Fluorine in PDB 6fer: Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
Enzymatic activity of Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
All present enzymatic activity of Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide:
2.7.10.1;
Protein crystallography data
The structure of Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, PDB code: 6fer
was solved by
M.Stihle,
H.Richter,
J.Benz,
B.Kuhn,
M.G.Rudolph,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.96 /
2.87
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.910,
155.790,
355.990,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20 /
28.7
|
Fluorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Page 4, Binding sites: 31 -
40;
Page 5, Binding sites: 41 -
50;
Page 6, Binding sites: 51 -
60;
Binding sites:
The binding sites of Fluorine atom in the Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
(pdb code 6fer). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 60 binding sites of Fluorine where determined in the
Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, PDB code: 6fer:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Fluorine binding site 1 out
of 60 in 6fer
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Fluorine Binding Sites List in 6fer
Fluorine binding site 1 out
of 60 in the Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
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 Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1001
b:50.1
occ:1.00
|
F29
|
A:D6Q1001
|
0.0
|
50.1
|
1.0
|
C28
|
A:D6Q1001
|
1.3
|
46.1
|
1.0
|
F31
|
A:D6Q1001
|
2.1
|
47.1
|
1.0
|
F30
|
A:D6Q1001
|
2.1
|
44.3
|
1.0
|
C27
|
A:D6Q1001
|
2.4
|
46.5
|
1.0
|
N26
|
A:D6Q1001
|
2.9
|
55.4
|
1.0
|
CZ
|
A:PHE753
|
3.4
|
65.4
|
1.0
|
CE1
|
A:PHE753
|
3.5
|
64.8
|
1.0
|
CD2
|
A:HIS755
|
3.5
|
46.5
|
1.0
|
CB
|
A:ASP775
|
4.0
|
54.2
|
1.0
|
NE2
|
A:HIS755
|
4.0
|
51.1
|
1.0
|
C24
|
A:D6Q1001
|
4.1
|
54.9
|
1.0
|
OD2
|
A:ASP775
|
4.2
|
73.7
|
1.0
|
O
|
A:ALA774
|
4.4
|
48.2
|
1.0
|
CG
|
A:HIS755
|
4.6
|
47.0
|
1.0
|
CE2
|
A:PHE753
|
4.6
|
65.0
|
1.0
|
CD1
|
A:PHE753
|
4.6
|
62.6
|
1.0
|
CG
|
A:ASP775
|
4.7
|
67.7
|
1.0
|
C
|
A:ALA774
|
4.7
|
52.2
|
1.0
|
O25
|
A:D6Q1001
|
4.8
|
61.5
|
1.0
|
CD1
|
A:LEU679
|
4.9
|
41.9
|
1.0
|
|
Fluorine binding site 2 out
of 60 in 6fer
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Fluorine Binding Sites List in 6fer
