Calcium in PDB 6p8x: Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
Protein crystallography data
The structure of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor., PDB code: 6p8x
was solved by
C.Mohr,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.86 /
2.11
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
33.327,
66.150,
78.629,
66.48,
78.75,
89.47
|
R / Rfree (%)
|
26.5 /
31.3
|
Other elements in 6p8x:
The structure of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
(pdb code 6p8x). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor., PDB code: 6p8x:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 6p8x
Go back to
Calcium Binding Sites List in 6p8x
Calcium binding site 1 out
of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:22.1
occ:1.00
|
O
|
A:HOH421
|
2.3
|
25.2
|
1.0
|
O
|
A:HOH442
|
2.3
|
21.8
|
1.0
|
O
|
A:HOH425
|
2.3
|
22.0
|
1.0
|
O
|
A:HOH413
|
2.3
|
20.5
|
1.0
|
OG
|
A:SER17
|
2.3
|
19.8
|
1.0
|
O1B
|
A:GDP304
|
2.4
|
24.8
|
1.0
|
CB
|
A:SER17
|
3.4
|
21.3
|
1.0
|
PB
|
A:GDP304
|
3.5
|
26.5
|
1.0
|
O3B
|
A:GDP304
|
3.5
|
26.4
|
1.0
|
OD2
|
A:ASP57
|
4.2
|
40.8
|
1.0
|
N
|
A:SER17
|
4.2
|
21.8
|
1.0
|
CD2
|
A:TYR32
|
4.2
|
40.8
|
1.0
|
O2A
|
A:GDP304
|
4.2
|
29.2
|
1.0
|
CA
|
A:SER17
|
4.4
|
21.6
|
1.0
|
O
|
A:ASP33
|
4.4
|
30.2
|
1.0
|
O3A
|
A:GDP304
|
4.5
|
27.6
|
1.0
|
O2B
|
A:GDP304
|
4.5
|
24.5
|
1.0
|
CA
|
A:PRO34
|
4.5
|
31.5
|
1.0
|
CE2
|
A:TYR32
|
4.6
|
43.4
|
1.0
|
O
|
A:PRO34
|
4.6
|
26.8
|
1.0
|
O
|
A:ILE36
|
4.6
|
29.3
|
1.0
|
O
|
A:THR58
|
4.7
|
29.3
|
1.0
|
OD1
|
A:ASP57
|
4.7
|
36.9
|
1.0
|
PA
|
A:GDP304
|
4.7
|
28.4
|
1.0
|
CG
|
A:ASP57
|
4.8
|
37.7
|
1.0
|
CE
|
A:LYS16
|
4.8
|
21.7
|
1.0
|
O1A
|
A:GDP304
|
4.8
|
29.1
|
1.0
|
C
|
A:PRO34
|
4.8
|
30.8
|
1.0
|
CB
|
A:ALA59
|
4.8
|
30.4
|
1.0
|
O04
|
A:O5V305
|
4.9
|
22.2
|
1.0
|
CB
|
A:LYS16
|
4.9
|
21.2
|
1.0
|
|
Calcium binding site 2 out
of 10 in 6p8x
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Calcium Binding Sites List in 6p8x
Calcium binding site 2 out
of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:30.6
occ:1.00
|
OE1
|
A:GLU63
|
2.7
|
30.5
|
1.0
|
OE2
|
A:GLU63
|
2.7
|
33.1
|
1.0
|
CD
|
A:GLU63
|
3.0
|
33.4
|
1.0
|
CG
|
A:GLU63
|
4.5
|
35.7
|
1.0
|
O
|
A:HOH433
|
4.9
|
27.9
|
1.0
|
OE1
|
A:GLN61
|
4.9
|
32.3
|
1.0
