Fluorine in PDB 8owg: Crystal Structure of D1228V C-Met Bound By Compound 2
Enzymatic activity of Crystal Structure of D1228V C-Met Bound By Compound 2
All present enzymatic activity of Crystal Structure of D1228V C-Met Bound By Compound 2:
2.7.10.1;
Protein crystallography data
The structure of Crystal Structure of D1228V C-Met Bound By Compound 2, PDB code: 8owg
was solved by
G.W.Collie,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
81.06 /
2.63
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
254.815,
46.198,
81.064,
90,
90,
90
|
R / Rfree (%)
|
28.1 /
32.9
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of D1228V C-Met Bound By Compound 2
(pdb code 8owg). 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 D1228V C-Met Bound By Compound 2, PDB code: 8owg:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 8owg
Go back to
Fluorine Binding Sites List in 8owg
Fluorine binding site 1 out
of 6 in the Crystal Structure of D1228V C-Met Bound By Compound 2
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 D1228V C-Met Bound By Compound 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1401
b:38.2
occ:1.00
|
F
|
A:W401401
|
0.0
|
38.2
|
1.0
|
C16
|
A:W401401
|
1.4
|
38.5
|
1.0
|
C17
|
A:W401401
|
2.3
|
38.7
|
1.0
|
C15
|
A:W401401
|
2.3
|
38.7
|
1.0
|
CD1
|
A:ILE1145
|
2.9
|
50.3
|
1.0
|
CA
|
A:GLY1128
|
3.4
|
40.4
|
1.0
|
CD2
|
A:LEU1142
|
3.4
|
41.9
|
1.0
|
C14
|
A:W401401
|
3.6
|
39.0
|
1.0
|
N
|
A:GLY1128
|
3.6
|
40.2
|
1.0
|
C12
|
A:W401401
|
3.6
|
38.7
|
1.0
|
CG1
|
A:ILE1145
|
3.7
|
49.1
|
1.0
|
CD1
|
A:LEU1142
|
3.9
|
42.0
|
1.0
|
C13
|
A:W401401
|
4.1
|
38.8
|
1.0
|
C
|
A:GLU1127
|
4.1
|
40.6
|
1.0
|
SD
|
A:MET1131
|
4.3
|
48.8
|
1.0
|
O
|
A:PHE1124
|
4.3
|
45.8
|
1.0
|
CG
|
A:LEU1142
|
4.3
|
41.2
|
1.0
|
CG2
|
A:VAL1155
|
4.5
|
36.9
|
1.0
|
O
|
A:GLU1127
|
4.5
|
40.6
|
1.0
|
CB
|
A:GLU1127
|
4.6
|
43.3
|
1.0
|
F1
|
A:W401401
|
4.7
|
39.3
|
1.0
|
C
|
A:GLY1128
|
4.7
|
40.6
|
1.0
|
CB
|
A:ILE1145
|
4.8
|
48.2
|
1.0
|
C9
|
A:W401401
|
4.8
|
38.4
|
1.0
|
CZ
|
A:PHE1124
|
4.8
|
47.9
|
1.0
|
CE1
|
A:PHE1124
|
4.8
|
48.1
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 8owg
Go back to
Fluorine Binding Sites List in 8owg
Fluorine binding site 2 out
of 6 in the Crystal Structure of D1228V C-Met Bound By Compound 2
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 D1228V C-Met Bound By Compound 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1401
b:39.3
occ:1.00
|
F1
|
A:W401401
|
0.0
|
39.3
|
1.0
|
C14
|
A:W401401
|
1.4
|
39.0
|
1.0
|
C15
|
A:W401401
|
2.3
|
38.7
|
1.0
|
C13
|
A:W401401
|
2.3
|
38.8
|
1.0
|
CD2
|
A:LEU1225
|
3.2
|
48.6
|
1.0
|
CD1
|
A:PHE1124
|
3.5
|
47.5
|
1.0
|
C16
|
A:W401401
|
3.6
|
38.5
|
1.0
|
C12
|
A:W401401
|
3.6
|
38.7
|
1.0
|
CG2
|
A:VAL1228
|
3.8
|
49.4
|
1.0
|
CE1
|
A:PHE1124
|
4.0
|
48.1
|
1.0
|
CB
|
A:GLU1127
|
4.0
|
43.3
|
1.0
|
C17
|
A:W401401
|
4.1
|
38.7
|
1.0
|
CG
|
A:GLU1127
|
4.1
|
