Fluorine in PDB 7xbi: The Crystal Structure of Human Trka Kinase Bound to the Inhibitor

Enzymatic activity of The Crystal Structure of Human Trka Kinase Bound to the Inhibitor

All present enzymatic activity of The Crystal Structure of Human Trka Kinase Bound to the Inhibitor:
2.7.10.1;

Protein crystallography data

The structure of The Crystal Structure of Human Trka Kinase Bound to the Inhibitor, PDB code: 7xbi was solved by C.Y.Wu, G.Wang, L.Ouyang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.16 / 2.16
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 52.01, 52.01, 229.51, 90, 90, 120
R / Rfree (%) 18.8 / 24.6

Other elements in 7xbi:

The structure of The Crystal Structure of Human Trka Kinase Bound to the Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Crystal Structure of Human Trka Kinase Bound to the Inhibitor (pdb code 7xbi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the The Crystal Structure of Human Trka Kinase Bound to the Inhibitor, PDB code: 7xbi:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 7xbi

Go back to Fluorine Binding Sites List in 7xbi
Fluorine binding site 1 out of 7 in the The Crystal Structure of Human Trka Kinase Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of Human Trka Kinase Bound to the Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:52.9
occ:1.00
 F26 A:CVY801 0.0 52.9 1.0
C25 A:CVY801 1.4 63.4 1.0
C24 A:CVY801 2.4 65.2 1.0
C20 A:CVY801 2.4 48.4 1.0
H191 A:CVY801 2.5 48.1 1.0
H241 A:CVY801 2.6 78.2 1.0
N19 A:CVY801 2.8 40.1 1.0
HG3 A:GLU560 2.9 61.7 1.0
OE2 A:GLU560 3.3 40.0 1.0
HD23 A:LEU563 3.5 57.7 1.0
C23 A:CVY801 3.6 58.3 1.0
C21 A:CVY801 3.7 47.5 1.0
CG A:GLU560 3.7 51.5 1.0
CD A:GLU560 3.8 49.6 1.0
HB3 A:ASP668 3.8 38.8 1.0
HG A:LEU564 3.8 41.8 1.0
C17 A:CVY801 4.1 41.8 1.0
C22 A:CVY801 4.1 44.5 1.0
HA A:GLU560 4.3 42.9 1.0
HG2 A:GLU560 4.3 61.7 1.0
CD2 A:LEU563 4.4 48.1 1.0
HD11 A:LEU564 4.4 50.4 1.0
H161 A:CVY801 4.4 45.4 1.0
HB2 A:GLU560 4.5 45.4 1.0
HD21 A:LEU563 4.5 57.7 1.0
HB3 A:LEU563 4.5 41.9 1.0
H231 A:CVY801 4.5 69.9 1.0
HG A:LEU563 4.5 57.5 1.0
H211 A:CVY801 4.6 57.0 1.0
CB A:GLU560 4.6 37.8 1.0
OD2 A:ASP668 4.7 49.2 1.0
CG A:LEU564 4.7 34.9 1.0
HD21 A:LEU564 4.7 40.9 1.0
CB A:ASP668 4.7 32.3 1.0
N16 A:CVY801 4.7 37.9 1.0
OE1 A:GLU560 4.8 55.2 1.0
O A:GLU560 4.9 32.2 1.0
CA A:GLU560 4.9 35.8 1.0
O18 A:CVY801 4.9 28.9 1.0
CG A:LEU563 4.9 47.9 1.0
HB2 A:ASP668 4.9 38.8 1.0
CD1 A:LEU564 4.9 42.0 1.0

