Fluorine in PDB 9bhp: Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977
Enzymatic activity of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977
All present enzymatic activity of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977:
3.6.5.2;
5.2.1.8;
Protein crystallography data
The structure of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977, PDB code: 9bhp
was solved by
Y.Pourfarjam,
Y.Goldgur,
A.Cuevas-Navarro,
P.Lito,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.81 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.456,
82.648,
127.829,
90,
90,
90
|
R / Rfree (%)
|
21 /
25.3
|
Other elements in 9bhp:
The structure of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977
(pdb code 9bhp). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977, PDB code: 9bhp:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 9bhp
Go back to
Fluorine Binding Sites List in 9bhp
Fluorine binding site 1 out
of 6 in the Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977
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 Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F201
b:28.8
occ:1.00
|
F1
|
A:AF3201
|
0.0
|
28.8
|
1.0
|
AL
|
A:AF3201
|
1.8
|
28.9
|
1.0
|
O
|
A:HOH342
|
2.5
|
24.9
|
1.0
|
OH
|
A:TYR32
|
2.6
|
33.1
|
1.0
|
SG
|
A:CYS12
|
2.6
|
46.6
|
1.0
|
O3B
|
A:GDP202
|
2.9
|
25.0
|
1.0
|
F2
|
A:AF3201
|
3.0
|
26.3
|
1.0
|
F3
|
A:AF3201
|
3.0
|
26.0
|
1.0
|
NE2
|
A:GLN61
|
3.5
|
32.4
|
1.0
|
CZ
|
A:TYR32
|
3.5
|
33.5
|
1.0
|
CE2
|
A:TYR32
|
3.6
|
28.4
|
1.0
|
CB
|
A:PRO34
|
3.6
|
28.3
|
1.0
|
CA
|
A:PRO34
|
3.8
|
28.2
|
1.0
|
CB
|
A:CYS12
|
3.9
|
28.5
|
1.0
|
OE1
|
A:GLN61
|
4.0
|
29.7
|
1.0
|
N
|
A:GLY13
|
4.0
|
27.9
|
1.0
|
CA
|
A:CYS12
|
4.1
|
27.8
|
1.0
|
CD
|
A:GLN61
|
4.2
|
30.3
|
1.0
|
N
|
A:THR35
|
4.3
|
25.4
|
1.0
|
PB
|
A:GDP202
|
4.4
|
25.5
|
1.0
|
C
|
A:PRO34
|
4.5
|
26.2
|
1.0
|
C
|
A:CYS12
|
4.5
|
28.6
|
1.0
|
CE1
|
A:TYR32
|
4.8
|
30.5
|
1.0
|
O
|
A:HOH313
|
4.8
|
24.7
|
1.0
|
MG
|
A:MG203
|
4.8
|
22.8
|
1.0
|
CA
|
A:GLY13
|
4.9
|
25.4
|
1.0
|
O1B
|
A:GDP202
|
4.9
|
22.3
|
1.0
|
CD2
|
A:TYR32
|
5.0
|
30.4
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 9bhp
Go back to
Fluorine Binding Sites List in 9bhp
Fluorine binding site 2 out
of 6 in the Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977
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 Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F201