47.8
|
1.0
|
CG
|
A:PHE1124
|
4.4
|
46.8
|
1.0
|
CA
|
A:PHE1124
|
4.4
|
45.8
|
1.0
|
O
|
A:PHE1124
|
4.6
|
45.8
|
1.0
|
CG
|
A:LEU1225
|
4.6
|
48.1
|
1.0
|
CB
|
A:PHE1124
|
4.7
|
45.9
|
1.0
|
F
|
A:W401401
|
4.7
|
38.2
|
1.0
|
C9
|
A:W401401
|
4.8
|
38.4
|
1.0
|
O
|
A:W401401
|
4.9
|
39.0
|
1.0
|
CB
|
A:VAL1228
|
5.0
|
48.8
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 8owg
Go back to
Fluorine Binding Sites List in 8owg
Fluorine binding site 3 out
of 6 in the Crystal Structure of D1228V C-Met Bound By Compound 2
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 D1228V C-Met Bound By Compound 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1401
b:36.3
occ:1.00
|
F
|
B:W401401
|
0.0
|
36.3
|
1.0
|
C16
|
B:W401401
|
1.4
|
36.1
|
1.0
|
C15
|
B:W401401
|
2.3
|
36.0
|
1.0
|
C17
|
B:W401401
|
2.3
|
35.7
|
1.0
|
CB
|
B:ALA1226
|
3.0
|
39.1
|
1.0
|
CD1
|
B:PHE1124
|
3.5
|
50.8
|
1.0
|
CD2
|
B:LEU1112
|
3.6
|
58.5
|
1.0
|
C14
|
B:W401401
|
3.6
|
35.8
|
1.0
|
C12
|
B:W401401
|
3.6
|
35.2
|
1.0
|
CE1
|
B:PHE1124
|
4.0
|
51.5
|
1.0
|
C13
|
B:W401401
|
4.1
|
35.2
|
1.0
|
CG
|
B:GLU1127
|
4.1
|
52.9
|
1.0
|
CB
|
B:GLU1127
|
4.2
|
47.5
|
1.0
|
CA
|
B:ALA1226
|
4.5
|
38.8
|
1.0
|
CG
|
B:PHE1124
|
4.5
|
49.9
|
1.0
|
CA
|
B:PHE1124
|
4.6
|
49.3
|
1.0
|
O
|
B:PHE1124
|
4.7
|
50.4
|
1.0
|
F1
|
B:W401401
|
4.7
|
36.1
|
1.0
|
CB
|
B:PHE1124
|
4.8
|
49.2
|
1.0
|
C9
|
B:W401401
|
4.8
|
35.0
|
1.0
|
O
|
B:W401401
|
4.9
|
35.3
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 8owg
Go back to
Fluorine Binding Sites List in 8owg
Fluorine binding site 4 out
of 6 in the Crystal Structure of D1228V C-Met Bound By Compound 2
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 D1228V C-Met Bound By Compound 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1401
b:36.1
occ:1.00
|
F1
|
B:W401401
|
0.0
|
36.1
|
1.0
|
C14
|
B:W401401
|
1.4
|
35.8
|
1.0
|
C15
|
B:W401401
|
2.3
|
36.0
|
1.0
|
C13
|
B:W401401
|
2.3
|
35.2
|
1.0
|
CD1
|
B:ILE1145
|
2.9
|
52.0
|
1.0
|
CA
|
B:GLY1128
|
3.2
|
41.6
|
1.0
|
CG1
|
B:ILE1145
|
3.5
|
50.4
|
1.0
|
CD2
|
B:LEU1142
|
3.6
|
33.3
|
1.0
|
C16
|
B:W401401
|
3.6
|
36.1
|
1.0
|
N
|
B:GLY1128
|
3.6
|
42.1
|
1.0
|
C12
|
B:W401401
|
3.6
|
35.2
|
1.0
|
O
|
B:PHE1124
|
4.1
|
50.4
|
1.0
|
CD1
|
B:LEU1142
|
4.1
|
33.7
|
1.0
|
C17
|
B:W401401
|
4.1
|
35.7
|
1.0
|
CG2
|
B:VAL1155
|
4.2
|
37.4
|
1.0
|
C
|
B:GLU1127
|
4.3
|
43.3
|
1.0
|
SD
|
B:MET1131
|
4.3
|
43.5
|
1.0
|
CG
|
B:LEU1142
|
4.5
|
33.4
|
1.0
|
C
|
B:GLY1128
|
4.5
|
40.7
|
1.0
|
O
|
B:GLU1127
|
4.6
|
43.3
|
1.0
|
CE1
|
B:PHE1124
|
4.6
|
51.5
|
1.0
|
CZ
|
B:PHE1124
|
4.6
|
51.2
|
1.0
|
F
|
B:W401401
|
4.7
|
36.3
|
1.0
|
C9
|
B:W401401
|
4.8
|
35.0
|
1.0
|
O
|
B:GLY1128
|
4.9
|
40.7
|
1.0
|
CD1
|
B:PHE1124
|
5.0
|
50.8
|
1.0
|
CB
|
B:MET1131
|
5.0
|
36.2
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 8owg
Go back to
Fluorine Binding Sites List in 8owg
Fluorine binding site 5 out