Fluorine binding site 2 out of 7 in 7xbi

Go back to Fluorine Binding Sites List in 7xbi
Fluorine binding site 2 out of 7 in the The Crystal Structure of Human Trka Kinase Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of Human Trka Kinase Bound to the Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:51.7
occ:1.00
 F28 A:CVY801 0.0 51.7 1.0
C27 A:CVY801 1.4 46.7 1.0
F30 A:CVY801 2.2 47.7 1.0
F29 A:CVY801 2.3 47.1 1.0
C22 A:CVY801 2.3 44.5 1.0
HG23 A:ILE572 2.4 30.4 1.0
H211 A:CVY801 2.5 57.0 1.0
C21 A:CVY801 2.7 47.5 1.0
CG2 A:ILE572 3.2 25.4 1.0
HG12 A:VAL573 3.2 41.0 1.0
HG21 A:ILE572 3.2 30.4 1.0
HA2 A:GLY667 3.3 32.6 1.0
O A:ILE666 3.4 28.8 1.0
HG22 A:ILE572 3.5 30.4 1.0
C23 A:CVY801 3.5 58.3 1.0
HD12 A:ILE572 3.5 45.2 1.0
HD12 A:LEU567 3.5 51.2 1.0
H231 A:CVY801 3.8 69.9 1.0
HD23 A:LEU564 3.9 40.9 1.0
HG22 A:ILE666 3.9 34.6 1.0
CG1 A:VAL573 4.0 34.2 1.0
C20 A:CVY801 4.0 48.4 1.0
HG13 A:VAL573 4.1 41.0 1.0
HD21 A:LEU641 4.1 39.8 1.0
HD13 A:LEU567 4.1 51.2 1.0
H A:VAL573 4.2 40.5 1.0
HG11 A:VAL573 4.2 41.0 1.0
CA A:GLY667 4.2 27.2 1.0
CD1 A:LEU567 4.3 42.7 1.0
C A:ILE666 4.3 29.7 1.0
HD11 A:LEU641 4.3 43.4 1.0
CD1 A:ILE572 4.4 37.7 1.0
HA A:ILE572 4.4 36.1 1.0
CB A:ILE572 4.4 27.5 1.0
HD13 A:ILE572 4.5 45.2 1.0
HB2 A:LEU567 4.5 49.1 1.0
C24 A:CVY801 4.6 65.2 1.0
N A:GLY667 4.7 26.9 1.0
HB A:ILE666 4.7 28.0 1.0
HB3 A:LEU567 4.7 49.1 1.0
HD21 A:LEU564 4.7 40.9 1.0
CD2 A:LEU564 4.8 34.1 1.0
N A:VAL573 4.8 33.8 1.0
C A:GLY667 4.8 26.9 1.0
C25 A:CVY801 4.8 63.4 1.0
HA3 A:GLY667 4.8 32.6 1.0
HD11 A:LEU567 4.8 51.2 1.0
CG1 A:ILE572 4.9 36.0 1.0
CG2 A:ILE666 4.9 28.9 1.0
CA A:ILE572 4.9 30.1 1.0
O18 A:CVY801 4.9 28.9 1.0
HG13 A:ILE572 4.9 43.2 1.0
HD2 A:HIS648 5.0 31.0 1.0

Fluorine binding site 3 out of 7 in 7xbi

Go back to Fluorine Binding Sites List in 7xbi
Fluorine binding site 3 out of 7 in the The Crystal Structure of Human Trka Kinase Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Crystal Structure of Human Trka Kinase Bound to the Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:47.1
occ:1.00
 F29 A:CVY801 0.0 47.1 1.0
C27 A:CVY801 1.4 46.7 1.0
F30 A:CVY801 2.3 47.7 1.0
F28 A:CVY801 2.3 51.7 1.0
H231 A:CVY801 2.3 69.9 1.0
C22 A:CVY801 2.3 44.5 1.0
C23 A:CVY801 2.7 58.3 1.0
HD11 A:LEU641 2.8 43.4 1.0
HE2 A:PHE646 2.8 59.1 1.0
HD21 A:LEU641 2.8 39.8 1.0
HD13 A:LEU567 3.2 51.2 1.0
HD12 A:LEU567 3.2 51.2 1.0
CE2 A:PHE646 3.3 49.2 1.0
HD13 A:LEU641 3.5 43.4 1.0
CD1 A:LEU641 3.5 36.1 1.0
C21 A:CVY801 3.6 47.5 1.0
CD1 A:LEU567 3.6 42.7 1.0
HD2 A:HIS648 3.6 31.0 1.0
CD2 A:LEU641 3.7 33.2 1.0
HD12 A:ILE572 3.7 45.2 1.0
HZ A:PHE646 3.7 56.1 1.0
HD22 A:LEU641 3.8 39.8 1.0
CZ A:PHE646 3.8 46.8 1.0
HD11 A:LEU567 3.9 51.2 1.0
H211 A:CVY801 4.0 57.0 1.0
HG22 A:ILE666 4.0 34.6 1.0
C24 A:CVY801 4.0 65.2 1.0
HG23 A:ILE572 4.1 30.4 1.0
CD2 A:PHE646 4.1 56.0 1.0
CG A:LEU641 4.2 34.5 1.0
HD2 A:PHE646 4.3 67.1 1.0
CD2 A:HIS648 4.3 25.8 1.0
HD12 A:LEU641 4.3 43.4 1.0
HD23 A:LEU641 4.4 39.8 1.0
HG21 A:ILE572 4.4 30.4 1.0
HG A:LEU641 4.7 41.4 1.0
C20 A:CVY801 4.7 48.4 1.0
HE2 A:HIS648 4.7 28.9 1.0
H241 A:CVY801 4.7 78.2 1.0
CD1 A:ILE572 4.7 37.7 1.0
CG2 A:ILE572 4.7 25.4 1.0
HA2 A:GLY667 4.7 32.6 1.0
HB3 A:LEU567 4.8 49.1 1.0
NE2 A:HIS648 4.8 24.1 1.0
C25 A:CVY801 4.9 63.4 1.0
CG2 A:ILE666 4.9 28.9 1.0
HB2 A:ASP668 4.9 38.8 1.0
CE1 A:PHE646 4.9 55.9 1.0
CG A:LEU567 4.9 37.8 1.0

