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Fluorine in PDB 5u6b: Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor

Enzymatic activity of Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor

All present enzymatic activity of Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor:
2.7.10.1;

Protein crystallography data

The structure of Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor, PDB code: 5u6b was solved by K.S.Gajiwala, N.Grodsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.81 / 2.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.680, 100.704, 81.921, 90.00, 93.97, 90.00
R / Rfree (%) 21.1 / 23.9

Other elements in 5u6b:

The structure of Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor (pdb code 5u6b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor, PDB code: 5u6b:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5u6b

Go back to Fluorine Binding Sites List in 5u6b
Fluorine binding site 1 out of 4 in the Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:50.8
occ:1.00
 F24 A:7YS9001 0.0 50.8 1.0
C21 A:7YS9001 1.4 48.6 1.0
C22 A:7YS9001 2.3 48.2 1.0
C20 A:7YS9001 2.4 47.6 1.0
CL25 A:7YS9001 2.8 52.0 1.0
CB A:ALA689 3.5 38.9 1.0
C A:ASN677 3.5 35.7 1.0
CA A:ASN677 3.6 30.3 1.0
C23 A:7YS9001 3.6 46.4 1.0
C16 A:7YS9001 3.6 44.9 1.0
CG A:MET679 3.7 44.4 1.0
SD A:MET679 3.7 48.9 1.0
O A:ASN677 3.7 34.8 1.0
O A:ARG676 4.0 37.6 1.0
N A:CYS678 4.1 34.0 1.0
C15 A:7YS9001 4.1 44.7 1.0
CB A:ASN677 4.5 31.8 1.0
N A:ASP690 4.5 43.3 1.0
C A:ALA689 4.5 43.3 1.0
OD1 A:ASN677 4.5 46.7 1.0
CA A:ALA689 4.6 38.4 1.0
N A:ASN677 4.6 30.7 1.0
C A:CYS678 4.7 40.4 1.0
C A:ARG676 4.7 36.4 1.0
N A:MET679 4.8 38.5 1.0
CA A:CYS678 4.8 33.7 1.0
CB A:ASP690 4.8 47.4 1.0
O A:CYS678 4.9 40.6 1.0
CB A:MET679 4.9 40.5 1.0
C17 A:7YS9001 5.0 42.5 1.0
CG A:ASN677 5.0 49.2 1.0

Fluorine binding site 2 out of 4 in 5u6b

Go back to Fluorine Binding Sites List in 5u6b
Fluorine binding site 2 out of 4 in the Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F9001

b:57.5
occ:1.00
 F24 B:7YS9001 0.0 57.5 1.0
C21 B:7YS9001 1.4 58.8 1.0
C22 B:7YS9001 2.3 58.7 1.0
C20 B:7YS9001 2.4 61.2 1.0
CL25 B:7YS9001 2.9 67.6 1.0
CB B:ALA689 3.4 41.4 1.0
C B:ASN677 3.5 36.6 1.0
CG B:MET679 3.6 41.1 1.0
C23 B:7YS9001 3.6 58.5 1.0
O B:ASN677 3.6 36.5 1.0
CA B:ASN677 3.6 33.8 1.0
C16 B:7YS9001 3.7 57.9 1.0
SD B:MET679 3.8 45.2 1.0
OD1 B:ASP690 4.0 59.0 1.0
O B:ARG676 4.0 39.1 1.0
N B:CYS678 4.1 32.6 1.0
C15 B:7YS9001 4.1 58.6 1.0
CG B:ASP690 4.3 59.3 1.0
N B:ASP690 4.4 37.8 1.0
C B:ALA689 4.5 41.8 1.0
CA B:ALA689 4.5 40.8 1.0
CB B:ASN677 4.5 32.2 1.0
CB B:ASP690 4.6 39.5 1.0
N B:ASN677 4.6 34.5 1.0
OD1 B:ASN677 4.6 45.2 1.0
C B:CYS678 4.6 38.4 1.0
C B:ARG676 4.7 38.3 1.0
N B:MET679 4.7 35.4 1.0
CA B:CYS678 4.8 32.6 1.0
CB B:MET679 4.8 37.5 1.0
OD2 B:ASP690 4.9 72.1 1.0
O B:CYS678 5.0 39.0 1.0
C17 B:7YS9001 5.0 52.7 1.0