Fluorine binding site 2 out
of 60 in the Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
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 Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1001
b:44.3
occ:1.00
|
F30
|
A:D6Q1001
|
0.0
|
44.3
|
1.0
|
C28
|
A:D6Q1001
|
1.3
|
46.1
|
1.0
|
F29
|
A:D6Q1001
|
2.1
|
50.1
|
1.0
|
F31
|
A:D6Q1001
|
2.2
|
47.1
|
1.0
|
C27
|
A:D6Q1001
|
2.3
|
46.5
|
1.0
|
N26
|
A:D6Q1001
|
2.5
|
55.4
|
1.0
|
C
|
A:ALA774
|
2.8
|
52.2
|
1.0
|
O
|
A:ALA774
|
2.8
|
48.2
|
1.0
|
C24
|
A:D6Q1001
|
3.1
|
54.9
|
1.0
|
CA
|
A:ALA774
|
3.2
|
47.7
|
1.0
|
CB
|
A:ASP775
|
3.2
|
54.2
|
1.0
|
N
|
A:ASP775
|
3.3
|
53.9
|
1.0
|
O25
|
A:D6Q1001
|
3.5
|
61.5
|
1.0
|
NE2
|
A:HIS755
|
3.8
|
51.1
|
1.0
|
CA
|
A:ASP775
|
3.9
|
53.1
|
1.0
|
N
|
A:ALA774
|
3.9
|
71.0
|
1.0
|
CD2
|
A:HIS755
|
3.9
|
46.5
|
1.0
|
O
|
A:ILE773
|
3.9
|
69.0
|
1.0
|
C23
|
A:D6Q1001
|
4.1
|
44.7
|
1.0
|
C
|
A:ILE773
|
4.2
|
69.3
|
1.0
|
CG
|
A:ASP775
|
4.4
|
67.7
|
1.0
|
CB
|
A:ALA774
|
4.5
|
50.4
|
1.0
|
OD2
|
A:ASP775
|
4.6
|
73.7
|
1.0
|
O22
|
A:D6Q1001
|
4.6
|
55.3
|
1.0
|
CG2
|
A:ILE773
|
4.8
|
45.2
|
1.0
|
|
Fluorine binding site 3 out
of 60 in 6fer
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Fluorine Binding Sites List in 6fer
Fluorine binding site 3 out
of 60 in the Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
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 Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1001
b:47.1
occ:1.00
|
F31
|
A:D6Q1001
|
0.0
|
47.1
|
1.0
|
C28
|
A:D6Q1001
|
1.3
|
46.1
|
1.0
|
F29
|
A:D6Q1001
|
2.1
|
50.1
|
1.0
|
F30
|
A:D6Q1001
|
2.2
|
44.3
|
1.0
|
C27
|
A:D6Q1001
|
2.4
|
46.5
|
1.0
|
N26
|
A:D6Q1001
|
3.6
|
55.4
|
1.0
|
CG2
|
A:ILE684
|
3.7
|
48.7
|
1.0
|
O
|
A:ILE773
|
3.8
|
69.0
|
1.0
|
CD2
|
A:HIS755
|
3.9
|
46.5
|
1.0
|
CD1
|
A:LEU748
|
4.2
|
44.6
|
1.0
|
CD1
|
A:LEU679
|
4.3
|
41.9
|
1.0
|
O
|
A:ALA774
|
4.3
|
48.2
|
1.0
|
CD2
|
A:LEU748
|
4.3
|
41.8
|
1.0
|
CD1
|
A:ILE684
|
4.3
|
38.8
|
1.0
|
C
|
A:ILE773
|
4.3
|
69.3
|
1.0
|
CG2
|
A:ILE773
|
4.4
|
45.2
|
1.0
|
C24
|
A:D6Q1001
|
4.4
|
54.9
|
1.0
|
NE2
|
A:HIS755
|
4.5
|
51.1
|
1.0
|
CE1
|
A:PHE753
|
4.5
|
64.8
|
1.0
|
O25
|
A:D6Q1001
|
4.5
|
61.5
|
1.0
|
C
|
A:ALA774
|
4.5
|
52.2
|
1.0
|
CA
|
A:ALA774
|
4.6
|
47.7
|
1.0
|
N
|
A:ALA774
|
4.6
|
71.0
|
1.0
|
CB
|
A:ILE773
|
4.7
|
44.4
|
1.0
|
CB
|
A:ILE684
|
4.8
|
35.4
|
1.0
|
CZ
|
A:PHE753
|
4.8
|
65.4
|