Fluorine binding site 4 out of 7 in 7xbi

Go back to Fluorine Binding Sites List in 7xbi
Fluorine binding site 4 out of 7 in the The Crystal Structure of Human Trka Kinase Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Crystal Structure of Human Trka Kinase Bound to the Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:47.7
occ:1.00
 F30 A:CVY801 0.0 47.7 1.0
C27 A:CVY801 1.4 46.7 1.0
F28 A:CVY801 2.2 51.7 1.0
F29 A:CVY801 2.3 47.1 1.0
C22 A:CVY801 2.3 44.5 1.0
HG22 A:ILE666 2.6 34.6 1.0
HA2 A:GLY667 2.7 32.6 1.0
H211 A:CVY801 2.8 57.0 1.0
C21 A:CVY801 2.9 47.5 1.0
HE2 A:HIS648 3.0 28.9 1.0
HD2 A:HIS648 3.1 31.0 1.0
C23 A:CVY801 3.3 58.3 1.0
C A:GLY667 3.3 26.9 1.0
CA A:GLY667 3.3 27.2 1.0
O A:GLY667 3.4 23.3 1.0
HB2 A:ASP668 3.4 38.8 1.0
NE2 A:HIS648 3.5 24.1 1.0
CD2 A:HIS648 3.5 25.8 1.0
H231 A:CVY801 3.5 69.9 1.0
CG2 A:ILE666 3.6 28.9 1.0
O A:ILE666 3.7 28.8 1.0
N A:GLY667 3.8 26.9 1.0
HG23 A:ILE666 3.9 34.6 1.0
C A:ILE666 3.9 29.7 1.0
HD11 A:LEU641 3.9 43.4 1.0
N A:ASP668 3.9 31.4 1.0
HG21 A:ILE666 4.0 34.6 1.0
C20 A:CVY801 4.1 48.4 1.0
HA3 A:GLY667 4.2 32.6 1.0
CB A:ASP668 4.2 32.3 1.0
HE2 A:PHE646 4.2 59.1 1.0
HG23 A:ILE572 4.3 30.4 1.0
H A:ASP668 4.3 37.7 1.0
H A:GLY667 4.3 32.3 1.0
HG12 A:VAL573 4.3 41.0 1.0
HB3 A:ASP668 4.4 38.8 1.0
HB A:ILE666 4.4 28.0 1.0
C24 A:CVY801 4.4 65.2 1.0
HD12 A:ILE572 4.5 45.2 1.0
CB A:ILE666 4.5 23.4 1.0
CA A:ASP668 4.7 32.0 1.0
CE1 A:HIS648 4.7 27.3 1.0
HD21 A:LEU641 4.8 39.8 1.0
CD1 A:LEU641 4.8 36.1 1.0
C25 A:CVY801 4.8 63.4 1.0
CG A:HIS648 4.8 27.8 1.0
O18 A:CVY801 4.8 28.9 1.0
CA A:ILE666 4.8 28.2 1.0
HD13 A:LEU641 4.9 43.4 1.0
HA A:ASP668 5.0 38.4 1.0
HZ A:PHE646 5.0 56.1 1.0
CE2 A:PHE646 5.0 49.2 1.0
HD12 A:LEU567 5.0 51.2 1.0