Fluorine binding site 3 out of 4 in 5u6b

Go back to Fluorine Binding Sites List in 5u6b
Fluorine binding site 3 out of 4 in the Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F9001

b:48.9
occ:1.00
 F24 C:7YS9001 0.0 48.9 1.0
C21 C:7YS9001 1.4 50.7 1.0
C20 C:7YS9001 2.3 50.2 1.0
C22 C:7YS9001 2.3 51.4 1.0
CL25 C:7YS9001 2.8 50.6 1.0
CB C:ALA689 3.5 42.6 1.0
C C:ASN677 3.5 38.0 1.0
CG C:MET679 3.5 45.8 1.0
CA C:ASN677 3.5 33.2 1.0
C23 C:7YS9001 3.6 49.3 1.0
C16 C:7YS9001 3.6 48.2 1.0
O C:ASN677 3.6 37.4 1.0
SD C:MET679 3.7 50.6 1.0
O C:ARG676 4.0 38.2 1.0
N C:CYS678 4.1 35.5 1.0
C15 C:7YS9001 4.1 47.9 1.0
CB C:ASN677 4.4 34.4 1.0
N C:ASP690 4.5 46.5 1.0
C C:ALA689 4.5 47.8 1.0
OD1 C:ASN677 4.5 45.6 1.0
N C:ASN677 4.5 33.7 1.0
CA C:ALA689 4.6 41.8 1.0
C C:CYS678 4.6 40.5 1.0
C C:ARG676 4.7 38.2 1.0
CB C:ASP690 4.7 49.2 1.0
N C:MET679 4.7 38.4 1.0
CA C:CYS678 4.8 34.8 1.0
CB C:MET679 4.8 41.4 1.0
O C:CYS678 4.9 40.4 1.0
C17 C:7YS9001 4.9 46.5 1.0
CG C:ASN677 5.0 47.4 1.0

Fluorine binding site 4 out of 4 in 5u6b

Go back to Fluorine Binding Sites List in 5u6b
Fluorine binding site 4 out of 4 in the Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Axl Kinase Domain in Complex with A Macrocyclic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F9001

b:47.4
occ:1.00
 F24 D:7YS9001 0.0 47.4 1.0
C21 D:7YS9001 1.3 48.0 1.0
C22 D:7YS9001 2.3 46.5 1.0
C20 D:7YS9001 2.4 52.7 1.0
CL25 D:7YS9001 2.9 59.5 1.0
CB D:ALA689 3.4 40.1 1.0
C D:ASN677 3.5 40.0 1.0
C23 D:7YS9001 3.6 46.8 1.0
O D:ASN677 3.6 38.5 1.0
CG D:MET679 3.6 50.4 1.0
CA D:ASN677 3.6 35.2 1.0
C16 D:7YS9001 3.7 49.5 1.0
SD D:MET679 3.8 54.7 1.0
O D:ARG676 4.0 38.7 1.0
N D:CYS678 4.1 38.3 1.0
C15 D:7YS9001 4.1 48.3 1.0
N D:ASP690 4.3 40.7 1.0
C D:ALA689 4.5 43.3 1.0
CA D:ALA689 4.5 39.5 1.0
CB D:ASP690 4.5 43.6 1.0
CB D:ASN677 4.6 32.7 1.0
OD2 D:ASP690 4.6 73.0 1.0
C D:CYS678 4.6 45.0 1.0
N D:ASN677 4.6 35.3 1.0
OD1 D:ASN677 4.6 52.2 1.0
C D:ARG676 4.7 38.5 1.0
CA D:CYS678 4.8 38.2 1.0
N D:MET679 4.8 43.6 1.0
O D:CYS678 4.9 45.0 1.0
CB D:MET679 4.9 46.5 1.0
C17 D:7YS9001 4.9 44.8 1.0
CA D:ASP690 5.0 41.0 1.0

Reference:

K.S.Gajiwala, N.Grodsky, B.Bolanos, J.Feng, R.Ferre, S.Timofeevski, M.Xu, B.W.Murray, T.W.Johnson, A.Stewart. The Axl Kinase Domain in Complex with A Macrocyclic Inhibitor Offers First Structural Insights Into An Active Tam Receptor Kinase. J. Biol. Chem. V. 292 15705 2017.
ISSN: ESSN 1083-351X
PubMed: 28724631
DOI: 10.1074/JBC.M116.771485
Page generated: Thu Aug 1 15:34:17 2024

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