Fluorine in PDB 8r9u: A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp
Protein crystallography data
The structure of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp, PDB code: 8r9u
was solved by
M.Mukherjee,
A.Cleasby,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
71.34 /
1.94
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.303,
127.711,
142.684,
90,
90,
90
|
R / Rfree (%)
|
27.5 /
34
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp
(pdb code 8r9u). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp, PDB code: 8r9u:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 8r9u
Go back to
Fluorine Binding Sites List in 8r9u
Fluorine binding site 1 out
of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:31.0
occ:0.93
|
F32
|
A:YNK401
|
0.0
|
31.0
|
0.9
|
C31
|
A:YNK401
|
1.3
|
29.7
|
0.9
|
F34
|
A:YNK401
|
2.1
|
29.1
|
0.9
|
F33
|
A:YNK401
|
2.1
|
29.4
|
0.9
|
C13
|
A:YNK401
|
2.4
|
29.5
|
0.9
|
H53
|
A:YNK401
|
2.8
|
28.1
|
0.9
|
C14
|
A:YNK401
|
3.0
|
29.6
|
0.9
|
C17
|
A:YNK401
|
3.0
|
28.1
|
0.9
|
C16
|
A:YNK401
|
3.1
|
28.7
|
0.9
|
C12
|
A:YNK401
|
3.5
|
30.0
|
0.9
|
CD
|
A:LYS41
|
3.5
|
51.5
|
1.0
|
CD1
|
A:PHE91
|
3.6
|
32.4
|
1.0
|
H52
|
A:YNK401
|
3.6
|
30.0
|
0.9
|
N18
|
A:YNK401
|
4.0
|
28.3
|
0.9
|
O
|
A:HOH510
|
4.1
|
20.0
|
1.0
|
CG1
|
A:VAL26
|
4.1
|
44.7
|
1.0
|
CE1
|
A:PHE91
|
4.1
|
33.2
|
1.0
|
C26
|
A:YNK401
|
4.2
|
28.6
|
0.9
|
NZ
|
A:LYS41
|
4.2
|
55.8
|
1.0
|
CB
|
A:ALA39
|
4.2
|
39.2
|
1.0
|
CE
|
A:LYS41
|
4.2
|
54.1
|
1.0
|
N15
|
A:YNK401
|
4.3
|
29.3
|
0.9
|
CG
|
A:PHE91
|
4.3
|
32.6
|
1.0
|
H38
|
A:YNK401
|
4.5
|
28.3
|
0.9
|
CB
|
A:PHE91
|
4.5
|
33.1
|
1.0
|
C19
|
A:YNK401
|
4.6
|
28.9
|
0.9
|
N11
|
A:YNK401
|
4.6
|
29.8
|
0.9
|
CG
|
A:LYS41
|
4.8
|
47.3
|
1.0
|
C10
|
A:YNK401
|
4.9
|
29.1
|
0.9
|
O
|
A:ALA39
|
4.9
|
39.0
|
1.0
|
CB
|
A:LYS41
|
5.0
|
42.5
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 8r9u
Go back to
Fluorine Binding Sites List in 8r9u
Fluorine binding site 2 out
of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:29.4
occ:0.93
|
F33
|
A:YNK401
|
0.0
|
29.4
|
0.9
|
C31
|
A:YNK401
|
1.3
|
29.7
|
0.9
|
F34
|
A:YNK401
|
2.1
|
29.1
|
0.9
|
F32
|
A:YNK401
|
2.1
|
31.0
|
0.9
|
H52
|
A:YNK401
|
2.3
|
30.0
|
0.9
|
C13
|
A:YNK401
|
2.4
|
29.5
|
0.9
|
C12
|
A:YNK401
|
2.7
|
30.0
|
0.9
|
CB
|
A:PHE91
|
3.0
|
33.1
|
1.0
|
CG
|
A:PHE91
|
3.3
|
32.6
|
1.0
|
CD1
|
A:PHE91
|
3.4
|
32.4
|
1.0
|
O
|
A:ASP92
|
3.6
|
31.4
|
1.0
|
CD1
|
A:ILE75
|
3.7
|
20.4
|
0.5
|
C14
|
A:YNK401
|
3.7
|
29.6
|
0.9
|
CG1
|
A:ILE75
|
3.9
|
20.5
|
0.5
|
H53
|
A:YNK401
|
3.9
|
28.1
|
0.9
|
CB
|
A:ALA39
|
4.0
|
39.2
|
1.0
|
N11
|
A:YNK401
|
4.0
|
29.8
|
0.9
|
CD2
|
A:PHE91
|
4.3
|
32.9
|
1.0
|
CE1
|
A:PHE91
|
4.4
|
33.2
|
1.0
|
CA
|
A:PHE91
|
4.4
|
34.0
|
1.0
|
CD1
|
A:ILE75
|
4.4
|
26.1
|
0.5
|
O
|
A:HOH510
|
4.4
|
20.0
|
1.0
|
C16
|
A:YNK401
|
4.4
|
28.7
|
0.9
|
C17
|
A:YNK401
|
4.4
|
28.1
|
0.9
|
CG2
|
A:ILE75
|
4.5
|
23.3
|
0.5
|
C
|
A:PHE91
|
4.6
|
34.4
|
1.0
|
N15
|
A:YNK401
|
4.7
|
29.3
|
0.9
|
CD1
|
A:LEU144
|
4.8
|
26.9
|
1.0
|
C10
|
A:YNK401
|
4.8
|
29.1
|
0.9
|
C
|
A:ASP92
|
4.8
|
31.3
|
1.0
|
O
|
A:ALA39
|
4.8
|
39.0
|
1.0
|
N
|
A:PHE91
|
4.9
|
35.6
|
1.0
|
O
|
A:PHE91
|
5.0
|
35.3
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 8r9u
Go back to
Fluorine Binding Sites List in 8r9u
Fluorine binding site 3 out
of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:29.1
occ:0.93
|
F34
|
A:YNK401
|
0.0
|
29.1
|
0.9
|
C31
|
A:YNK401
|
1.3
|
29.7
|
0.9
|
H53
|
A:YNK401
|
2.0
|
28.1
|
0.9
|
F33
|
A:YNK401
|
2.1
|
29.4
|
0.9
|
F32
|
A:YNK401
|
2.1
|
31.0
|
0.9
|
C13
|
A:YNK401
|
2.4
|
29.5
|
0.9
|
C17
|
A:YNK401
|
2.8
|
28.1
|
0.9
|
C14
|
A:YNK401
|
3.1
|
29.6
|
0.9
|
O
|
A:HOH510
|
3.3
|
20.0
|
1.0
|
C16
|
A:YNK401
|
3.3
|
28.7
|
0.9
|
C12
|
A:YNK401
|
3.3
|
30.0
|
0.9
|
H52
|
A:YNK401
|
3.5
|
30.0
|
0.9
|
CD1
|
A:LEU144
|
3.8
|
26.9
|
1.0
|
CB
|
A:ALA154
|
3.8
|
21.3
|
1.0
|
CD1
|
A:ILE75
|
4.0
|
26.1
|
0.5
|
N18
|
A:YNK401
|
4.0
|
28.3
|
0.9
|
NZ
|
A:LYS41
|
4.2
|
55.8
|
1.0
|
N15
|
A:YNK401
|
4.3
|
29.3
|
0.9
|
H38
|
A:YNK401
|
4.3
|
28.3
|
0.9
|
OD1
|
A:ASP155
|
4.4
|
36.2
|
1.0
|
CD1
|
A:ILE75
|
4.4
|
20.4
|
0.5
|
CD1
|
A:PHE91
|
4.5
|
32.4
|
1.0
|
N11
|
A:YNK401
|
4.5
|
29.8
|
0.9
|
CG1
|
A:ILE75
|
4.5
|
20.5
|
0.5
|
C26
|
A:YNK401
|
4.6
|
28.6
|
0.9
|
CG
|
A:PHE91
|
4.6
|
32.6
|
1.0
|
CG2
|
A:ILE75
|
4.7
|
23.3
|
0.5
|
CD
|
A:LYS41
|
4.8
|
51.5
|
1.0
|
CB
|
A:PHE91
|
4.8
|
33.1
|
1.0
|
C10
|
A:YNK401
|
4.8
|
29.1
|
0.9
|
CE1
|