Fluorine binding site 5 out of 7 in 7xbi

Go back to Fluorine Binding Sites List in 7xbi
Fluorine binding site 5 out of 7 in the The Crystal Structure of Human Trka Kinase Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Crystal Structure of Human Trka Kinase Bound to the Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:51.1
occ:1.00
 F32 A:CVY801 0.0 51.1 1.0
C31 A:CVY801 1.4 64.0 1.0
F33 A:CVY801 2.2 58.3 1.0
F34 A:CVY801 2.3 66.0 1.0
C11 A:CVY801 2.4 57.9 1.0
HB2 A:LYS544 2.5 38.4 1.0
HD3 A:LYS544 2.7 69.1 1.0
C08 A:CVY801 2.8 56.3 1.0
HG22 A:VAL524 2.9 49.6 1.0
C10 A:CVY801 2.9 47.5 1.0
O09 A:CVY801 3.0 38.5 1.0
H051 A:CVY801 3.2 57.5 1.0
HG21 A:VAL524 3.3 49.6 1.0
CB A:LYS544 3.3 32.0 1.0
N07 A:CVY801 3.4 43.6 1.0
CD A:LYS544 3.4 57.6 1.0
HG3 A:LYS544 3.4 57.2 1.0
CG2 A:VAL524 3.5 41.4 1.0
C12 A:CVY801 3.5 57.2 1.0
CG A:LYS544 3.5 47.7 1.0
HD2 A:LYS544 3.6 69.1 1.0
HE1 A:PHE589 3.7 42.4 1.0
HB3 A:LYS544 3.8 38.4 1.0
H121 A:CVY801 3.8 68.6 1.0
H071 A:CVY801 3.9 52.3 1.0
C05 A:CVY801 3.9 48.0 1.0
C04 A:CVY801 4.0 47.3 1.0
HG23 A:VAL524 4.0 49.6 1.0
HG11 A:VAL524 4.1 35.1 1.0
CE1 A:PHE589 4.1 35.4 1.0
C15 A:CVY801 4.3 43.2 1.0
HG13 A:VAL524 4.3 35.1 1.0
HD1 A:PHE589 4.3 33.9 1.0
HZ3 A:LYS544 4.4 116.0 1.0
CA A:LYS544 4.4 27.4 1.0
HA A:LYS544 4.4 32.8 1.0
CD1 A:PHE589 4.5 28.2 1.0
HG2 A:LYS544 4.5 57.2 1.0
CG1 A:VAL524 4.5 29.3 1.0
HZ2 A:LYS544 4.6 116.0 1.0
CB A:VAL524 4.6 29.8 1.0
C13 A:CVY801 4.7 43.8 1.0
CE A:LYS544 4.7 70.2 1.0
N A:LYS544 4.8 28.3 1.0
NZ A:LYS544 4.8 96.7 1.0
H A:LYS544 4.8 34.0 1.0
CZ A:PHE589 4.9 34.7 1.0
H151 A:CVY801 5.0 51.8 1.0

