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Fluorine in PDB 6dkb: Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.

Enzymatic activity of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.

All present enzymatic activity of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B., PDB code: 6dkb was solved by S.E.Greasley, E.Johnson, M.L.Kraus, C.N.Cronin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.00 / 2.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.490, 45.970, 79.270, 90.00, 126.97, 90.00
R / Rfree (%) 21.6 / 24.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B. (pdb code 6dkb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B., PDB code: 6dkb:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6dkb

Go back to Fluorine Binding Sites List in 6dkb
Fluorine binding site 1 out of 4 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.


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 Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:81.8
occ:1.00
F31 A:FKY4000 0.0 81.8 1.0
C30 A:FKY4000 1.3 78.7 1.0
F33 A:FKY4000 2.1 76.9 1.0
F32 A:FKY4000 2.1 80.3 1.0
O29 A:FKY4000 2.2 73.4 1.0
C26 A:FKY4000 2.7 69.2 1.0
O A:ILE666 2.9 55.6 1.0
C25 A:FKY4000 3.2 69.4 1.0
C A:ILE666 3.3 55.1 1.0
CA A:GLY667 3.6 51.3 1.0
N A:GLY667 3.6 51.7 1.0
C27 A:FKY4000 3.7 66.2 1.0
CG2 A:ILE666 3.7 54.4 1.0
O A:GLY667 3.7 54.1 1.0
C A:GLY667 3.8 55.6 1.0
CB A:ILE666 4.0 53.1 1.0
CD1 A:ILE572 4.2 59.2 1.0
CD2 A:HIS648 4.2 64.8 1.0
CG2 A:ILE572 4.2 57.8 1.0
NE2 A:HIS648 4.2 64.4 1.0
CA A:ILE666 4.3 50.2 1.0
C24 A:FKY4000 4.4 68.2 1.0
C28 A:FKY4000 4.7 65.0 1.0
N A:ASP668 4.8 53.4 1.0
CD1 A:LEU641 4.9 59.5 1.0
CB A:ILE572 5.0 57.8 1.0

Fluorine binding site 2 out of 4 in 6dkb

Go back to Fluorine Binding Sites List in 6dkb
Fluorine binding site 2 out of 4 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.


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 Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:80.3
occ:1.00
F32 A:FKY4000 0.0 80.3 1.0
C30 A:FKY4000 1.3 78.7 1.0
F33 A:FKY4000 2.1 76.9 1.0
O29 A:FKY4000 2.1 73.4 1.0
F31 A:FKY4000 2.1 81.8 1.0
C26 A:FKY4000 3.4 69.2 1.0
CD2 A:LEU641 3.6 58.5 1.0
CD1 A:LEU641 3.8 59.5 1.0
CE1 A:PHE646 3.9 74.0 1.0
CD1 A:LEU567 4.0 73.1 1.0
CD2 A:HIS648 4.2 64.8 1.0
CD1 A:ILE572 4.2 59.2 1.0
CZ A:PHE646 4.2 73.1 1.0
CG A:LEU641 4.3 60.7 1.0
C25 A:FKY4000 4.3 69.4 1.0
C27 A:FKY4000 4.3 66.2 1.0
CG2 A:ILE572 4.4 57.8 1.0
CD1 A:PHE646 4.6 74.0 1.0
NE2 A:HIS648 4.8 64.4 1.0
O A:ILE666 4.9 55.6 1.0
CG A:LEU567 5.0 73.0 1.0
CG2 A:ILE666 5.0 54.4 1.0
CD2 A:LEU567 5.0 73.0 1.0

Fluorine binding site 3 out of 4 in 6dkb

Go back to Fluorine Binding Sites List in 6dkb
Fluorine binding site 3 out of 4 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.