A:PHE91
|
4.9
|
33.2
|
1.0
|
CE
|
A:LYS41
|
4.9
|
54.1
|
1.0
|
C19
|
A:YNK401
|
4.9
|
28.9
|
0.9
|
N
|
A:ASP155
|
5.0
|
26.2
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 8r9u
Go back to
Fluorine Binding Sites List in 8r9u
Fluorine binding site 4 out
of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:26.8
occ:0.84
|
F32
|
B:YNK401
|
0.0
|
26.8
|
0.8
|
C31
|
B:YNK401
|
1.3
|
27.9
|
0.8
|
F34
|
B:YNK401
|
2.1
|
28.8
|
0.8
|
F33
|
B:YNK401
|
2.1
|
26.6
|
0.8
|
H52
|
B:YNK401
|
2.3
|
30.1
|
0.8
|
C13
|
B:YNK401
|
2.4
|
29.2
|
0.8
|
C12
|
B:YNK401
|
2.7
|
30.1
|
0.8
|
O
|
B:ASP92
|
2.8
|
42.7
|
1.0
|
CB
|
B:PHE91
|
2.9
|
40.9
|
1.0
|
CD1
|
B:ILE75
|
3.4
|
23.4
|
0.5
|
CG
|
B:PHE91
|
3.5
|
40.7
|
1.0
|
CG1
|
B:ILE75
|
3.7
|
22.8
|
0.5
|
C14
|
B:YNK401
|
3.7
|
29.3
|
0.8
|
CB
|
B:ALA39
|
3.8
|
52.0
|
1.0
|
CD1
|
B:PHE91
|
3.9
|
40.6
|
1.0
|
N11
|
B:YNK401
|
4.0
|
30.3
|
0.8
|
C
|
B:ASP92
|
4.0
|
41.1
|
1.0
|
H53
|
B:YNK401
|
4.1
|
29.6
|
0.8
|
C
|
B:PHE91
|
4.1
|
40.8
|
1.0
|
CA
|
B:PHE91
|
4.1
|
41.5
|
1.0
|
CD2
|
B:PHE91
|
4.3
|
41.1
|
1.0
|
N
|
B:ASP92
|
4.3
|
41.6
|
1.0
|
O
|
B:PHE91
|
4.5
|
39.4
|
1.0
|
C16
|
B:YNK401
|
4.5
|
29.4
|
0.8
|
O
|
B:ALA39
|
4.5
|
51.8
|
1.0
|
C17
|
B:YNK401
|
4.6
|
29.6
|
0.8
|
CG2
|
B:ILE75
|
4.6
|
25.7
|
0.5
|
N15
|
B:YNK401
|
4.8
|
29.7
|
0.8
|
CA
|
B:ASP92
|
4.8
|
42.4
|
1.0
|
CD1
|
B:LEU144
|
4.8
|
19.0
|
1.0
|
C10
|
B:YNK401
|
4.8
|
30.2
|
0.8
|
CG
|
B:MET94
|
4.9
|
33.0
|
1.0
|
CE1
|
B:PHE91
|
5.0
|
40.9
|
1.0
|
N
|
B:PHE91
|
5.0
|
42.5
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 8r9u
Go back to
Fluorine Binding Sites List in 8r9u
Fluorine binding site 5 out
of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:26.6
occ:0.84
|
F33
|
B:YNK401
|
0.0
|
26.6
|
0.8
|
C31
|
B:YNK401
|
1.3
|
27.9
|
0.8
|
H53
|
B:YNK401
|
2.1
|
29.6
|
0.8
|
F32
|
B:YNK401
|
2.1
|
26.8
|
0.8
|
F34
|
B:YNK401
|
2.1
|
28.8
|
0.8
|
C13
|
B:YNK401
|
2.4
|
29.2
|
0.8
|
C17
|
B:YNK401
|
2.7
|
29.6
|
0.8
|
C14
|
B:YNK401
|
3.1
|
29.3
|
0.8
|
C16
|
B:YNK401
|
3.2
|
29.4
|
0.8
|
C12
|
B:YNK401
|
3.5
|
30.1
|
0.8
|
H52
|
B:YNK401
|
3.7
|
30.1
|
0.8
|
N18
|
B:YNK401
|
3.9
|
30.2
|
0.8
|
CD1
|
B:PHE91
|
4.1
|
40.6
|
1.0
|
CG
|
B:PHE91
|
4.1
|
40.7
|
1.0
|
CG1
|
B:ILE75
|
4.2
|
22.8