1.0
|
CG
|
A:LEU748
|
4.9
|
41.7
|
1.0
|
CG1
|
A:ILE684
|
4.9
|
37.7
|
1.0
|
|
Fluorine binding site 4 out
of 60 in 6fer
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Fluorine Binding Sites List in 6fer
Fluorine binding site 4 out
of 60 in the Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
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 Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1001
b:38.2
occ:1.00
|
F36
|
A:D6Q1001
|
0.0
|
38.2
|
1.0
|
C35
|
A:D6Q1001
|
1.3
|
32.2
|
1.0
|
C18
|
A:D6Q1001
|
2.3
|
31.4
|
1.0
|
C34
|
A:D6Q1001
|
2.4
|
30.1
|
1.0
|
F37
|
A:D6Q1001
|
2.7
|
31.4
|
1.0
|
C15
|
A:D6Q1001
|
3.0
|
33.1
|
1.0
|
C16
|
A:D6Q1001
|
3.1
|
26.4
|
1.0
|
OG1
|
A:THR701
|
3.1
|
48.0
|
1.0
|
C14
|
A:D6Q1001
|
3.5
|
37.6
|
1.0
|
C19
|
A:D6Q1001
|
3.6
|
37.4
|
1.0
|
C33
|
A:D6Q1001
|
3.6
|
30.3
|
1.0
|
C32
|
A:D6Q1001
|
4.1
|
35.9
|
1.0
|
CB
|
A:THR701
|
4.2
|
54.9
|
1.0
|
CB
|
A:LYS655
|
4.2
|
32.9
|
1.0
|
C9
|
A:D6Q1001
|
4.3
|
57.9
|
1.0
|
C17
|
A:D6Q1001
|
4.4
|
45.1
|
1.0
|
C21
|
A:D6Q1001
|
4.4
|
44.3
|
1.0
|
C10
|
A:D6Q1001
|
4.6
|
51.0
|
1.0
|
N20
|
A:D6Q1001
|
4.6
|
44.4
|
1.0
|
N
|
A:LYS655
|
4.6
|
36.4
|
1.0
|
N12
|
A:D6Q1001
|
4.6
|
50.1
|
1.0
|
CB
|
A:ALA653
|
4.7
|
43.8
|
1.0
|
CG2
|
A:ILE685
|
4.7
|
30.2
|
1.0
|
C13
|
A:D6Q1001
|
4.7
|
40.4
|
1.0
|
O11
|
A:D6Q1001
|
4.8
|
60.2
|
1.0
|
O
|
A:ALA653
|
4.9
|
54.3
|
1.0
|
C1
|
A:D6Q1001
|
4.9
|
51.6
|
1.0
|
|
Fluorine binding site 5 out
of 60 in 6fer
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Fluorine Binding Sites List in 6fer
Fluorine binding site 5 out
of 60 in the Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
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 Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1001
b:31.4
occ:1.00
|
F37
|
A:D6Q1001
|
0.0
|
31.4
|
1.0
|
C34
|
A:D6Q1001
|
1.3
|
30.1
|
1.0
|
C33
|
A:D6Q1001
|
2.3
|
30.3
|
1.0
|
C35
|
A:D6Q1001
|
2.4
|
32.2
|
1.0
|
F36
|
A:D6Q1001
|
2.7
|
38.2
|
1.0
|
OG1
|
A:THR701
|
3.0
|
48.0
|
1.0
|
CB
|
A:MET699
|
3.3
|
50.8
|
1.0
|
C
|
A:MET699
|
3.6
|
63.5
|
1.0
|
C18
|
A:D6Q1001
|
3.6
|
31.4
|
1.0
|
C32
|
A:D6Q1001
|
3.6
|
35.9
|
1.0
|
O
|
A:MET699
|
3.7
|
78.3
|
1.0
|
CB
|
A:LYS655
|
3.8
|
32.9
|
1.0
|
N
|
A:ILE700
|
3.8
|
61.6
|
1.0
|
C
|
A:ILE700
|
4.0
|
56.6
|
1.0
|
C19
|
A:D6Q1001
|
4.1
|
37.4
|
1.0
|
CA
|
A:MET699
|
4.1
|
51.5
|
1.0
|
N
|
A:LYS655
|
4.1
|
36.4
|
1.0
|
O
|
A:ILE700