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 Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:76.9
occ:1.00
F33 A:FKY4000 0.0 76.9 1.0
C30 A:FKY4000 1.3 78.7 1.0
F32 A:FKY4000 2.1 80.3 1.0
F31 A:FKY4000 2.1 81.8 1.0
O29 A:FKY4000 2.2 73.4 1.0
C26 A:FKY4000 2.8 69.2 1.0
C27 A:FKY4000 3.1 66.2 1.0
CD2 A:HIS648 3.2 64.8 1.0
NE2 A:HIS648 3.2 64.4 1.0
O A:GLY667 3.8 54.1 1.0
C25 A:FKY4000 4.0 69.4 1.0
C A:GLY667 4.1 55.6 1.0
CB A:ASP668 4.1 55.9 1.0
C28 A:FKY4000 4.3 65.0 1.0
CG A:HIS648 4.3 64.2 1.0
CE1 A:PHE646 4.3 74.0 1.0
CE1 A:HIS648 4.4 64.0 1.0
CZ A:PHE646 4.5 73.1 1.0
CA A:GLY667 4.6 51.3 1.0
N A:ASP668 4.7 53.4 1.0
CG2 A:ILE666 4.8 54.4 1.0
CD1 A:LEU641 4.9 59.5 1.0
O A:ILE666 4.9 55.6 1.0
OD2 A:ASP668 4.9 87.6 1.0
N A:GLY667 5.0 51.7 1.0
ND1 A:HIS648 5.0 65.2 1.0

Fluorine binding site 4 out of 4 in 6dkb

Go back to Fluorine Binding Sites List in 6dkb
Fluorine binding site 4 out of 4 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.


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 Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:61.9
occ:1.00
F34 A:FKY4000 0.0 61.9 1.0
C15 A:FKY4000 1.4 61.2 1.0
C14 A:FKY4000 2.4 61.7 1.0
C16 A:FKY4000 2.4 61.9 1.0
O13 A:FKY4000 2.7 61.9 1.0
N17 A:FKY4000 2.9 65.7 1.0
C19 A:FKY4000 3.0 63.6 1.0
CG A:PHE589 3.3 55.3 1.0
CB A:PHE589 3.5 55.3 1.0
N36 A:FKY4000 3.5 68.6 1.0
C20 A:FKY4000 3.5 67.3 1.0
C18 A:FKY4000 3.5 64.1 1.0
CD1 A:PHE589 3.6 56.9 1.0
CD2 A:PHE589 3.8 56.0 1.0
C22 A:FKY4000 3.9 65.9 1.0
C10 A:FKY4000 4.0 63.4 1.0
O21 A:FKY4000 4.3 67.9 1.0
CE1 A:PHE589 4.3 56.8 1.0
C35 A:FKY4000 4.4 68.7 1.0
CG2 A:VAL573 4.4 61.7 1.0
CE2 A:PHE589 4.4 58.3 1.0
CB A:ALA542 4.4 56.6 1.0
CD1 A:LEU657 4.5 57.4 1.0
CZ A:PHE589 4.6 56.2 1.0
C9 A:FKY4000 4.6 65.5 1.0
N11 A:FKY4000 4.9 62.8 1.0
CG1 A:VAL573 4.9 61.8 1.0
CA A:PHE589 5.0 54.3 1.0

Reference:

S.K.Bagal, M.Andrews, B.M.Bechle, J.Bian, J.Bilsland, D.C.Blakemore, J.F.Braganza, P.J.Bungay, M.S.Corbett, C.N.Cronin, J.J.Cui, R.Dias, N.J.Flanagan, S.E.Greasley, R.Grimley, K.James, E.Johnson, L.Kitching, M.L.Kraus, I.Mcalpine, A.Nagata, S.Ninkovic, K.Omoto, S.Scales, S.E.Skerratt, J.Sun, M.Tran-Dube, G.J.Waldron, F.Wang, J.S.Warmus. Discovery of Potent, Selective, and Peripherally Restricted Pan-Trk Kinase Inhibitors For the Treatment of Pain. J. Med. Chem. V. 61 6779 2018.
ISSN: ISSN 1520-4804
PubMed: 29944371
DOI: 10.1021/ACS.JMEDCHEM.8B00633
Page generated: Tue Jul 15 10:47:12 2025

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