of 6 in the Crystal Structure of D1228V C-Met Bound By Compound 2
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 D1228V C-Met Bound By Compound 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1401
b:49.1
occ:1.00
|
F
|
C:W401401
|
0.0
|
49.1
|
1.0
|
C16
|
C:W401401
|
1.4
|
48.9
|
1.0
|
C17
|
C:W401401
|
2.3
|
48.7
|
1.0
|
C15
|
C:W401401
|
2.3
|
48.9
|
1.0
|
CG2
|
C:ILE1145
|
2.9
|
54.0
|
1.0
|
CA
|
C:GLY1128
|
3.3
|
49.3
|
1.0
|
N
|
C:GLY1128
|
3.3
|
50.1
|
1.0
|
CD2
|
C:LEU1142
|
3.4
|
51.6
|
1.0
|
C14
|
C:W401401
|
3.6
|
49.0
|
1.0
|
C12
|
C:W401401
|
3.6
|
48.3
|
1.0
|
C
|
C:GLU1127
|
3.9
|
51.1
|
1.0
|
O
|
C:PHE1124
|
4.1
|
55.5
|
1.0
|
C13
|
C:W401401
|
4.1
|
48.8
|
1.0
|
CB
|
C:GLU1127
|
4.2
|
53.4
|
1.0
|
CB
|
C:ILE1145
|
4.4
|
53.5
|
1.0
|
O
|
C:GLU1127
|
4.4
|
51.3
|
1.0
|
SD
|
C:MET1131
|
4.6
|
55.5
|
1.0
|
CG
|
C:LEU1142
|
4.6
|
51.2
|
1.0
|
CD1
|
C:LEU1142
|
4.7
|
51.5
|
1.0
|
CE1
|
C:PHE1124
|
4.7
|
60.4
|
1.0
|
C
|
C:GLY1128
|
4.7
|
48.5
|
1.0
|
F1
|
C:W401401
|
4.7
|
49.4
|
1.0
|
CA
|
C:GLU1127
|
4.7
|
51.4
|
1.0
|
CE
|
C:MET1131
|
4.7
|
55.1
|
1.0
|
CZ
|
C:PHE1124
|
4.8
|
60.2
|
1.0
|
CD1
|
C:ILE1145
|
4.8
|
55.2
|
1.0
|
C9
|
C:W401401
|
4.8
|
47.4
|
1.0
|
CG1
|
C:ILE1145
|
4.8
|
54.1
|
1.0
|
CD1
|
C:PHE1124
|
5.0
|
59.7
|
1.0
|
CG1
|
C:VAL1155
|
5.0
|
54.9
|
1.0
|
CG2
|
C:VAL1155
|
5.0
|
54.9
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 8owg
Go back to
Fluorine Binding Sites List in 8owg
Fluorine binding site 6 out
of 6 in the Crystal Structure of D1228V C-Met Bound By Compound 2
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 D1228V C-Met Bound By Compound 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1401
b:49.4
occ:1.00
|
F1
|
C:W401401
|
0.0
|
49.4
|
1.0
|
C14
|
C:W401401
|
1.4
|
49.0
|
1.0
|
C15
|
C:W401401
|
2.3
|
48.9
|
1.0
|
C13
|
C:W401401
|
2.3
|
48.8
|
1.0
|
OE1
|
C:GLU1127
|
2.9
|
68.9
|
1.0
|
CD
|
C:GLU1127
|
3.3
|
66.3
|
1.0
|
OE2
|
C:GLU1127
|
3.3
|
67.6
|
1.0
|
C16
|
C:W401401
|
3.6
|
48.9
|
1.0
|
C12
|
C:W401401
|
3.6
|
48.3
|
1.0
|
CD1
|
C:PHE1124
|
3.8
|
59.7
|
1.0
|
CE1
|
C:PHE1124
|
3.9
|
60.4
|
1.0
|
C17
|
C:W401401
|
4.1
|
48.7
|
1.0
|
CG
|
C:GLU1127
|
4.4
|
58.6
|
1.0
|
CB
|
C:GLU1127
|
4.4
|
53.4
|
1.0
|
F
|
C:W401401
|
4.7
|
49.1
|
1.0
|
CE
|
C:MET1131
|
4.8
|
55.1
|
1.0
|
C9
|
C:W401401
|
4.8
|
47.4
|
1.0
|
O
|
C:W401401
|
4.9
|
47.5
|
1.0
|
CG
|
C:PHE1124
|
4.9
|
58.4
|
1.0
|
|
Reference:
I.N.Michaelides,
G.W.Collie,
U.Borjesson,
C.Vasalou,
O.Alkhatib,
L.Barlind,
T.Cheung,
I.L.Dale,
K.J.Embrey,
E.J.Hennessy,
P.Khurana,
C.M.Koh,
M.L.Lamb,
J.Liu,
T.A.Moss,
D.J.O'neill,
C.Phillips,
J.Shaw,
A.Snijder,
R.I.Storer,
C.J.Stubbs,
F.Han,
C.Li,
J.Qiao,
D.Q.Sun,
J.Wang,
P.Wang,
W.Yang.
Discovery and Optimization of the First Atp Competitive Type-III C-Met Inhibitor. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37343272
DOI: 10.1021/ACS.JMEDCHEM.3C00401
Page generated: Fri Aug 2 21:18:00 2024
|