|
4.2
|
46.8
|
1.0
|
CA
|
A:ILE700
|
4.3
|
55.2
|
1.0
|
N
|
A:THR701
|
4.3
|
68.0
|
1.0
|
CB
|
A:THR701
|
4.4
|
54.9
|
1.0
|
CD1
|
A:LEU687
|
4.5
|
46.0
|
1.0
|
CG
|
A:MET699
|
4.5
|
51.0
|
1.0
|
SD
|
A:MET699
|
4.5
|
62.6
|
1.0
|
CA
|
A:LYS655
|
4.6
|
47.3
|
1.0
|
CE
|
A:MET699
|
4.6
|
52.5
|
1.0
|
CD
|
A:LYS655
|
4.7
|
33.3
|
1.0
|
O
|
A:ALA653
|
4.8
|
54.3
|
1.0
|
CG
|
A:LYS655
|
4.9
|
34.2
|
1.0
|
CA
|
A:THR701
|
5.0
|
47.8
|
1.0
|
C15
|
A:D6Q1001
|
5.0
|
33.1
|
1.0
|
N
|
A:MET699
|
5.0
|
53.8
|
1.0
|
|
Fluorine binding site 6 out
of 60 in 6fer
Go back to
Fluorine Binding Sites List in 6fer
Fluorine binding site 6 out
of 60 in the Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
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 Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1001
b:48.1
occ:1.00
|
F29
|
B:D6Q1001
|
0.0
|
48.1
|
1.0
|
C28
|
B:D6Q1001
|
1.3
|
41.3
|
1.0
|
F31
|
B:D6Q1001
|
2.1
|
46.3
|
1.0
|
F30
|
B:D6Q1001
|
2.2
|
37.6
|
1.0
|
C27
|
B:D6Q1001
|
2.5
|
32.2
|
1.0
|
N26
|
B:D6Q1001
|
2.9
|
51.1
|
1.0
|
CE2
|
B:PHE753
|
3.5
|
38.2
|
1.0
|
CD2
|
B:HIS755
|
3.6
|
39.4
|
1.0
|
NE2
|
B:HIS755
|
3.6
|
39.1
|
1.0
|
CB
|
B:ASP775
|
3.8
|
39.7
|
1.0
|
C24
|
B:D6Q1001
|
3.9
|
56.0
|
1.0
|
CZ
|
B:PHE753
|
4.1
|
54.1
|
1.0
|
O25
|
B:D6Q1001
|
4.3
|
60.7
|
1.0
|
OD2
|
B:ASP775
|
4.4
|
36.8
|
1.0
|
CG
|
B:HIS755
|
4.5
|
37.4
|
1.0
|
CE1
|
B:HIS755
|
4.5
|
41.1
|
1.0
|
CG
|
B:ASP775
|
4.5
|
45.7
|
1.0
|
CD2
|
B:PHE753
|
4.5
|
56.8
|
1.0
|
C
|
B:ALA774
|
4.7
|
40.6
|
1.0
|
N
|
B:ASP775
|
4.7
|
45.3
|
1.0
|
O
|
B:ALA774
|
4.7
|
34.6
|
1.0
|
CA
|
B:ASP775
|
4.8
|
44.5
|
1.0
|
C23
|
B:D6Q1001
|
4.9
|
45.3
|
1.0
|
ND1
|
B:HIS755
|
4.9
|
33.7
|
1.0
|
|
Fluorine binding site 7 out
of 60 in 6fer
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Fluorine Binding Sites List in 6fer
Fluorine binding site 7 out
of 60 in the Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1001
b:37.6
occ:1.00
|
F30
|
B:D6Q1001
|
0.0
|
37.6
|
1.0
|
C28
|
B:D6Q1001
|
1.3
|
41.3
|
1.0
|
F31
|
B:D6Q1001
|
2.1
|
46.3
|
1.0
|
F29
|
B:D6Q1001
|
2.2
|
48.1
|
1.0
|
C27
|
B:D6Q1001
|
2.4
|
32.2
|
1.0
|
N26
|
B:D6Q1001
|
2.9
|
51.1
|
1.0
|
O25
|
B:D6Q1001
|
3.0
|
60.7
|
1.0
|
C
|
B:ALA774
|
3.1
|
40.6
|
1.0
|
C24
|
B:D6Q1001
|
3.1
|
56.0
|
1.0
|
CA
|
B:ALA774
|
3.2
|
44.6
|
1.0
|
O
|
B:ALA774
|
3.4
|
34.6
|
1.0
|
NE2
|
B:HIS755
|
3.5
|
39.1
|
1.0
|
O
|
B:ILE773
|
3.5
