Atomistry » Fluorine » PDB 4xyf-4ymo » 4ybj
Atomistry »
  Fluorine »
    PDB 4xyf-4ymo »
      4ybj »

Fluorine in PDB 4ybj: Type II Dasatinib Analog Crystallized with C-Src Kinase

Enzymatic activity of Type II Dasatinib Analog Crystallized with C-Src Kinase

All present enzymatic activity of Type II Dasatinib Analog Crystallized with C-Src Kinase:
2.7.10.2;

Protein crystallography data

The structure of Type II Dasatinib Analog Crystallized with C-Src Kinase, PDB code: 4ybj was solved by F.E.Kwarcinski, K.B.Brandvold, T.K.Johnson, S.Phadke, J.L.Meagher, M.A.Seeliger, J.A.Stuckey, M.B.Soellner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.56 / 2.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.117, 120.062, 63.319, 90.00, 90.26, 90.00
R / Rfree (%) 21.8 / 25

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Type II Dasatinib Analog Crystallized with C-Src Kinase (pdb code 4ybj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Type II Dasatinib Analog Crystallized with C-Src Kinase, PDB code: 4ybj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 1 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:48.3
occ:1.00
 F3 A:4A9601 0.0 48.3 1.0
C11 A:4A9601 1.3 49.3 1.0
F1 A:4A9601 2.1 50.0 1.0
F2 A:4A9601 2.1 49.5 1.0
C10 A:4A9601 2.4 49.8 1.0
H8 A:4A9601 2.4 49.9 0.0
C12 A:4A9601 2.8 49.9 1.0
CD1 A:LEU317 3.6 42.5 1.0
C9 A:4A9601 3.7 49.9 1.0
CD1 A:LEU322 4.0 30.1 1.0
H7 A:4A9601 4.1 49.8 0.0
C13 A:4A9601 4.1 49.6 1.0
CE2 A:TYR382 4.2 41.4 1.0
CD2 A:HIS384 4.5 27.4 1.0
CD2 A:LEU322 4.7 31.8 1.0
CD2 A:TYR382 4.7 40.8 1.0
CG2 A:VAL377 4.8 26.8 1.0
CG A:LEU322 4.8 29.5 1.0
H9 A:4A9601 4.8 49.6 0.0
C8 A:4A9601 4.8 49.5 1.0
CG A:LEU317 4.9 43.4 1.0
CB A:LEU322 4.9 24.6 1.0
CZ A:TYR382 5.0 49.6 1.0
C14 A:4A9601 5.0 49.6 1.0

Fluorine binding site 2 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 2 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:49.5
occ:1.00
 F2 A:4A9601 0.0 49.5 1.0
C11 A:4A9601 1.3 49.3 1.0
F1 A:4A9601 2.1 50.0 1.0
F3 A:4A9601 2.1 48.3 1.0
C10 A:4A9601 2.4 49.8 1.0
H7 A:4A9601 2.7 49.8 0.0
C9 A:4A9601 2.9 49.9 1.0
O A:VAL402 3.3 30.1 1.0
CB A:LEU322 3.5 24.6 1.0
C12 A:4A9601 3.6 49.9 1.0
CD1 A:LEU322 3.7 30.1 1.0
H8 A:4A9601 3.9 49.9 0.0
CG A:LEU322 4.0 29.5 1.0
CD2 A:LEU322 4.1 31.8 1.0
N A:VAL323 4.1 27.4 1.0
C A:VAL402 4.1 30.5 1.0
CA A:LEU322 4.2 24.3 1.0
C8 A:4A9601 4.3 49.5 1.0
O A:VAL323 4.4 33.0 1.0
C A:LEU322 4.5 30.0 1.0
CA A:ALA403 4.6 28.7 1.0
N A:ALA403 4.7 28.3 1.0
C13 A:4A9601 4.7 49.6 1.0
CG1 A:VAL402 4.8 28.3 1.0
CB A:VAL402 4.8 28.7 1.0
CD1 A:LEU317 5.0 42.5 1.0

Fluorine binding site 3 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 3 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:50.0
occ:1.00
 F1 A:4A9601 0.0 50.0 1.0
C11 A:4A9601 1.3 49.3 1.0
F3 A:4A9601 2.1 48.3 1.0
F2 A:4A9601 2.1 49.5 1.0
C10 A:4A9601 2.4 49.8 1.0
C9 A:4A9601 3.2 49.9 1.0
H7 A:4A9601 3.3 49.8 0.0
C12 A:4A9601 3.3 49.9 1.0
CG1 A:VAL402 3.3 28.3 1.0
H8 A:4A9601 3.4 49.9 0.0
O A:VAL402 3.5 30.1 1.0
CD2 A:HIS384 3.5 27.4 1.0
NE2 A:HIS384 3.6 26.6 1.0
C A:VAL402 3.6 30.5 1.0
N A:ALA403 3.8 28.3 1.0
CA A:ALA403 3.9 28.7 1.0
CB A:VAL402 3.9 28.7 1.0
O A:ALA403 4.0 33.1 1.0
C A:ALA403 4.0 33.7 1.0
CA A:VAL402 4.4 25.0 1.0
C8 A:4A9601 4.4 49.5 1.0
C13 A:4A9601 4.5 49.6 1.0
CD2 A:LEU322 4.5 31.8 1.0
N A:ASP404 4.8 31.7 1.0
CG A:HIS384 4.8 26.3 1.0
CD1 A:LEU322 4.9 30.1 1.0
CE1 A:HIS384 4.9 26.2 1.0
C14 A:4A9601 4.9 49.6 1.0