b:26.3
occ:1.00
|
F2
|
A:AF3201
|
0.0
|
26.3
|
1.0
|
AL
|
A:AF3201
|
1.8
|
28.9
|
1.0
|
MG
|
A:MG203
|
1.9
|
22.8
|
1.0
|
O3B
|
A:GDP202
|
2.6
|
25.0
|
1.0
|
O
|
A:HOH313
|
2.8
|
24.7
|
1.0
|
N
|
A:THR35
|
2.8
|
25.4
|
1.0
|
O
|
A:HOH342
|
2.8
|
24.9
|
1.0
|
O1B
|
A:GDP202
|
2.9
|
22.3
|
1.0
|
F1
|
A:AF3201
|
3.0
|
28.8
|
1.0
|
OG1
|
A:THR35
|
3.0
|
25.9
|
1.0
|
O
|
A:HOH307
|
3.0
|
25.1
|
1.0
|
F3
|
A:AF3201
|
3.1
|
26.0
|
1.0
|
CB
|
A:THR35
|
3.2
|
25.4
|
1.0
|
PB
|
A:GDP202
|
3.3
|
25.5
|
1.0
|
CA
|
A:THR35
|
3.6
|
25.3
|
1.0
|
C
|
A:PRO34
|
3.8
|
26.2
|
1.0
|
CA
|
A:PRO34
|
3.8
|
28.2
|
1.0
|
OG
|
A:SER17
|
3.9
|
23.8
|
1.0
|
O
|
A:THR58
|
4.3
|
24.3
|
1.0
|
O
|
A:THR35
|
4.3
|
23.8
|
1.0
|
O2B
|
A:GDP202
|
4.4
|
21.8
|
1.0
|
C
|
A:THR35
|
4.5
|
25.1
|
1.0
|
O3A
|
A:GDP202
|
4.5
|
25.7
|
1.0
|
O
|
A:ASP33
|
4.5
|
26.9
|
1.0
|
NZ
|
A:LYS16
|
4.5
|
24.3
|
1.0
|
O2A
|
A:GDP202
|
4.6
|
24.9
|
1.0
|
CG2
|
A:THR35
|
4.6
|
25.0
|
1.0
|
CB
|
A:PRO34
|
4.7
|
28.3
|
1.0
|
CE
|
A:LYS16
|
4.8
|
26.4
|
1.0
|
CE2
|
A:TYR32
|
4.9
|
28.4
|
1.0
|
CB
|
A:SER17
|
4.9
|
23.6
|
1.0
|
O
|
A:PRO34
|
5.0
|
26.1
|
1.0
|
N
|
A:PRO34
|
5.0
|
27.8
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 9bhp
Go back to
Fluorine Binding Sites List in 9bhp
Fluorine binding site 3 out
of 6 in the Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977
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 Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F201
b:26.0
occ:1.00
|
F3
|
A:AF3201
|
0.0
|
26.0
|
1.0
|
AL
|
A:AF3201
|
1.8
|
28.9
|
1.0
|
N
|
A:GLY60
|
2.7
|
28.0
|
1.0
|
NZ
|
A:LYS16
|
2.7
|
24.3
|
1.0
|
O
|
A:HOH342
|
2.9
|
24.9
|
1.0
|
O3B
|
A:GDP202
|
2.9
|
25.0
|
1.0
|
F1
|
A:AF3201
|
3.0
|
28.8
|
1.0
|
F2
|
A:AF3201
|
3.1
|
26.3
|
1.0
|
CA
|
A:GLY60
|
3.3
|
27.8
|
1.0
|
CE
|
A:LYS16
|
3.4
|
26.4
|
1.0
|
CA
|
A:CYS12
|
3.6
|
27.8
|
1.0
|
C
|
A:ALA59
|
3.7
|
28.0
|
1.0
|
CA
|
A:ALA59
|
3.8
|
26.1
|
1.0
|
O
|
A:THR58
|
3.9
|
24.3
|
1.0
|
PB
|
A:GDP202
|
4.0
|
25.5
|
1.0
|
O2B
|
A:GDP202
|
4.2
|
21.8
|
1.0
|
CB
|
A:CYS12
|
4.2
|
28.5
|
1.0
|
OE1
|
A:GLN61
|
4.2
|
29.7
|
1.0
|
SG
|
A:CYS12
|
4.2
|
46.6
|
1.0
|
O
|
A:HOH307
|
4.2
|
25.1
|
1.0
|
N
|
A:CYS12
|
4.3
|
27.0
|
1.0
|
O
|
A:ALA11
|
4.3
|
27.5
|
1.0
|
N
|
A:GLY13
|
4.3
|
27.9
|
1.0
|
C
|
A:GLY60
|
4.3
|
30.4
|
1.0
|
O1B
|
A:GDP202
|
4.4