|
|
Calcium binding site 3 out
of 10 in 6p8x
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Calcium Binding Sites List in 6p8x
Calcium binding site 3 out
of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca303
b:40.1
occ:1.00
|
O
|
A:HOH445
|
2.3
|
37.1
|
1.0
|
OD1
|
A:ASP105
|
2.3
|
30.4
|
1.0
|
OD2
|
A:ASP105
|
2.3
|
31.4
|
1.0
|
O
|
A:HOH428
|
2.3
|
35.8
|
1.0
|
CG
|
A:ASP105
|
2.7
|
29.5
|
1.0
|
CB
|
A:ASP105
|
4.2
|
28.4
|
1.0
|
O
|
A:ASP105
|
4.3
|
23.4
|
1.0
|
C
|
A:ASP105
|
4.8
|
25.8
|
1.0
|
CA
|
A:ASP105
|
4.9
|
27.2
|
1.0
|
|
Calcium binding site 4 out
of 10 in 6p8x
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Calcium Binding Sites List in 6p8x
Calcium binding site 4 out
of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:23.2
occ:1.00
|
OG
|
B:SER17
|
2.3
|
22.4
|
1.0
|
O
|
B:HOH413
|
2.3
|
20.1
|
1.0
|
O
|
B:HOH429
|
2.3
|
23.6
|
1.0
|
O
|
B:HOH412
|
2.3
|
22.4
|
1.0
|
O
|
B:HOH410
|
2.3
|
27.2
|
1.0
|
O1B
|
B:GDP304
|
2.4
|
24.9
|
1.0
|
CB
|
B:SER17
|
3.3
|
23.6
|
1.0
|
PB
|
B:GDP304
|
3.5
|
25.9
|
1.0
|
O3B
|
B:GDP304
|
3.6
|
24.6
|
1.0
|
O2A
|
B:GDP304
|
4.1
|
22.1
|
1.0
|
N
|
B:SER17
|
4.1
|
22.7
|
1.0
|
OD2
|
B:ASP57
|
4.3
|
37.2
|
1.0
|
CA
|
B:SER17
|
4.3
|
22.8
|
1.0
|
OD1
|
B:ASP57
|
4.3
|
33.2
|
1.0
|
CD2
|
B:TYR32
|
4.5
|
40.5
|
1.0
|
O3A
|
B:GDP304
|
4.5
|
25.4
|
1.0
|
O
|
B:ILE36
|
4.5
|
39.1
|
1.0
|
O
|
B:ASP33
|
4.6
|
29.8
|
1.0
|
O2B
|
B:GDP304
|
4.6
|
24.2
|
1.0
|
PA
|
B:GDP304
|
4.6
|
25.6
|
1.0
|
CA
|
B:PRO34
|
4.6
|
30.7
|
1.0
|
O
|
B:PRO34
|
4.7
|
25.2
|
1.0
|
O1A
|
B:GDP304
|
4.7
|
24.6
|
1.0
|
CG
|
B:ASP57
|
4.7
|
33.9
|
1.0
|
O
|
B:THR58
|
4.7
|
31.0
|
1.0
|
O04
|
B:O5V305
|
4.8
|
37.3
|
1.0
|
CB
|
B:ALA59
|
4.9
|
33.9
|
1.0
|
CE
|
B:LYS16
|
4.9
|
20.1
|
1.0
|
CB
|
B:LYS16
|
4.9
|
21.0
|
1.0
|
C
|
B:PRO34
|
4.9
|
28.8
|
1.0
|
|
Calcium binding site 5 out
of 10 in 6p8x
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Calcium Binding Sites List in 6p8x
Calcium binding site 5 out
of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca302
b:26.4
occ:1.00
|
OE1
|
B:GLU63
|
2.3
|
27.6
|
1.0
|
OE2
|
B:GLU63
|
2.4
|
32.1
|
1.0
|
CD
|
B:GLU63
|
2.7
|
33.6
|
1.0
|
CG
|
B:GLU63
|
4.3
|
36.1
|
1.0
|
O
|
B:HOH427
|
4.9
|
21.5
|
1.0
|
|
Calcium binding site 6 out
of 10 in 6p8x
Go back to
Calcium Binding Sites List in 6p8x