|
0.5
|
CB
|
B:PHE91
|
4.2
|
40.9
|
1.0
|
CD1
|
B:LEU144
|
4.3
|
19.0
|
1.0
|
H38
|
B:YNK401
|
4.3
|
30.2
|
0.8
|
N15
|
B:YNK401
|
4.3
|
29.7
|
0.8
|
CB
|
B:ALA154
|
4.4
|
31.6
|
1.0
|
CD1
|
B:ILE75
|
4.4
|
29.0
|
0.5
|
CD1
|
B:ILE75
|
4.4
|
23.4
|
0.5
|
C26
|
B:YNK401
|
4.5
|
29.9
|
0.8
|
CE1
|
B:PHE91
|
4.6
|
40.9
|
1.0
|
CD2
|
B:PHE91
|
4.6
|
41.1
|
1.0
|
OD1
|
B:ASP155
|
4.7
|
44.9
|
1.0
|
N11
|
B:YNK401
|
4.7
|
30.3
|
0.8
|
CG2
|
B:ILE75
|
4.8
|
25.7
|
0.5
|
C19
|
B:YNK401
|
4.8
|
30.3
|
0.8
|
O
|
B:ASP92
|
4.9
|
42.7
|
1.0
|
CB
|
B:ALA39
|
4.9
|
52.0
|
1.0
|
C10
|
B:YNK401
|
5.0
|
30.2
|
0.8
|
|
Fluorine binding site 6 out
of 6 in 8r9u
Go back to
Fluorine Binding Sites List in 8r9u
Fluorine binding site 6 out
of 6 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:28.8
occ:0.84
|
F34
|
B:YNK401
|
0.0
|
28.8
|
0.8
|
C31
|
B:YNK401
|
1.3
|
27.9
|
0.8
|
F32
|
B:YNK401
|
2.1
|
26.8
|
0.8
|
F33
|
B:YNK401
|
2.1
|
26.6
|
0.8
|
C13
|
B:YNK401
|
2.4
|
29.2
|
0.8
|
CB
|
B:ALA39
|
3.0
|
52.0
|
1.0
|
C14
|
B:YNK401
|
3.2
|
29.3
|
0.8
|
C12
|
B:YNK401
|
3.3
|
30.1
|
0.8
|
H52
|
B:YNK401
|
3.4
|
30.1
|
0.8
|
CD1
|
B:PHE91
|
3.5
|
40.6
|
1.0
|
H53
|
B:YNK401
|
3.5
|
29.6
|
0.8
|
C16
|
B:YNK401
|
3.5
|
29.4
|
0.8
|
O
|
B:ALA39
|
3.6
|
51.8
|
1.0
|
C17
|
B:YNK401
|
3.7
|
29.6
|
0.8
|
CB
|
B:PHE91
|
3.7
|
40.9
|
1.0
|
CG
|
B:PHE91
|
3.8
|
40.7
|
1.0
|
C
|
B:ALA39
|
4.2
|
51.4
|
1.0
|
CA
|
B:ALA39
|
4.2
|
52.0
|
1.0
|
CE1
|
B:PHE91
|
4.3
|
40.9
|
1.0
|
N15
|
B:YNK401
|
4.4
|
29.7
|
0.8
|
O
|
B:ASP92
|
4.4
|
42.7
|
1.0
|
N11
|
B:YNK401
|
4.5
|
30.3
|
0.8
|
C26
|
B:YNK401
|
4.5
|
29.9
|
0.8
|
CG1
|
B:VAL26
|
4.6
|
58.8
|
1.0
|
N18
|
B:YNK401
|
4.7
|
30.2
|
0.8
|
CD
|
B:LYS41
|
4.9
|
53.4
|
1.0
|
CD2
|
B:PHE91
|
4.9
|
41.1
|
1.0
|
C10
|
B:YNK401
|
4.9
|
30.2
|
0.8
|
CA
|
B:PHE91
|
4.9
|
41.5
|
1.0
|
CB
|
B:LYS41
|
4.9
|
50.4
|
1.0
|
|
Reference:
M.Mukherjee,
P.Day,
D.Laverty,
J.A.Bueren-Calabuig,
A.Woodhead,
C.Griffiths-Jones,
S.Hiscock,
C.East,
S.Boyd,
M.O'reilly.
Protein Engineering Enables A Soakable Crystal Form of Human CDK7 Primed For High-Throughput Crystallography and Structure-Based Drug Design To Be Published.
Page generated: Fri Aug 2 22:39:11 2024
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