|
39.1
|
1.0
|
N
|
B:ASP775
|
3.5
|
45.3
|
1.0
|
N
|
B:ALA774
|
3.8
|
50.0
|
1.0
|
C
|
B:ILE773
|
3.9
|
46.8
|
1.0
|
CB
|
B:ASP775
|
3.9
|
39.7
|
1.0
|
CD2
|
B:HIS755
|
3.9
|
39.4
|
1.0
|
CG2
|
B:ILE773
|
4.3
|
33.8
|
1.0
|
CA
|
B:ASP775
|
4.3
|
44.5
|
1.0
|
C23
|
B:D6Q1001
|
4.4
|
45.3
|
1.0
|
CB
|
B:ALA774
|
4.5
|
47.6
|
1.0
|
CE1
|
B:HIS755
|
4.6
|
41.1
|
1.0
|
CB
|
B:ILE773
|
4.8
|
34.2
|
1.0
|
CA
|
B:ILE773
|
5.0
|
34.7
|
1.0
|
|
Fluorine binding site 8 out
of 60 in 6fer
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Fluorine Binding Sites List in 6fer
Fluorine binding site 8 out
of 60 in the Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1001
b:46.3
occ:1.00
|
F31
|
B:D6Q1001
|
0.0
|
46.3
|
1.0
|
C28
|
B:D6Q1001
|
1.3
|
41.3
|
1.0
|
F29
|
B:D6Q1001
|
2.1
|
48.1
|
1.0
|
F30
|
B:D6Q1001
|
2.1
|
37.6
|
1.0
|
C27
|
B:D6Q1001
|
2.4
|
32.2
|
1.0
|
CD2
|
B:LEU748
|
3.5
|
37.0
|
1.0
|
N26
|
B:D6Q1001
|
3.6
|
51.1
|
1.0
|
CD2
|
B:HIS755
|
3.8
|
39.4
|
1.0
|
CE2
|
B:PHE753
|
3.9
|
38.2
|
1.0
|
CD1
|
B:LEU748
|
4.0
|
35.0
|
1.0
|
NE2
|
B:HIS755
|
4.1
|
39.1
|
1.0
|
CG2
|
B:ILE684
|
4.2
|
36.4
|
1.0
|
CD1
|
B:LEU679
|
4.3
|
46.7
|
1.0
|
CG
|
B:LEU748
|
4.3
|
40.8
|
1.0
|
O25
|
B:D6Q1001
|
4.4
|
60.7
|
1.0
|
CD2
|
B:PHE753
|
4.5
|
56.8
|
1.0
|
C24
|
B:D6Q1001
|
4.5
|
56.0
|
1.0
|
O
|
B:ILE773
|
4.5
|
39.1
|
1.0
|
CD1
|
B:ILE684
|
4.6
|
47.4
|
1.0
|
CZ
|
B:PHE753
|
4.7
|
54.1
|
1.0
|
CG2
|
B:ILE773
|
4.8
|
33.8
|
1.0
|
CG
|
B:HIS755
|
5.0
|
37.4
|
1.0
|
|
Fluorine binding site 9 out
of 60 in 6fer
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Fluorine Binding Sites List in 6fer
Fluorine binding site 9 out
of 60 in the Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 9 of Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1001
b:40.0
occ:1.00
|
F36
|
B:D6Q1001
|
0.0
|
40.0
|
1.0
|
C35
|
B:D6Q1001
|
1.3
|
30.8
|
1.0
|
C18
|
B:D6Q1001
|
2.3
|
30.4
|
1.0
|
C34
|
B:D6Q1001
|
2.3
|
34.3
|
1.0
|
F37
|
B:D6Q1001
|
2.7
|
37.8
|
1.0
|
C15
|
B:D6Q1001
|
2.9
|
36.9
|
1.0
|
C16
|
B:D6Q1001
|
3.1
|
33.8
|
1.0
|
C14
|
B:D6Q1001
|
3.1
|
42.8
|
1.0
|
OG1
|
B:THR701
|
3.4
|
53.7
|
1.0
|
C19
|
B:D6Q1001
|
3.6
|
34.9
|
1.0
|
C33
|
B:D6Q1001
|
3.6
|
26.6
|
1.0
|
CB
|
B:LYS655
|
3.9
|
67.5
|
1.0
|
C32
|
B:D6Q1001
|
4.1
|
28.2
|
1.0
|
CB
|
B:THR701
|
4.2
|
55.3
|
1.0
|
C17
|
B:D6Q1001
|
4.4
|
42.2
|
1.0
|
C13
|
B:D6Q1001
|
4.4
|
51.1
|
1.0
|
C21
|
B:D6Q1001
|
4.4
|
43.8
|
1.0
|
N12
|
B:D6Q1001
|
4.5
|
46.7
|
1.0
|
O
|
B:MET699
|
4.6
|
74.5
|
1.0
|
N20
|
B:D6Q1001
|
4.6
|
43.2
|
1.0
|
N
|
B:LYS655
|
4.7
|
68.0
|
1.0
|
CG2
|
B:THR701
|
4.7
|
44.1
|
1.0
|
CD
|
B:LYS655
|
4.7
|
49.5
|
1.0
|
CG2
|
B:VAL624
|
4.8
|
75.6
|
1.0
|
CA
|
B:LYS655
|
4.8
|
72.5
|
1.0
|
C9
|
B:D6Q1001
|
4.9
|
52.6
|
1.0
|
CG2
|
B:ILE685
|
4.9
|
44.0
|
1.0
|
CG
|
B:LYS655
|
5.0
|
56.4
|
1.0
|
|
Fluorine binding site 10 out
of 60 in 6fer
Go back to
Fluorine Binding Sites List in 6fer
Fluorine binding site 10 out
of 60 in the Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 10 of Crystal Structure of Human DDR2 Kinase in Complex with 2-[4,5- Difluoro-2-Oxo-1'-(1H-Pyrazolo[3,4-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1001
b:37.8
occ:1.00
|
F37
|
B:D6Q1001
|
0.0
|
37.8
|
1.0
|
C34
|
B:D6Q1001
|
1.3
|
34.3
|
1.0
|
C35
|
B:D6Q1001
|
2.4
|
30.8
|
1.0
|
C33
|
B:D6Q1001
|
2.4
|
26.6
|
1.0
|
F36
|
B:D6Q1001
|
2.7
|
40.0
|
1.0
|
O
|
B:MET699
|
2.9
|
74.5
|
1.0
|
CB
|
B:MET699
|
3.0
|
51.6
|
1.0
|
OG1
|
B:THR701
|
3.1
|
53.7
|
1.0
|
C
|
B:MET699
|
3.5
|
61.8
|
1.0
|
C18
|
B:D6Q1001
|
3.6
|
30.4
|
1.0
|
CB
|
B:LYS655
|
3.6
|
67.5
|
1.0
|
C32
|
B:D6Q1001
|
3.7
|
28.2
|
1.0
|
CA
|
B:MET699
|
3.8
|
58.4
|
1.0
|
CE
|
B:MET699
|
4.1
|
69.3
|
1.0
|
SD
|
B:MET699
|
4.1
|
51.8
|
1.0
|
C19
|
B:D6Q1001
|
4.1
|
34.9
|
1.0
|
CG
|
B:MET699
|
4.1
|
50.5
|
1.0
|
N
|
B:LYS655
|
4.3
|
68.0
|
1.0
|
N
|
B:ILE700
|
4.4
|
54.8
|
1.0
|
CB
|
B:THR701
|
4.5
|
55.3
|
1.0
|
CD
|
B:LYS655
|
4.6
|
49.5
|
1.0
|
CA
|
B:LYS655
|
4.6
|
72.5
|
1.0
|
CG
|
B:LYS655
|
4.6
|
56.4
|
1.0
|
O
|
B:ILE700
|
4.6
|
54.3
|
1.0
|
C
|
B:ILE700
|
4.7
|
52.5
|
1.0
|
N
|
B:MET699
|
4.7
|
64.2
|
1.0
|
CD1
|
B:LEU687
|
4.8
|
65.0
|
1.0
|
C15
|
B:D6Q1001
|
4.9
|
36.9
|
1.0
|
CA
|
B:ILE700
|
5.0
|
50.8
|
1.0
|
|
Reference:
H.Richter,
A.L.Satz,
M.Bedoucha,
B.Buettelmann,
A.C.Petersen,
A.Harmeier,
R.Hermosilla,
R.Hochstrasser,
D.Burger,
B.Gsell,
R.Gasser,
S.Huber,
M.N.Hug,
B.Kocer,
B.Kuhn,
M.Ritter,
M.G.Rudolph,
F.Weibel,
J.Molina-David,
J.J.Kim,
J.V.Santos,
M.Stihle,
G.J.Georges,
R.D.Bonfil,
R.Fridman,
S.Uhles,
S.Moll,
C.Faul,
A.Fornoni,
M.Prunotto.
Dna-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in A Genetic Mouse Model of Alport Syndrome. Acs Chem.Biol. V. 14 37 2019.
ISSN: ESSN 1554-8937
PubMed: 30452219
DOI: 10.1021/ACSCHEMBIO.8B00866
Page generated: Thu Aug 1 19:55:07 2024
|