Calcium binding site 6 out
of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca303
b:37.7
occ:1.00
|
OD1
|
B:ASP105
|
2.3
|
26.2
|
1.0
|
O
|
B:HOH411
|
2.3
|
32.9
|
1.0
|
OD2
|
B:ASP105
|
2.5
|
27.9
|
1.0
|
CG
|
B:ASP105
|
2.7
|
26.4
|
1.0
|
CB
|
B:ASP105
|
4.2
|
25.8
|
1.0
|
O
|
B:ASP105
|
4.3
|
22.0
|
1.0
|
CA
|
B:ASP105
|
4.8
|
26.8
|
1.0
|
C
|
B:ASP105
|
4.9
|
25.6
|
1.0
|
|
Calcium binding site 7 out
of 10 in 6p8x
Go back to
Calcium Binding Sites List in 6p8x
Calcium binding site 7 out
of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca301
b:26.4
occ:1.00
|
O1B
|
C:GDP303
|
2.3
|
21.7
|
1.0
|
O
|
C:HOH413
|
2.3
|
23.0
|
1.0
|
OG
|
C:SER17
|
2.3
|
18.9
|
1.0
|
O
|
C:HOH417
|
2.3
|
25.2
|
1.0
|
O
|
C:HOH408
|
2.3
|
21.2
|
1.0
|
O
|
C:HOH437
|
2.3
|
26.0
|
1.0
|
CB
|
C:SER17
|
3.3
|
19.6
|
1.0
|
PB
|
C:GDP303
|
3.5
|
22.2
|
1.0
|
O3B
|
C:GDP303
|
3.7
|
21.7
|
1.0
|
N
|
C:SER17
|
4.1
|
19.0
|
1.0
|
O2A
|
C:GDP303
|
4.2
|
23.2
|
1.0
|
CA
|
C:SER17
|
4.3
|
19.2
|
1.0
|
OD2
|
C:ASP57
|
4.4
|
42.9
|
1.0
|
O3A
|
C:GDP303
|
4.5
|
22.9
|
1.0
|
CA
|
C:PRO34
|
4.5
|
36.8
|
1.0
|
O2B
|
C:GDP303
|
4.5
|
20.3
|
1.0
|
O
|
C:ASP33
|
4.5
|
30.6
|
1.0
|
O
|
C:PRO34
|
4.6
|
38.0
|
1.0
|
OD1
|
C:ASP57
|
4.6
|
42.1
|
1.0
|
CD2
|
C:TYR32
|
4.6
|
36.0
|
1.0
|
O
|
C:ILE36
|
4.6
|
34.5
|
1.0
|
PA
|
C:GDP303
|
4.7
|
25.0
|
1.0
|
O1A
|
C:GDP303
|
4.8
|
23.1
|
1.0
|
O
|
C:THR58
|
4.8
|
31.7
|
1.0
|
C
|
C:PRO34
|
4.8
|
37.0
|
1.0
|
CB
|
C:ALA59
|
4.9
|
32.9
|
1.0
|
CG
|
C:ASP57
|
4.9
|
38.8
|
1.0
|
CE
|
C:LYS16
|
4.9
|
23.3
|
1.0
|
CB
|
C:LYS16
|
5.0
|
21.4
|
1.0
|
O
|
C:TYR32
|
5.0
|
36.6
|
1.0
|
|
Calcium binding site 8 out
of 10 in 6p8x
Go back to
Calcium Binding Sites List in 6p8x
Calcium binding site 8 out
of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca302
b:21.5
occ:1.00
|
O
|
C:HOH427
|
2.3
|
23.6
|
1.0
|
OE2
|
C:GLU63
|
2.3
|
22.5
|
1.0
|
O
|
C:HOH432
|
2.3
|
19.2
|
1.0
|
OE1
|
C:GLU63
|
2.3
|
20.1
|
1.0
|
O
|
C:HOH407
|
2.3
|
23.7
|
1.0
|
CD
|
C:GLU63
|
2.7
|
24.7
|
1.0
|
CG
|
C:GLU63
|
4.2
|
26.7
|
1.0
|
OE1
|
C:GLN61
|
4.3
|
32.3
|
1.0
|
CB
|
C:GLN61
|
4.7
|
30.9
|
1.0
|
CG
|
C:GLN61
|
4.7
|
31.6
|
1.0
|
CD
|
C:GLN61
|
4.9
|
31.6
|
1.0
|
CB
|
C:GLU63
|
4.9
|
28.5
|
1.0
|
|
Calcium binding site 9 out
of 10 in 6p8x
Go back to