Fluorine binding site 4 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 4 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:49.2
occ:1.00
 F3 B:4A9601 0.0 49.2 1.0
C11 B:4A9601 1.3 48.4 1.0
F2 B:4A9601 2.1 46.9 1.0
F1 B:4A9601 2.1 49.0 1.0
C10 B:4A9601 2.4 48.8 1.0
C9 B:4A9601 3.1 48.9 1.0
H7 B:4A9601 3.2 49.0 0.0
NE2 B:HIS384 3.3 30.7 1.0
C12 B:4A9601 3.3 49.0 1.0
CD2 B:HIS384 3.4 31.2 1.0
CG1 B:VAL402 3.4 26.8 1.0
O B:ALA403 3.4 30.2 1.0
H8 B:4A9601 3.5 49.0 0.0
O B:VAL402 3.5 29.5 1.0
C B:ALA403 3.6 31.2 1.0
C B:VAL402 3.7 29.4 1.0
N B:ALA403 3.8 26.4 1.0
CA B:ALA403 3.8 26.7 1.0
CB B:VAL402 4.1 27.1 1.0
N B:ASP404 4.3 29.5 1.0
C8 B:4A9601 4.4 48.8 1.0
CB B:ASP404 4.5 32.3 1.0
CA B:VAL402 4.5 23.6 1.0
C13 B:4A9601 4.5 49.3 1.0
CE1 B:HIS384 4.5 30.2 1.0
CG B:LEU322 4.7 35.5 1.0
CG B:HIS384 4.7 29.9 1.0
CD2 B:LEU322 4.9 38.2 1.0
C14 B:4A9601 5.0 49.3 1.0
CA B:ASP404 5.0 30.1 1.0

Fluorine binding site 5 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 5 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:46.9
occ:1.00
 F2 B:4A9601 0.0 46.9 1.0
C11 B:4A9601 1.3 48.4 1.0
F3 B:4A9601 2.1 49.2 1.0
F1 B:4A9601 2.1 49.0 1.0
C10 B:4A9601 2.4 48.8 1.0
H8 B:4A9601 2.5 49.0 0.0
C12 B:4A9601 2.8 49.0 1.0
C9 B:4A9601 3.7 48.9 1.0
CD1 B:LEU317 3.7 47.8 1.0
CD2 B:LEU322 3.8 38.2 1.0
H7 B:4A9601 4.1 49.0 0.0
CE2 B:TYR382 4.1 40.1 1.0
C13 B:4A9601 4.2 49.3 1.0
CG B:LEU322 4.2 35.5 1.0
CD2 B:HIS384 4.4 31.2 1.0
CD2 B:TYR382 4.7 39.5 1.0
NE2 B:HIS384 4.8 30.7 1.0
C8 B:4A9601 4.8 48.8 1.0
H9 B:4A9601 4.8 49.3 0.0
CZ B:TYR382 4.9 49.2 1.0
OH B:TYR382 4.9 50.3 1.0
CG2 B:VAL377 4.9 30.1 1.0
O B:VAL402 4.9 29.5 1.0
CG1 B:VAL402 4.9 26.8 1.0

Fluorine binding site 6 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 6 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:49.0
occ:1.00
 F1 B:4A9601 0.0 49.0 1.0
C11 B:4A9601 1.3 48.4 1.0
F2 B:4A9601 2.1 46.9 1.0
F3 B:4A9601 2.1 49.2 1.0
C10 B:4A9601 2.4 48.8 1.0
H7 B:4A9601 2.7 49.0 0.0
C9 B:4A9601 2.9 48.9 1.0
O B:VAL402 3.1 29.5 1.0
CG B:LEU322 3.3 35.5 1.0
CD2 B:LEU322 3.4 38.2 1.0
C12 B:4A9601 3.6 49.0 1.0
H8 B:4A9601 3.9 49.0 0.0
C B:VAL402 3.9 29.4 1.0
CB B:LEU322 4.0 31.4 1.0
N B:VAL323 4.3 35.6 1.0
C8 B:4A9601 4.3 48.8 1.0
CA B:ALA403 4.4 26.7 1.0
CA B:LEU322 4.4 31.1 1.0
CD1 B:LEU322 4.4 35.0 1.0
N B:ALA403 4.5 26.4 1.0
CG1 B:VAL402 4.6 26.8 1.0
O B:VAL323 4.6 42.4 1.0
CB B:VAL402 4.7 27.1 1.0
C B:LEU322 4.7 37.1 1.0
C13 B:4A9601 4.7 49.3 1.0
C B:ALA403 4.8 31.2 1.0
CA B:VAL402 4.9 23.6 1.0

Reference:

F.E.Kwarcinski, K.R.Brandvold, S.Phadke, O.M.Beleh, T.K.Johnson, J.L.Meagher, M.A.Seeliger, J.A.Stuckey, M.B.Soellner. Conformation-Selective Analogues of Dasatinib Reveal Insight Into Kinase Inhibitor Binding and Selectivity. Acs Chem.Biol. V. 11 1296 2016.
ISSN: ESSN 1554-8937
PubMed: 26895387
DOI: 10.1021/ACSCHEMBIO.5B01018
Page generated: Tue Jul 15 01:41:17 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy