Fluorine in PDB 6x3p: Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor
Enzymatic activity of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor
All present enzymatic activity of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor:
2.7.10.2;
Protein crystallography data
The structure of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor, PDB code: 6x3p
was solved by
T.O.Fischmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.33 /
1.34
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.010,
104.640,
38.000,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.4 /
21.7
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor
(pdb code 6x3p). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor, PDB code: 6x3p:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6x3p
Go back to
Fluorine Binding Sites List in 6x3p
Fluorine binding site 1 out
of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:16.9
occ:1.00
|
F37
|
A:UM4701
|
0.0
|
16.9
|
1.0
|
C36
|
A:UM4701
|
1.3
|
15.4
|
1.0
|
F38
|
A:UM4701
|
2.1
|
15.6
|
1.0
|
F39
|
A:UM4701
|
2.1
|
14.8
|
1.0
|
C34
|
A:UM4701
|
2.3
|
9.7
|
1.0
|
C35
|
A:UM4701
|
2.8
|
10.4
|
1.0
|
CZ
|
A:PHE442
|
3.3
|
17.8
|
1.0
|
C33
|
A:UM4701
|
3.5
|
10.4
|
1.0
|
CD1
|
A:ILE472
|
3.6
|
15.5
|
1.0
|
CE1
|
A:PHE442
|
3.6
|
19.2
|
1.0
|
CG1
|
A:ILE472
|
3.8
|
13.5
|
1.0
|
CB
|
A:ALA446
|
3.9
|
11.5
|
1.0
|
CG2
|
A:ILE472
|
4.1
|
11.7
|
1.0
|
CE2
|
A:PHE442
|
4.1
|
21.6
|
1.0
|
CD2
|
A:LEU542
|
4.2
|
16.6
|
1.0
|
C30
|
A:UM4701
|
4.2
|
10.3
|
1.0
|
CD1
|
A:LEU542
|
4.2
|
14.3
|
1.0
|
CD1
|
A:PHE442
|
4.6
|
18.6
|
1.0
|
CB
|
A:ILE472
|
4.6
|
11.1
|
1.0
|
O28
|
A:UM4701
|
4.6
|
10.6
|
1.0
|
CA
|
A:ALA446
|
4.6
|
10.0
|
1.0
|
C32
|
A:UM4701
|
4.6
|
9.6
|
1.0
|
CG
|
A:LEU542
|
4.8
|
13.7
|
1.0
|
N31
|
A:UM4701
|
4.9
|
10.3
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6x3p
Go back to
Fluorine Binding Sites List in 6x3p
Fluorine binding site 2 out
of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:15.6
occ:1.00
|
F38
|
A:UM4701
|
0.0
|
15.6
|
1.0
|
C36
|
A:UM4701
|
1.3
|
15.4
|
1.0
|
F37
|
A:UM4701
|
2.1
|
16.9
|
1.0
|
F39
|
A:UM4701
|
2.1
|
14.8
|
1.0
|
C34
|
A:UM4701
|
2.3
|
9.7
|
1.0
|
C35
|
A:UM4701
|
3.0
|
10.4
|
1.0
|
C33
|
A:UM4701
|
3.3
|
10.4
|
1.0
|
CG2
|
A:ILE472
|
3.5
|
11.7
|
1.0
|
CD1
|
A:LEU460
|
3.5
|
12.9
|
1.0
|
CB
|
A:ALA446
|
3.6
|
11.5
|
1.0
|
CD2
|
A:LEU460
|
3.8
|
11.0
|
1.0
|
CA
|
A:ALA446
|
4.0
|
10.0
|
1.0
|
CD1
|
A:ILE472
|
4.2
|
15.5
|
1.0
|
CG
|
A:LEU460
|
4.2
|
10.1
|
1.0
|
CE
|
A:MET450
|
4.2
|
10.9
|
1.0
|
C30
|
A:UM4701
|
4.3
|
10.3
|
1.0
|
C32
|
A:UM4701
|
4.5
|
9.6
|
1.0
|
CG1
|
A:ILE472
|
4.5
|
13.5
|
1.0
|
O
|
A:ALA446
|
4.6
|
11.6
|
1.0
|
CB
|
A:ILE472
|
4.7
|
11.1
|
1.0
|
C
|
A:ALA446
|
4.7
|
11.8
|
1.0
|
CB
|
A:LEU460
|
4.8
|
8.4
|
1.0
|
CG1
|
A:VAL463
|
4.8
|
14.7
|
1.0
|
N31
|
A:UM4701
|
4.9
|
10.3
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6x3p
Go back to
Fluorine Binding Sites List in 6x3p
Fluorine binding site 3 out
of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:14.8
occ:1.00
|
F39
|
A:UM4701
|
0.0
|
14.8
|
1.0
|
C36
|
A:UM4701
|
1.3
|
15.4
|
1.0
|
F37
|
A:UM4701
|
2.1
|
16.9
|
1.0
|
F38
|
A:UM4701
|
2.1
|
15.6
|
1.0
|
C34
|
A:UM4701
|
2.3
|
9.7
|
1.0
|
C33
|
A:UM4701
|
2.7
|
10.4
|
1.0
|
CA
|
A:ALA446
|
3.3
|
10.0
|
1.0
|
CB
|
A:ALA446
|
3.3
|
11.5
|
1.0
|
C35
|
A:UM4701
|
3.6
|
10.4
|
1.0
|
CD2
|
A:LEU542
|
3.6
|
16.6
|
1.0
|
SD
|
A:MET449
|
4.0
|
12.2
|
1.0
|
N
|
A:ALA446
|
4.1
|
10.4
|
1.0
|
C32
|
A:UM4701
|
4.1
|
9.6
|
1.0
|
CD1
|
A:LEU460
|
4.3
|
12.9
|
1.0
|
C
|
A:ALA446
|
4.5
|
11.8
|
1.0
|
O
|
A:ALA446
|
4.6
|
11.6
|
1.0
|
CE1
|
A:PHE442
|
4.7
|
19.2
|
1.0
|
CD1
|
A:LEU542
|
4.7
|
14.3
|
1.0
|
CB
|
A:MET449
|
4.7
|
9.9
|
1.0
|
C30
|
A:UM4701
|
4.7
|
10.3
|
1.0
|
CG
|
A:LEU542
|
4.7
|
13.7
|
1.0
|
C
|
A:GLU445
|
4.8
|
11.5
|
1.0
|
CZ
|
A:PHE442
|
4.8
|
17.8
|
1.0
|
O
|
A:PHE442
|
4.9
|
12.0
|
1.0
|
O
|
A:GLU445
|
4.9
|
11.1
|
1.0
|
N31
|
A:UM4701
|
4.9
|
10.3
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6x3p
Go back to
Fluorine Binding Sites List in 6x3p
Fluorine binding site 4 out
of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F702
b:14.6
occ:1.00
|
F37
|
A:UM4702
|
0.0
|
14.6
|
1.0
|
C36
|
A:UM4702
|
1.3
|
15.7
|
1.0
|
F39
|
A:UM4702
|
2.1
|
15.8
|
1.0
|
F38
|
A:UM4702
|
2.1
|
16.2
|
1.0
|
C34
|
A:UM4702
|
2.3
|
11.8
|
1.0
|
C35
|
A:UM4702
|
2.7
|
11.0
|
1.0
|
CE2
|
A:TYR461
|
3.3
|
9.9
|
1.0
|
CD2
|
A:TYR461
|
3.4
|
9.1
|
1.0
|
O
|
A:HOH982
|
3.5
|
36.3
|
1.0
|
C33
|
A:UM4702
|
3.6
|
12.1
|
1.0
|
CG1
|
A:VAL427
|
3.7
|
9.9
|
1.0
|
CZ
|
A:TYR461
|
3.8
|
10.8
|
1.0
|
O
|
A:HOH955
|
3.8
|
27.6
|
1.0
|
CB
|
A:TYR425
|
3.9
|
11.9
|
1.0
|
CG
|
A:TYR461
|
4.0
|
8.5
|
1.0
|
C30
|
A:UM4702
|
4.1
|
10.0
|
1.0
|
CE1
|
A:TYR461
|
4.3
|
10.5
|
1.0
|
O
|
A:ASP426
|
4.3
|
11.3
|
1.0
|
OH
|
A:TYR461
|
4.3
|
13.2
|
1.0
|
CD1
|
A:TYR461
|
4.4
|
8.9
|
1.0
|
O28
|
A:UM4702
|
4.4
|
12.7
|
1.0
|
CG
|
A:TYR425
|
4.5
|
15.7
|
1.0
|
CD1
|
A:TYR425
|
4.6
|
19.0
|
1.0
|
C32
|
A:UM4702
|
4.7
|
13.6
|
1.0
|
CB
|
A:TYR461
|
4.8
|
9.7
|
1.0
|
N31
|
A:UM4702
|
4.9
|
12.4
|
1.0
|
CE3
|
A:TRP421
|
5.0
|
11.3
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6x3p
Go back to
Fluorine Binding Sites List in 6x3p
Fluorine binding site 5 out
of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F702
