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Fluorine in PDB 5h3q: Crystal Structure of Trka Kinase with Ligand

Enzymatic activity of Crystal Structure of Trka Kinase with Ligand

All present enzymatic activity of Crystal Structure of Trka Kinase with Ligand:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Trka Kinase with Ligand, PDB code: 5h3q was solved by F.Noritaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.81 / 2.10
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 140.845, 157.195, 52.306, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 21.5

Other elements in 5h3q:

The structure of Crystal Structure of Trka Kinase with Ligand also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Trka Kinase with Ligand (pdb code 5h3q). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Trka Kinase with Ligand, PDB code: 5h3q:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5h3q

Go back to Fluorine Binding Sites List in 5h3q
Fluorine binding site 1 out of 2 in the Crystal Structure of Trka Kinase with Ligand


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 Trka Kinase with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:39.4
occ:1.00
FBF A:7HF1001 0.0 39.4 1.0
CAK A:7HF1001 1.4 37.2 1.0
CAQ A:7HF1001 2.4 39.5 1.0
CAP A:7HF1001 2.4 35.5 1.0
FBG A:7HF1001 2.6 38.9 1.0
O A:HOH1145 3.2 41.2 1.0
CA A:ILE490 3.4 37.0 1.0
O A:GLY488 3.5 37.0 1.0
O A:HIS648 3.5 30.0 1.0
N A:ILE490 3.6 35.4 1.0
ND2 A:ASN493 3.6 35.4 1.0
O A:HIS489 3.6 35.8 1.0
C A:HIS489 3.6 40.0 1.0
CAD A:7HF1001 3.7 35.6 1.0
O A:VAL647 3.7 35.2 1.0
C A:GLY488 3.7 34.3 1.0
CAN A:7HF1001 3.7 37.0 1.0
CA A:HIS648 3.7 33.8 1.0
C A:HIS648 4.0 29.9 1.0
CAA A:7HF1001 4.2 39.4 1.0
CB A:ILE490 4.2 35.6 1.0
CA A:GLY488 4.2 33.5 1.0
N A:HIS489 4.2 35.9 1.0
C A:ILE490 4.4 37.4 1.0
CG A:HIS648 4.4 31.1 1.0
CA A:HIS489 4.5 36.8 1.0
CD1 A:ILE490 4.5 47.7 1.0
C A:VAL647 4.5 35.0 1.0
O A:ILE490 4.5 39.2 1.0
CD2 A:HIS648 4.5 33.6 1.0
CB A:HIS648 4.6 30.2 1.0
N A:HIS648 4.6 33.9 1.0
ND1 A:HIS648 4.8 32.0 1.0
CG A:ASN493 4.8 39.4 1.0
CG1 A:ILE490 4.9 41.0 1.0
N A:GLY488 4.9 30.7 1.0
CBJ A:7HF1001 4.9 33.5 1.0
NH1 A:ARG649 5.0 55.0 1.0

Fluorine binding site 2 out of 2 in 5h3q

Go back to Fluorine Binding Sites List in 5h3q
Fluorine binding site 2 out of 2 in the Crystal Structure of Trka Kinase with Ligand


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 Trka Kinase with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:38.9
occ:1.00
FBG A:7HF1001 0.0 38.9 1.0
CAQ A:7HF1001 1.3 39.5 1.0
CAK A:7HF1001 2.3 37.2 1.0
CAD A:7HF1001 2.3 35.6 1.0
FBF A:7HF1001 2.6 39.4 1.0
O A:VAL647 3.2 35.2 1.0
ND2 A:ASN493 3.2 35.4 1.0
CA A:HIS648 3.5 33.8 1.0
C A:VAL647 3.5 35.0 1.0
CAP A:7HF1001 3.5 35.5 1.0
CAA A:7HF1001 3.6 39.4 1.0
N A:HIS648 3.7 33.9 1.0
CD2 A:PHE646 3.8 48.4 1.0
CB A:PHE646 3.9 44.4 1.0
CAN A:7HF1001 4.1 37.0 1.0
CG A:ASN493 4.1 39.4 1.0
CB A:HIS648 4.1 30.2 1.0
N A:VAL647 4.1 36.6 1.0
CD1 A:ILE490 4.2 47.7 1.0
CG A:PHE646 4.3 52.8 1.0
OD1 A:ASN493 4.3 37.9 1.0
CA A:VAL647 4.5 36.2 1.0
CG A:HIS648 4.5 31.1 1.0
CD2 A:HIS648 4.5 33.6 1.0
CD1 A:LEU641 4.6 35.9 1.0
C A:PHE646 4.6 42.0 1.0
C A:HIS648 4.6 29.9 1.0
CA A:PHE646 4.8 42.7 1.0
CE2 A:PHE646 4.8 54.4 1.0
O A:HIS648 4.8 30.0 1.0
CD2 A:LEU641 4.9 36.2 1.0
CA A:ILE490 4.9 37.0 1.0

Reference:

N.Furuya, T.Momose, K.Katsuno, N.Fushimi, H.Muranaka, C.Handa, T.Ozawa, T.Kinoshita. The Juxtamembrane Region of Trka Kinase Is Critical For Inhibitor Selectivity Bioorg. Med. Chem. Lett. V. 27 1233 2017.
ISSN: ESSN 1464-3405
PubMed: 28159414
DOI: 10.1016/J.BMCL.2017.01.056
Page generated: Sun Dec 13 12:23:13 2020

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