|
22.3
|
1.0
|
MG
|
A:MG203
|
4.5
|
22.8
|
1.0
|
N
|
A:GLN61
|
4.5
|
30.1
|
1.0
|
C
|
A:CYS12
|
4.6
|
28.6
|
1.0
|
C
|
A:ALA11
|
4.6
|
28.4
|
1.0
|
O
|
A:GLY10
|
4.7
|
26.7
|
1.0
|
C
|
A:THR58
|
4.7
|
26.9
|
1.0
|
N
|
A:ALA59
|
4.7
|
24.8
|
1.0
|
O
|
A:ALA59
|
4.8
|
27.6
|
1.0
|
CD
|
A:LYS16
|
4.8
|
27.4
|
1.0
|
CB
|
A:ALA59
|
4.9
|
25.6
|
1.0
|
CD
|
A:GLN61
|
4.9
|
30.3
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 9bhp
Go back to
Fluorine Binding Sites List in 9bhp
Fluorine binding site 4 out
of 6 in the Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F201
b:56.9
occ:1.00
|
F1
|
C:AF3201
|
0.0
|
56.9
|
1.0
|
AL
|
C:AF3201
|
1.8
|
56.5
|
1.0
|
O
|
C:HOH328
|
2.4
|
50.0
|
1.0
|
N
|
C:GLY60
|
2.7
|
55.1
|
1.0
|
NZ
|
C:LYS16
|
2.9
|
59.8
|
1.0
|
F2
|
C:AF3201
|
3.0
|
57.4
|
1.0
|
O2B
|
C:GDP202
|
3.0
|
56.2
|
1.0
|
F3
|
C:AF3201
|
3.0
|
49.8
|
1.0
|
CA
|
C:ALA59
|
3.5
|
49.6
|
1.0
|
C
|
C:ALA59
|
3.6
|
52.8
|
1.0
|
CA
|
C:GLY60
|
3.6
|
59.9
|
1.0
|
CE
|
C:LYS16
|
3.6
|
55.1
|
1.0
|
CA
|
C:CYS12
|
3.7
|
70.6
|
1.0
|
O1B
|
C:GDP202
|
3.8
|
57.4
|
1.0
|
PB
|
C:GDP202
|
3.9
|
55.3
|
1.0
|
OE1
|
C:GLN61
|
4.0
|
53.1
|
1.0
|
O
|
C:THR58
|
4.0
|
48.3
|
1.0
|
SG
|
C:CYS12
|
4.1
|
71.0
|
1.0
|
CB
|
C:CYS12
|
4.1
|
70.4
|
1.0
|
O3B
|
C:GDP202
|
4.2
|
52.0
|
1.0
|
O
|
C:ALA11
|
4.3
|
66.6
|
1.0
|
O
|
C:HOH308
|
4.4
|
46.1
|
1.0
|
CB
|
C:ALA59
|
4.4
|
48.0
|
1.0
|
N
|
C:CYS12
|
4.4
|
72.7
|
1.0
|
C
|
C:GLY60
|
4.4
|
59.8
|
1.0
|
N
|
C:GLY13
|
4.5
|
65.5
|
1.0
|
MG
|
C:MG203
|
4.5
|
47.6
|
1.0
|
C
|
C:ALA11
|
4.6
|
69.5
|
1.0
|
N
|
C:GLN61
|
4.6
|
58.8
|
1.0
|
N
|
C:ALA59
|
4.6
|
47.9
|
1.0
|
NE2
|
C:GLN61
|
4.6
|
55.0
|
1.0
|
CD
|
C:GLN61
|
4.6
|
54.8
|
1.0
|
C
|
C:CYS12
|
4.7
|
72.1
|
1.0
|
C
|
C:THR58
|
4.7
|
47.4
|
1.0
|
O
|
C:ALA59
|
4.7
|
53.1
|
1.0
|
O
|
C:GLY10
|
4.9
|
64.5
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 9bhp
Go back to
Fluorine Binding Sites List in 9bhp
Fluorine binding site 5 out
of 6 in the Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F201
b:57.4
occ:1.00
|
F2
|
C:AF3201
|
0.0
|
57.4
|
1.0
|
AL
|
C:AF3201
|
1.8
|
56.5
|
1.0
|
OH
|
C:TYR32
|
2.4
|
62.4
|
1.0
|
O
|
C:HOH328
|
2.4
|
50.0
|
1.0
|
O2B
|
C:GDP202
|
2.6
|
56.2
|
1.0
|
F1
|
C:AF3201
|
3.0
|
56.9
|
1.0
|
F3
|
C:AF3201
|
3.1
|
49.8
|
1.0
|
CZ
|
C:TYR32
|
3.4
|
60.9
|
1.0
|
NE2
|
C:GLN61
|
3.5
|
55.0
|
1.0
|
CE1
|
C:TYR32
|