Calcium Binding Sites List in 6p8x
Calcium binding site 9 out
of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca301
b:21.9
occ:1.00
|
O1B
|
D:GDP303
|
2.3
|
23.4
|
1.0
|
OG
|
D:SER17
|
2.3
|
21.2
|
1.0
|
O
|
D:HOH407
|
2.3
|
21.8
|
1.0
|
O
|
D:HOH429
|
2.3
|
21.6
|
1.0
|
O
|
D:HOH423
|
2.3
|
17.7
|
1.0
|
O
|
D:HOH439
|
2.3
|
18.8
|
1.0
|
CB
|
D:SER17
|
3.4
|
20.7
|
1.0
|
PB
|
D:GDP303
|
3.5
|
24.7
|
1.0
|
O3B
|
D:GDP303
|
3.8
|
24.9
|
1.0
|
N
|
D:SER17
|
4.1
|
21.4
|
1.0
|
OD2
|
D:ASP57
|
4.2
|
37.2
|
1.0
|
CA
|
D:SER17
|
4.3
|
20.7
|
1.0
|
OD1
|
D:ASP57
|
4.4
|
39.6
|
1.0
|
O2B
|
D:GDP303
|
4.4
|
22.3
|
1.0
|
O
|
D:ILE36
|
4.5
|
38.5
|
1.0
|
O2A
|
D:GDP303
|
4.5
|
21.3
|
1.0
|
O
|
D:PRO34
|
4.6
|
42.0
|
1.0
|
O
|
D:THR58
|
4.6
|
31.2
|
1.0
|
CA
|
D:PRO34
|
4.6
|
41.6
|
1.0
|
O3A
|
D:GDP303
|
4.7
|
24.9
|
1.0
|
CG
|
D:ASP57
|
4.7
|
37.8
|
1.0
|
O
|
D:ASP33
|
4.7
|
38.1
|
1.0
|
CD2
|
D:TYR32
|
4.7
|
42.1
|
1.0
|
CE
|
D:LYS16
|
4.8
|
19.5
|
1.0
|
CB
|
D:ALA59
|
4.8
|
34.4
|
1.0
|
O04
|
D:O5V304
|
4.8
|
21.8
|
1.0
|
O1A
|
D:GDP303
|
4.9
|
22.2
|
1.0
|
CB
|
D:LYS16
|
4.9
|
20.9
|
1.0
|
C
|
D:PRO34
|
4.9
|
40.0
|
1.0
|
PA
|
D:GDP303
|
4.9
|
24.4
|
1.0
|
|
Calcium binding site 10 out
of 10 in 6p8x
Go back to
Calcium Binding Sites List in 6p8x
Calcium binding site 10 out
of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca302
b:20.5
occ:1.00
|
O
|
D:HOH447
|
2.3
|
23.5
|
1.0
|
O
|
D:HOH421
|
2.3
|
26.0
|
1.0
|
OE1
|
D:GLU63
|
2.3
|
21.6
|
1.0
|
OE2
|
D:GLU63
|
2.4
|
25.4
|
1.0
|
CD
|
D:GLU63
|
2.7
|
25.9
|
1.0
|
O
|
D:HOH451
|
4.1
|
26.6
|
1.0
|
CG
|
D:GLU63
|
4.2
|
28.1
|
1.0
|
O
|
D:HOH418
|
4.4
|
29.6
|
1.0
|
OE1
|
D:GLN61
|
4.8
|
36.0
|
1.0
|
|
Reference:
Y.Shin,
J.W.Jeong,
R.P.Wurz,
P.Achanta,
T.Arvedson,
M.D.Bartberger,
I.D.G.Campuzano,
R.Fucini,
S.K.Hansen,
J.Ingersoll,
J.S.Iwig,
J.R.Lipford,
V.Ma,
D.J.Kopecky,
J.Mccarter,
T.San Miguel,
C.Mohr,
S.Sabet,
A.Y.Saiki,
A.Sawayama,
S.Sethofer,
C.M.Tegley,
L.P.Volak,
K.Yang,
B.A.Lanman,
D.A.Erlanson,
V.J.Cee.
Discovery Ofn-(1-Acryloylazetidin-3-Yl)-2-(1H-Indol-1-Yl) Acetamides As Covalent Inhibitors of KRASG12C. Acs Med.Chem.Lett. V. 10 1302 2019.
ISSN: ISSN 1948-5875
PubMed: 31531201
DOI: 10.1021/ACSMEDCHEMLETT.9B00258
Page generated: Tue Jul 16 12:49:01 2024
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