b:16.2
occ:1.00
|
F38
|
A:UM4702
|
0.0
|
16.2
|
1.0
|
C36
|
A:UM4702
|
1.3
|
15.7
|
1.0
|
F37
|
A:UM4702
|
2.1
|
14.6
|
1.0
|
F39
|
A:UM4702
|
2.1
|
15.8
|
1.0
|
C34
|
A:UM4702
|
2.3
|
11.8
|
1.0
|
C35
|
A:UM4702
|
3.1
|
11.0
|
1.0
|
CG
|
A:TYR425
|
3.1
|
15.7
|
1.0
|
CB
|
A:TYR425
|
3.2
|
11.9
|
1.0
|
C33
|
A:UM4702
|
3.2
|
12.1
|
1.0
|
CE3
|
A:TRP421
|
3.3
|
11.3
|
1.0
|
CD1
|
A:TYR425
|
3.4
|
19.0
|
1.0
|
CZ3
|
A:TRP421
|
3.8
|
13.0
|
1.0
|
CD2
|
A:TYR425
|
3.8
|
16.4
|
1.0
|
CD2
|
A:TRP421
|
4.1
|
9.4
|
1.0
|
CE1
|
A:TYR425
|
4.2
|
20.9
|
1.0
|
O
|
A:HOH982
|
4.2
|
36.3
|
1.0
|
C30
|
A:UM4702
|
4.3
|
10.0
|
1.0
|
C32
|
A:UM4702
|
4.3
|
13.6
|
1.0
|
CB
|
A:TRP421
|
4.5
|
9.2
|
1.0
|
CE2
|
A:TYR425
|
4.6
|
17.8
|
1.0
|
CG
|
A:TRP421
|
4.6
|
9.1
|
1.0
|
O
|
A:HOH955
|
4.6
|
27.6
|
1.0
|
CA
|
A:TYR425
|
4.7
|
10.1
|
1.0
|
CZ
|
A:TYR425
|
4.7
|
23.7
|
1.0
|
CH2
|
A:TRP421
|
4.8
|
13.5
|
1.0
|
N31
|
A:UM4702
|
4.9
|
12.4
|
1.0
|
CG1
|
A:VAL427
|
4.9
|
9.9
|
1.0
|
CE2
|
A:TRP421
|
5.0
|
12.0
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6x3p
Go back to
Fluorine Binding Sites List in 6x3p
Fluorine binding site 6 out
of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F702
b:15.8
occ:1.00
|
F39
|
A:UM4702
|
0.0
|
15.8
|
1.0
|
C36
|
A:UM4702
|
1.3
|
15.7
|
1.0
|
F37
|
A:UM4702
|
2.1
|
14.6
|
1.0
|
F38
|
A:UM4702
|
2.1
|
16.2
|
1.0
|
C34
|
A:UM4702
|
2.3
|
11.8
|
1.0
|
C33
|
A:UM4702
|
2.8
|
12.1
|
1.0
|
CB
|
A:TRP421
|
3.1
|
9.2
|
1.0
|
CG1
|
A:VAL427
|
3.2
|
9.9
|
1.0
|
CG
|
A:TRP421
|
3.4
|
9.1
|
1.0
|
CE3
|
A:TRP421
|
3.4
|
11.3
|
1.0
|
CD2
|
A:TRP421
|
3.5
|
9.4
|
1.0
|
C35
|
A:UM4702
|
3.6
|
11.0
|
1.0
|
CB
|
A:TYR425
|
3.8
|
11.9
|
1.0
|
C32
|
A:UM4702
|
4.2
|
13.6
|
1.0
|
CD1
|
A:TRP421
|
4.2
|
11.6
|
1.0
|
CD2
|
A:TYR461
|
4.3
|
9.1
|
1.0
|
CE2
|
A:TRP421
|
4.4
|
12.0
|
1.0
|
CZ3
|
A:TRP421
|
4.4
|
13.0
|
1.0
|
CG
|
A:TYR425
|
4.5
|
15.7
|
1.0
|
CA
|
A:TRP421
|
4.5
|
9.4
|
1.0
|
O
|
A:TYR425
|
4.6
|
10.9
|
1.0
|
CE2
|
A:TYR461
|
4.7
|
9.9
|
1.0
|
C30
|
A:UM4702
|
4.7
|
10.0
|
1.0
|
CB
|
A:VAL427
|
4.7
|
10.6
|
1.0
|
NE1
|
A:TRP421
|
4.8
|
12.1
|
1.0
|
CG
|
A:TYR461
|
4.9
|
8.5
|
1.0
|
N
|
A:TRP421
|
4.9
|
9.0
|
1.0
|
N31
|
A:UM4702
|
5.0
|
12.4
|
1.0
|
|
Reference:
J.Liu,
D.Guiadeen,
A.Krikorian,
X.Gao,
J.Wang,
S.Babu Boga,
A.B.Alhassan,
W.Yu,
O.Selyutin,
Y.Yu,
R.Anand,
J.Xu,
J.Kelly,
J.L.Duffy,
S.Liu,
C.Yang,
H.Wu,
J.Cai,
C.Bennett,
K.M.Maloney,
S.Tyagarajan,
Y.D.Gao,
T.O.Fischmann,
J.Presland,
M.Mansueto,
Z.Xu,
E.Leccese,
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ISSN: ESSN 1464-3405
PubMed: 32738973
DOI: 10.1016/J.BMCL.2020.127390
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