3.5
|
57.8
|
1.0
|
CB
|
C:CYS12
|
3.6
|
70.4
|
1.0
|
N
|
C:GLY13
|
3.7
|
65.5
|
1.0
|
CB
|
C:PRO34
|
3.8
|
48.9
|
1.0
|
CA
|
C:CYS12
|
3.9
|
70.6
|
1.0
|
CA
|
C:PRO34
|
4.1
|
50.1
|
1.0
|
PB
|
C:GDP202
|
4.1
|
55.3
|
1.0
|
SG
|
C:CYS12
|
4.2
|
71.0
|
1.0
|
C
|
C:CYS12
|
4.3
|
72.1
|
1.0
|
CD
|
C:GLN61
|
4.4
|
54.8
|
1.0
|
OE1
|
C:GLN61
|
4.4
|
53.1
|
1.0
|
N
|
C:THR35
|
4.6
|
44.6
|
1.0
|
CA
|
C:GLY13
|
4.7
|
66.3
|
1.0
|
CE2
|
C:TYR32
|
4.7
|
61.0
|
1.0
|
O3B
|
C:GDP202
|
4.8
|
52.0
|
1.0
|
C
|
C:PRO34
|
4.8
|
47.1
|
1.0
|
O1B
|
C:GDP202
|
4.8
|
57.4
|
1.0
|
CD1
|
C:TYR32
|
4.9
|
59.0
|
1.0
|
O2A
|
C:GDP202
|
4.9
|
52.9
|
1.0
|
MG
|
C:MG203
|
5.0
|
47.6
|
1.0
|
O
|
C:HOH311
|
5.0
|
47.2
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 9bhp
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Fluorine Binding Sites List in 9bhp
Fluorine binding site 6 out
of 6 in the Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F201
b:49.8
occ:1.00
|
F3
|
C:AF3201
|
0.0
|
49.8
|
1.0
|
AL
|
C:AF3201
|
1.8
|
56.5
|
1.0
|
MG
|
C:MG203
|
2.0
|
47.6
|
1.0
|
O
|
C:HOH328
|
2.5
|
50.0
|
1.0
|
O2B
|
C:GDP202
|
2.5
|
56.2
|
1.0
|
O3B
|
C:GDP202
|
2.7
|
52.0
|
1.0
|
O
|
C:HOH311
|
2.8
|
47.2
|
1.0
|
N
|
C:THR35
|
2.9
|
44.6
|
1.0
|
O
|
C:HOH308
|
3.0
|
46.1
|
1.0
|
F1
|
C:AF3201
|
3.0
|
56.9
|
1.0
|
F2
|
C:AF3201
|
3.1
|
57.4
|
1.0
|
OG1
|
C:THR35
|
3.1
|
45.0
|
1.0
|
PB
|
C:GDP202
|
3.1
|
55.3
|
1.0
|
CB
|
C:THR35
|
3.3
|
42.7
|
1.0
|
CA
|
C:THR35
|
3.7
|
42.6
|
1.0
|
CA
|
C:PRO34
|
3.9
|
50.1
|
1.0
|
C
|
C:PRO34
|
3.9
|
47.1
|
1.0
|
OG
|
C:SER17
|
3.9
|
47.5
|
1.0
|
O2A
|
C:GDP202
|
4.0
|
52.9
|
1.0
|
O1B
|
C:GDP202
|
4.1
|
57.4
|
1.0
|
O
|
C:THR58
|
4.3
|
48.3
|
1.0
|
O
|
C:THR35
|
4.3
|
44.1
|
1.0
|
O3A
|
C:GDP202
|
4.4
|
56.8
|
1.0
|
C
|
C:THR35
|
4.5
|
42.0
|
1.0
|
O
|
C:ASP33
|
4.6
|
50.5
|
1.0
|
NZ
|
C:LYS16
|
4.6
|
59.8
|
1.0
|
CB
|
C:PRO34
|
4.6
|
48.9
|
1.0
|
CG2
|
C:THR35
|
4.7
|
40.2
|
1.0
|
PA
|
C:GDP202
|
4.8
|
54.9
|
1.0
|
CE1
|
C:TYR32
|
4.9
|
57.8
|
1.0
|
CE
|
C:LYS16
|
4.9
|
55.1
|
1.0
|
CA
|
C:ALA59
|
5.0
|
49.6
|
1.0
|
CB
|
C:SER17
|
5.0
|
47.4
|
1.0
|
|
Reference:
Y.Pourfarjam,
Y.Goldgur,
A.Cuevas-Navarro,
P.Lito.
Crystal Structure of Kras G12S in A Transition State Mimetic Complex with Cypa and Rmc-7977 To Be Published.
Page generated: Wed Nov 13 08:39:06 2024
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