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Fluorine in PDB 6hd6: ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571)

Enzymatic activity of ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571)

All present enzymatic activity of ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571):
2.7.10.2;

Protein crystallography data

The structure of ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571), PDB code: 6hd6 was solved by S.W.Cowan-Jacob, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.25 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.080, 65.201, 66.347, 73.30, 79.82, 84.54
R / Rfree (%) 17.5 / 23.8

Other elements in 6hd6:

The structure of ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571) (pdb code 6hd6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571), PDB code: 6hd6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6hd6

Go back to Fluorine Binding Sites List in 6hd6
Fluorine binding site 1 out of 6 in the ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:33.6
occ:0.50
 F1 A:FYH602 0.0 33.6 0.5
F1 A:FYH602 0.5 28.8 0.5
C2 A:FYH602 1.4 32.8 0.5
C2 A:FYH602 1.8 28.5 0.5
F3 A:FYH602 2.2 34.0 0.5
F4 A:FYH602 2.2 32.3 0.5
O5 A:FYH602 2.3 33.2 0.5
F3 A:FYH602 2.5 31.4 0.5
O5 A:FYH602 2.6 27.0 0.5
F4 A:FYH602 2.7 28.1 0.5
C6 A:FYH602 2.9 33.2 0.5
C6 A:FYH602 3.1 26.4 0.5
CD1 A:LEU448 3.2 15.0 1.0
C14 A:FYH602 3.3 32.5 0.5
C14 A:FYH602 3.5 25.3 0.5
CG1 A:VAL487 3.7 22.0 1.0
C7 A:FYH602 3.9 32.8 0.5
CG2 A:ILE451 3.9 18.5 1.0
O A:LEU448 4.1 13.9 1.0
C7 A:FYH602 4.1 26.3 0.5
CG A:LEU448 4.1 14.7 1.0
N A:ALA452 4.3 18.2 1.0
CB A:ALA363 4.4 14.0 1.0
CB A:ALA452 4.4 18.7 1.0
CB A:ILE451 4.5 18.3 1.0
C12 A:FYH602 4.5 33.6 0.5
CA A:ALA452 4.6 17.7 1.0
C12 A:FYH602 4.6 25.9 0.5
CB A:VAL487 4.8 23.5 1.0
O A:LEU359 4.9 17.3 1.0
C A:LEU448 4.9 14.2 1.0
C9 A:FYH602 4.9 32.3 0.5
C A:LEU359 4.9 15.9 1.0
C A:ILE451 5.0 18.8 1.0
CB A:LEU359 5.0 13.9 1.0

Fluorine binding site 2 out of 6 in 6hd6

Go back to Fluorine Binding Sites List in 6hd6
Fluorine binding site 2 out of 6 in the ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:28.8
occ:0.50
 F1 A:FYH602 0.0 28.8 0.5
F1 A:FYH602 0.5 33.6 0.5
C2 A:FYH602 0.9 32.8 0.5
C2 A:FYH602 1.4 28.5 0.5
F4 A:FYH602 1.8 32.3 0.5
F3 A:FYH602 1.9 34.0 0.5
O5 A:FYH602 2.0 33.2 0.5
F3 A:FYH602 2.2 31.4 0.5
F4 A:FYH602 2.2 28.1 0.5
O5 A:FYH602 2.3 27.0 0.5
C6 A:FYH602 2.8 33.2 0.5
C6 A:FYH602 3.0 26.4 0.5
CD1 A:LEU448 3.3 15.0 1.0
C14 A:FYH602 3.3 32.5 0.5
C14 A:FYH602 3.5 25.3 0.5
CG1 A:VAL487 3.6 22.0 1.0
C7 A:FYH602 3.7 32.8 0.5
C7 A:FYH602 4.0 26.3 0.5
CG2 A:ILE451 4.1 18.5 1.0
CB A:ALA363 4.3 14.0 1.0
CG A:LEU448 4.4 14.7 1.0
O A:LEU448 4.5 13.9 1.0
C12 A:FYH602 4.6 33.6 0.5
O A:LEU359 4.6 17.3 1.0
N A:LEU360 4.7 17.3 1.0
C A:LEU359 4.7 15.9 1.0
CA A:LEU360 4.7 17.5 1.0
CB A:VAL487 4.7 23.5 1.0
C12 A:FYH602 4.7 25.9 0.5
CB A:ILE451 4.7 18.3 1.0
N A:ALA452 4.8 18.2 1.0
CG2 A:VAL487 4.8 23.1 1.0
CB A:ALA452 4.9 18.7 1.0
C9 A:FYH602 4.9 32.3 0.5
CB A:LEU359 4.9 13.9 1.0
CA A:ALA452 5.0 17.7 1.0