Fluorine binding site 6 out of 7 in 7xbi

Go back to Fluorine Binding Sites List in 7xbi
Fluorine binding site 6 out of 7 in the The Crystal Structure of Human Trka Kinase Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Crystal Structure of Human Trka Kinase Bound to the Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:58.3
occ:1.00
 F33 A:CVY801 0.0 58.3 1.0
C31 A:CVY801 1.4 64.0 1.0
HD3 A:LYS544 2.2 69.1 1.0
H121 A:CVY801 2.2 68.6 1.0
F32 A:CVY801 2.2 51.1 1.0
F34 A:CVY801 2.2 66.0 1.0
C11 A:CVY801 2.3 57.9 1.0
C12 A:CVY801 2.5 57.2 1.0
HZ3 A:LYS544 2.7 116.0 1.0
HE1 A:PHE589 2.9 42.4 1.0
HZ2 A:LYS544 3.0 116.0 1.0
HB2 A:LYS544 3.1 38.4 1.0
CD A:LYS544 3.1 57.6 1.0
NZ A:LYS544 3.2 96.7 1.0
CE1 A:PHE589 3.5 35.4 1.0
HB3 A:LYS544 3.5 38.4 1.0
C10 A:CVY801 3.6 47.5 1.0
CB A:LYS544 3.6 32.0 1.0
HZ A:PHE589 3.6 41.6 1.0
HD2 A:LYS544 3.7 69.1 1.0
CE A:LYS544 3.8 70.2 1.0
CG A:LYS544 3.8 47.7 1.0
CZ A:PHE589 3.9 34.7 1.0
C13 A:CVY801 3.9 43.8 1.0
HZ1 A:LYS544 4.0 116.0 1.0
HB2 A:MET587 4.0 44.5 1.0
SD A:MET587 4.1 54.3 1.0
C08 A:CVY801 4.2 56.3 1.0
HG3 A:LYS544 4.2 57.2 1.0
H051 A:CVY801 4.3 57.5 1.0
HE2 A:LYS544 4.3 84.2 1.0
H161 A:CVY801 4.3 45.4 1.0
O09 A:CVY801 4.3 38.5 1.0
CD1 A:PHE589 4.5 28.2 1.0
HE3 A:LYS544 4.5 84.2 1.0
N16 A:CVY801 4.6 37.9 1.0
HG2 A:LYS544 4.6 57.2 1.0
HD1 A:PHE589 4.6 33.9 1.0
C15 A:CVY801 4.7 43.2 1.0
HG22 A:VAL524 4.8 49.6 1.0
CB A:MET587 4.8 37.1 1.0
HB3 A:MET587 4.8 44.5 1.0
C14 A:CVY801 4.8 44.2 1.0
OE1 A:GLU560 4.9 55.2 1.0
HE1 A:MET587 5.0 51.0 1.0

Fluorine binding site 7 out of 7 in 7xbi

Go back to Fluorine Binding Sites List in 7xbi
Fluorine binding site 7 out of 7 in the The Crystal Structure of Human Trka Kinase Bound to the Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of The Crystal Structure of Human Trka Kinase Bound to the Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:66.0
occ:1.00
 F34 A:CVY801 0.0 66.0 1.0
C31 A:CVY801 1.4 64.0 1.0
HD3 A:LYS544 2.2 69.1 1.0
F33 A:CVY801 2.2 58.3 1.0
F32 A:CVY801 2.3 51.1 1.0
C11 A:CVY801 2.4 57.9 1.0
O09 A:CVY801 2.7 38.5 1.0
HD2 A:LYS544 2.7 69.1 1.0
CD A:LYS544 2.9 57.6 1.0
C10 A:CVY801 3.2 47.5 1.0
HZ2 A:LYS544 3.2 116.0 1.0
C08 A:CVY801 3.2 56.3 1.0
C12 A:CVY801 3.3 57.2 1.0
H121 A:CVY801 3.4 68.6 1.0
HZ3 A:LYS544 3.7 116.0 1.0
NZ A:LYS544 3.7 96.7 1.0
CE A:LYS544 3.9 70.2 1.0
CG A:LYS544 3.9 47.7 1.0
HB2 A:LYS544 3.9 38.4 1.0
HG3 A:LYS544 3.9 57.2 1.0
HG22 A:VAL524 4.1 49.6 1.0
HE3 A:LYS544 4.2 84.2 1.0
HG21 A:VAL524 4.3 49.6 1.0
CB A:LYS544 4.4 32.0 1.0
C15 A:CVY801 4.4 43.2 1.0
N07 A:CVY801 4.4 43.6 1.0
C13 A:CVY801 4.5 43.8 1.0
CG2 A:VAL524 4.6 41.4 1.0
HZ1 A:LYS544 4.6 116.0 1.0
HG23 A:VAL524 4.6 49.6 1.0
HE2 A:LYS544 4.7 84.2 1.0
HB3 A:LYS544 4.7 38.4 1.0
HG2 A:LYS544 4.7 57.2 1.0
HG A:SER672 4.8 80.7 1.0
H051 A:CVY801 4.8 57.5 1.0
H071 A:CVY801 4.8 52.3 1.0
C14 A:CVY801 5.0 44.2 1.0
HE1 A:PHE589 5.0 42.4 1.0
HA A:PHE669 5.0 53.3 1.0

Reference:

C.Y.Wu, G.Wang, L.Ouyang. The Crystal Structure of Human Trka Kinase Bound to the Inhibitor To Be Published.
Page generated: Fri Aug 2 15:23:09 2024

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