6
|
27.4
|
1.0
|
CD1
|
D:ILE73
|
4.6
|
19.4
|
1.0
|
CB
|
D:LYS70
|
4.6
|
26.6
|
1.0
|
C
|
D:LYS70
|
4.6
|
27.1
|
1.0
|
CB
|
D:ALA105
|
4.7
|
21.8
|
1.0
|
S48
|
D:QNG300
|
4.7
|
35.3
|
1.0
|
C
|
D:ILE73
|
4.8
|
23.8
|
1.0
|
CG2
|
D:THR107
|
4.8
|
25.2
|
1.0
|
CG1
|
D:ILE73
|
4.9
|
19.7
|
1.0
|
N14
|
D:QNG300
|
4.9
|
25.1
|
1.0
|
CB
|
D:ASN74
|
4.9
|
29.1
|
1.0
|
CA
|
D:ASN74
|
4.9
|
26.5
|
1.0
|
O51
|
D:QNG300
|
4.9
|
34.5
|
1.0
|
CD
|
D:LYS70
|
4.9
|
30.9
|
1.0
|
CA
|
D:ILE73
|
4.9
|
21.0
|
1.0
|
CE
|
D:LYS70
|
5.0
|
29.4
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 6v2f
Go back to
Chlorine Binding Sites List in 6v2f
Chlorine binding site 5 out
of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl300
b:29.6
occ:1.00
|
CL47
|
E:QNG300
|
0.0
|
29.6
|
1.0
|
C10
|
E:QNG300
|
1.7
|
24.5
|
1.0
|
C09
|
E:QNG300
|
2.7
|
24.7
|
1.0
|
C11
|
E:QNG300
|
2.7
|
22.1
|
1.0
|
N17
|
E:QNG300
|
3.1
|
26.4
|
1.0
|
C16
|
E:QNG300
|
3.3
|
25.4
|
1.0
|
CG2
|
E:ILE73
|
3.5
|
21.9
|
1.0
|
ND2
|
E:ASN74
|
3.6
|
30.4
|
1.0
|
OD1
|
E:ASN74
|
3.8
|
35.0
|
1.0
|
CG
|
E:ASN74
|
3.8
|
28.8
|
1.0
|
C12
|
E:QNG300
|
4.0
|
20.2
|
1.0
|
C08
|
E:QNG300
|
4.0
|
25.0
|
1.0
|
O
|
E:LYS70
|
4.0
|
23.1
|
1.0
|
CB
|
E:ILE73
|
4.0
|
23.9
|
1.0
|
N
|
E:ASN74
|
4.5
|
22.4
|
1.0
|
C07
|
E:QNG300
|
4.5
|
20.3
|
1.0
|
N15
|
E:QNG300
|
4.6
|
22.6
|
1.0
|
CA
|
E:LYS70
|
4.6
|
20.2
|
1.0
|
S48
|
E:QNG300
|
4.6
|
29.3
|
1.0
|
CB
|
E:LYS70
|
4.7
|
25.4
|
1.0
|
C
|
E:LYS70
|
4.7
|
23.5
|
1.0
|
CB
|
E:ALA105
|
4.7
|
22.4
|
1.0
|
CE
|
E:LYS70
|
4.8
|
27.4
|
1.0
|
CD1
|
E:ILE73
|
4.8
|
21.7
|
1.0
|
CG2
|
E:THR107
|
4.8
|
26.8
|
1.0
|
CG
|
E:LYS70
|
4.8
|
31.0
|
1.0
|
C
|
E:ILE73
|
4.9
|
24.6
|
1.0
|
N14
|
E:QNG300
|
4.9
|
24.2
|
1.0
|
CB
|
E:ASN74
|
4.9
|
28.0
|
1.0
|
CA
|
E:ASN74
|
4.9
|
27.6
|
1.0
|
O50
|
E:QNG300
|
4.9
|
31.5
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 6v2f
Go back to
Chlorine Binding Sites List in 6v2f
Chlorine binding site 6 out
of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl300
b:29.0
occ:1.00
|
CL47
|
F:QNG300
|
0.0
|
29.0
|
1.0
|
C10
|
F:QNG300
|
1.7
|
23.8
|
1.0
|
C09
|
F:QNG300
|
2.7
|
22.2
|
1.0
|
C11
|
F:QNG300
|
2.7
|
22.7
|
1.0
|
N17
|
F:QNG300
|
3.1
|
24.2
|
1.0
|
C16
|
F:QNG300
|
3.3
|
24.8
|
1.0
|
CG2
|
F:ILE73
|
3.5
|
20.4
|
1.0
|
OD1
|
F:ASN74
|
3.7
|
35.1
|
1.0
|
ND2
|
F:ASN74
|
3.8
|
31.4
|
1.0
|
CG
|
F:ASN74
|
3.9
|
27.5
|
1.0
|
O
|
F:LYS70
|
4.0
|
22.4
|
1.0
|
C12
|
F:QNG300
|
4.0
|
21.7
|
1.0
|
C08
|
F:QNG300
|
4.0
|
24.3
|
1.0
|
CB
|
F:ILE73
|
4.0
|
20.6
|
1.0
|
N
|
F:ASN74
|
4.5
|
20.5
|
1.0
|
C07
|
F:QNG300
|
4.5
|
21.4
|
1.0
|
N15
|
F:QNG300
|
4.6
|
23.0
|
1.0
|
CG
|
F:LYS70
|
4.6
|
31.4
|
1.0
|
CA
|
F:LYS70
|
4.6
|
20.6
|
1.0
|
S48
|
F:QNG300
|
4.7
|
27.0
|
1.0
|
C
|
F:LYS70
|
4.7
|
23.7
|
1.0
|
CB
|
F:ALA105
|
4.7
|
20.8
|
1.0
|
CB
|
F:LYS70
|
4.8
|
25.6
|
1.0
|
CD1
|
F:ILE73
|
4.8
|
22.8
|
1.0
|
CE
|
F:LYS70
|
4.8
|
27.8
|
1.0
|
C
|
F:ILE73
|
4.8
|
22.8
|
1.0
|
CG2
|
F:THR107
|
4.8
|
26.3
|
1.0
|
N14
|
F:QNG300
|
4.9
|
22.9
|
1.0
|
CB
|
F:ASN74
|
4.9
|
26.8
|
1.0
|
CA
|
F:ASN74
|
4.9
|
25.0
|
1.0
|
O51
|
F:QNG300
|
4.9
|
31.9
|
1.0
|
|
Reference:
J.O.Link,
M.S.Rhee,
W.C.Tse,
J.Zheng,
J.R.Somoza,
W.Rowe,
R.Begley,
A.Chiu,
A.Mulato,
D.Hansen,
E.Singer,
L.K.Tsai,
R.A.Bam,
C.H.Chou,
E.Canales,
G.Brizgys,
J.R.Zhang,
J.Li,
M.Graupe,
P.Morganelli,
Q.Liu,
Q.Wu,
R.L.Halcomb,
R.D.Saito,
S.D.Schroeder,
S.E.Lazerwith,
S.Bondy,
D.Jin,
M.Hung,
N.Novikov,
X.Liu,
A.G.Villasenor,
C.E.Cannizzaro,
E.Y.Hu,
R.L.Anderson,
T.C.Appleby,
B.Lu,
J.Mwangi,
A.Liclican,
A.Niedziela-Majka,
G.A.Papalia,
M.H.Wong,
S.A.Leavitt,
Y.Xu,
D.Koditek,
G.J.Stepan,
H.Yu,
N.Pagratis,
S.Clancy,
S.Ahmadyar,
T.Z.Cai,
S.Sellers,
S.A.Wolckenhauer,
J.Ling,
C.Callebaut,
N.Margot,
R.R.Ram,
Y.P.Liu,
R.Hyland,
G.I.Sinclair,
P.J.Ruane,
G.E.Crofoot,
C.K.Mcdonald,
D.M.Brainard,
L.Lad,
S.Swaminathan,
W.I.Sundquist,
R.Sakowicz,
A.E.Chester,
W.E.Lee,
E.S.Daar,
S.R.Yant,
T.Cihlar.
Clinical Targeting of Hiv Capsid Protein with A Long-Acting Small Molecule. Nature V. 584 614 2020.
ISSN: ESSN 1476-4687
PubMed: 32612233
DOI: 10.1038/S41586-020-2443-1
Page generated: Mon Jul 29 16:03:41 2024
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