Fluorine binding site 3 out of 6 in 6hd6

Go back to Fluorine Binding Sites List in 6hd6
Fluorine binding site 3 out of 6 in the ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:34.0
occ:0.50
 F3 A:FYH602 0.0 34.0 0.5
F3 A:FYH602 0.9 31.4 0.5
C2 A:FYH602 1.4 32.8 0.5
C2 A:FYH602 1.6 28.5 0.5
F1 A:FYH602 1.9 28.8 0.5
F4 A:FYH602 2.2 32.3 0.5
F1 A:FYH602 2.2 33.6 0.5
F4 A:FYH602 2.3 28.1 0.5
O5 A:FYH602 2.3 33.2 0.5
C A:LEU359 2.8 15.9 1.0
N A:LEU360 2.8 17.3 1.0
O5 A:FYH602 2.9 27.0 0.5
O A:LEU359 3.0 17.3 1.0
C6 A:FYH602 3.1 33.2 0.5
CA A:LEU360 3.1 17.5 1.0
C7 A:FYH602 3.4 32.8 0.5
CB A:LEU359 3.4 13.9 1.0
C6 A:FYH602 3.5 26.4 0.5
CG2 A:ILE451 3.6 18.5 1.0
CA A:LEU359 3.7 14.7 1.0
C7 A:FYH602 3.8 26.3 0.5
CB A:ALA363 4.0 14.0 1.0
CB A:LEU360 4.1 17.7 1.0
C14 A:FYH602 4.2 32.5 0.5
C A:LEU360 4.2 16.9 1.0
C14 A:FYH602 4.4 25.3 0.5
C9 A:FYH602 4.6 32.3 0.5
O A:LEU360 4.6 16.9 1.0
CD1 A:LEU448 4.7 15.0 1.0
O A:ALA356 4.7 19.6 1.0
CB A:ILE451 4.7 18.3 1.0
CG A:LEU359 4.7 13.5 1.0
CD1 A:LEU360 4.8 18.5 1.0
N A:LEU359 4.9 14.3 1.0
C9 A:FYH602 4.9 24.0 0.5
CD1 A:ILE521 4.9 27.0 1.0
N A:ALA363 4.9 15.3 1.0

Fluorine binding site 4 out of 6 in 6hd6

Go back to Fluorine Binding Sites List in 6hd6
Fluorine binding site 4 out of 6 in the ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:31.4
occ:0.50
 F3 A:FYH602 0.0 31.4 0.5
F3 A:FYH602 0.9 34.0 0.5
C2 A:FYH602 1.4 28.5 0.5
C2 A:FYH602 1.4 32.8 0.5
O5 A:FYH602 1.8 33.2 0.5
F1 A:FYH602 2.2 28.8 0.5
F4 A:FYH602 2.2 28.1 0.5
O5 A:FYH602 2.3 27.0 0.5
F4 A:FYH602 2.4 32.3 0.5
C6 A:FYH602 2.4 33.2 0.5
F1 A:FYH602 2.5 33.6 0.5
C7 A:FYH602 2.6 32.8 0.5
N A:LEU360 2.7 17.3 1.0
C6 A:FYH602 2.9 26.4 0.5
C7 A:FYH602 3.0 26.3 0.5
C A:LEU359 3.0 15.9 1.0
CA A:LEU360 3.1 17.5 1.0
CB A:LEU359 3.3 13.9 1.0
O A:LEU359 3.5 17.3 1.0
C14 A:FYH602 3.7 32.5 0.5
CB A:LEU360 3.8 17.7 1.0
CA A:LEU359 3.8 14.7 1.0
C9 A:FYH602 3.9 32.3 0.5
C14 A:FYH602 4.0 25.3 0.5
O A:ALA356 4.1 19.6 1.0
CD1 A:ILE521 4.1 27.0 1.0
C9 A:FYH602 4.2 24.0 0.5
CG2 A:ILE451 4.2 18.5 1.0
C A:LEU360 4.4 16.9 1.0
CD1 A:LEU360 4.6 18.5 1.0
CG A:LEU359 4.7 13.5 1.0
C12 A:FYH602 4.7 33.6 0.5
CB A:ALA363 4.8 14.0 1.0
C11 A:FYH602 4.8 32.3 0.5
N A:LEU359 4.8 14.3 1.0
CG A:LEU360 4.8 20.0 1.0
O A:LEU360 4.9 16.9 1.0
CD1 A:LEU359 4.9 11.4 1.0
C12 A:FYH602 4.9 25.9 0.5

Fluorine binding site 5 out of 6 in 6hd6

Go back to Fluorine Binding Sites List in 6hd6
Fluorine binding site 5 out of 6 in the ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:32.3
occ:0.50
 F4 A:FYH602 0.0 32.3 0.5
F4 A:FYH602 0.8 28.1 0.5
C2 A:FYH602 1.4 32.8 0.5
C2 A:FYH602 1.5 28.5 0.5
F1 A:FYH602 1.8 28.8 0.5
F3 A:FYH602 2.2 34.0 0.5
F1 A:FYH602 2.2 33.6 0.5
O5 A:FYH602 2.3 33.2 0.5
F3 A:FYH602 2.4 31.4 0.5
O5 A:FYH602 2.7 27.0 0.5
CE1 A:PHE512 3.6 22.9 1.0
CB A:ALA363 3.6 14.0 1.0
C6 A:FYH602 3.6 33.2 0.5
CD1 A:LEU448 3.6 15.0 1.0
CA A:LEU360 3.7 17.5 1.0
CD1 A:LEU360 3.8 18.5 1.0
CG1 A:VAL487 3.8 22.0 1.0
C6 A:FYH602 3.9 26.4 0.5
N A:LEU360 4.2 17.3 1.0
CZ A:PHE512 4.2 20.2 1.0
CB A:LEU360 4.3 17.7 1.0
CG2 A:VAL487 4.3 23.1 1.0
O A:LEU359 4.4 17.3 1.0
CD1 A:PHE512 4.4 22.2 1.0
C7 A:FYH602 4.5 32.8 0.5
C14 A:FYH602 4.5 32.5 0.5
C A:LEU359 4.5 15.9 1.0
O A:LEU360 4.5 16.9 1.0
C A:LEU360 4.6 16.9 1.0
CB A:VAL487 4.7 23.5 1.0
CG A:LEU360 4.7 20.0 1.0
C7 A:FYH602 4.7 26.3 0.5
C14 A:FYH602 4.8 25.3 0.5
CD1 A:ILE521 4.8 27.0 1.0
CG A:LEU448 4.9 14.7 1.0

Fluorine binding site 6 out of 6 in 6hd6

Go back to Fluorine Binding Sites List in 6hd6
Fluorine binding site 6 out of 6 in the ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of ABL1 in Complex with COMPOUND6 and Imatinib (Sti-571) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:28.1
occ:0.50
 F4 A:FYH602 0.0 28.1 0.5
F4 A:FYH602 0.8 32.3 0.5
C2 A:FYH602 1.4 28.5 0.5
C2 A:FYH602 1.5 32.8 0.5
O5 A:FYH602 1.9 33.2 0.5
F1 A:FYH602 2.2 28.8 0.5
F3 A:FYH602 2.2 31.4 0.5
O5 A:FYH602 2.3 27.0 0.5
F3 A:FYH602 2.3 34.0 0.5
F1 A:FYH602 2.7 33.6 0.5
CD1 A:LEU360 3.3 18.5 1.0
C6 A:FYH602 3.3 33.2 0.5
CA A:LEU360 3.4 17.5 1.0
C6 A:FYH602 3.6 26.4 0.5
CE1 A:PHE512 3.8 22.9 1.0
CB A:LEU360 3.8 17.7 1.0
CG1 A:VAL487 3.8 22.0 1.0
CG2 A:VAL487 3.9 23.1 1.0
N A:LEU360 4.0 17.3 1.0
CD1 A:ILE521 4.1 27.0 1.0
C7 A:FYH602 4.1 32.8 0.5
CG A:LEU360 4.2 20.0 1.0
CB A:ALA363 4.2 14.0 1.0
C14 A:FYH602 4.3 32.5 0.5
C7 A:FYH602 4.3 26.3 0.5
CD1 A:LEU448 4.3 15.0 1.0
CD1 A:PHE512 4.5 22.2 1.0
C A:LEU360 4.5 16.9 1.0
CB A:VAL487 4.5 23.5 1.0
C A:LEU359 4.6 15.9 1.0
O A:LEU360 4.6 16.9 1.0
O A:LEU359 4.6 17.3 1.0
C14 A:FYH602 4.6 25.3 0.5
CZ A:PHE512 4.6 20.2 1.0

Reference:

J.Schoepfer, W.Jahnke, G.Berellini, S.Buonamici, S.Cotesta, S.W.Cowan-Jacob, S.Dodd, P.Drueckes, D.Fabbro, T.Gabriel, J.M.Groell, R.M.Grotzfeld, A.Q.Hassan, C.Henry, V.Iyer, D.Jones, F.Lombardo, A.Loo, P.W.Manley, X.Pelle, G.Rummel, B.Salem, M.Warmuth, A.A.Wylie, T.Zoller, A.L.Marzinzik, P.Furet. Discovery of Asciminib (ABL001), An Allosteric Inhibitor of the Tyrosine Kinase Activity of Bcr-ABL1. J. Med. Chem. V. 61 8120 2018.
ISSN: ISSN 1520-4804
PubMed: 30137981
DOI: 10.1021/ACS.JMEDCHEM.8B01040
Page generated: Thu Aug 1 21:00:41 2024

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