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Fluorine in PDB 6u65: Mcl-1 Bound to Compound 19

Protein crystallography data

The structure of Mcl-1 Bound to Compound 19, PDB code: 6u65 was solved by J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.12 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.712, 85.223, 109.753, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Mcl-1 Bound to Compound 19 (pdb code 6u65). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Mcl-1 Bound to Compound 19, PDB code: 6u65:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6u65

Go back to Fluorine Binding Sites List in 6u65
Fluorine binding site 1 out of 4 in the Mcl-1 Bound to Compound 19


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mcl-1 Bound to Compound 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:38.9
occ:1.00
F A:Q0A401 0.0 38.9 1.0
C9 A:Q0A401 1.4 37.8 1.0
C8 A:Q0A401 2.3 35.5 1.0
C10 A:Q0A401 2.4 36.6 1.0
CD1 A:LEU290 3.3 21.9 1.0
C7 A:Q0A401 3.6 31.6 1.0
C11 A:Q0A401 3.6 34.2 1.0
CG2 A:VAL274 3.7 20.6 1.0
CD1 A:ILE294 3.8 22.8 1.0
CA A:GLY271 3.9 16.7 1.0
CB A:VAL274 4.1 21.1 1.0
C6 A:Q0A401 4.1 29.0 1.0
CD2 A:PHE270 4.2 18.7 1.0
CG1 A:ILE294 4.2 20.6 1.0
CG A:LEU290 4.3 21.2 1.0
CD1 A:LEU246 4.4 33.6 1.0
CE2 A:PHE270 4.4 20.6 1.0
N A:GLY271 4.4 18.3 1.0
CG1 A:VAL274 4.4 21.8 1.0
CD2 A:LEU290 4.6 21.1 1.0
SD A:MET250 4.6 34.9 1.0
O A:PHE270 4.6 18.9 1.0
C A:PHE270 4.7 20.4 1.0

Fluorine binding site 2 out of 4 in 6u65

Go back to Fluorine Binding Sites List in 6u65
Fluorine binding site 2 out of 4 in the Mcl-1 Bound to Compound 19


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mcl-1 Bound to Compound 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:30.8
occ:1.00
F B:Q0A401 0.0 30.8 1.0
C9 B:Q0A401 1.4 26.6 1.0
C8 B:Q0A401 2.3 23.9 1.0
C10 B:Q0A401 2.3 25.7 1.0
CD1 B:LEU290 3.4 24.3 1.0
C7 B:Q0A401 3.6 19.9 1.0
C11 B:Q0A401 3.6 23.3 1.0
CA B:GLY271 3.7 18.4 1.0
CD1 B:ILE294 3.9 22.3 1.0
CG2 B:VAL274 4.0 21.0 1.0
C6 B:Q0A401 4.1 20.6 1.0
CD1 B:LEU246 4.1 26.7 1.0
CG1 B:ILE294 4.2 20.9 1.0
N B:GLY271 4.2 18.6 1.0
CD2 B:PHE270 4.3 19.4 1.0
CB B:VAL274 4.3 20.9 1.0
CG B:LEU290 4.4 23.4 1.0
CD2 B:LEU290 4.5 26.6 1.0
SD B:MET250 4.6 29.5 1.0
O B:PHE270 4.6 20.9 1.0
C B:PHE270 4.6 21.1 1.0
CG1 B:VAL274 4.7 20.2 1.0
CE2 B:PHE270 4.7 20.5 1.0
C B:GLY271 4.9 20.9 1.0
O B:GLY271 5.0 20.6 1.0
CB B:LEU246 5.0 22.7 1.0

Fluorine binding site 3 out of 4 in 6u65

Go back to Fluorine Binding Sites List in 6u65
Fluorine binding site 3 out of 4 in the Mcl-1 Bound to Compound 19


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Mcl-1 Bound to Compound 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:33.1
occ:1.00
F C:Q0A401 0.0 33.1 1.0
C9 C:Q0A401 1.4 31.6 1.0
C10 C:Q0A401 2.4 30.6 1.0
C8 C:Q0A401 2.4 28.9 1.0
CD1 C:LEU290 3.4 35.0 1.0
C11 C:Q0A401 3.6 31.0 1.0
C7 C:Q0A401 3.6 29.6 1.0
CG2 C:VAL274 3.8 27.0 1.0
CA C:GLY271 3.9 24.4 1.0
CD1 C:ILE294 4.0 27.6 1.0
C6 C:Q0A401 4.1 31.1 1.0
CB C:VAL274 4.1 27.6 1.0
CD2 C:PHE270 4.3 29.3 1.0
CD1 C:LEU246 4.3 36.7 1.0
CG C:LEU290 4.3 33.4 1.0
N C:GLY271 4.3 24.8 1.0
CG1 C:ILE294 4.3 25.9 1.0
CD2 C:LEU290 4.5 34.0 1.0
SD C:MET250 4.5 39.8 1.0
CG1 C:VAL274 4.5 28.1 1.0
O C:PHE270 4.6 26.0 1.0
CE2 C:PHE270 4.6 31.2 1.0
C C:PHE270 4.7 27.3 1.0
C C:GLY271 4.9 27.8 1.0
O C:GLY271 4.9 27.9 1.0

Fluorine binding site 4 out of 4 in 6u65

Go back to Fluorine Binding Sites List in 6u65
Fluorine binding site 4 out of 4 in the Mcl-1 Bound to Compound 19


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Mcl-1 Bound to Compound 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:39.8
occ:1.00
F D:Q0A401 0.0 39.8 1.0
C9 D:Q0A401 1.4 37.7 1.0
C10 D:Q0A401 2.3 35.1 1.0
C8 D:Q0A401 2.3 37.8 1.0
CD1 D:LEU290 3.3 42.0 1.0
C11 D:Q0A401 3.6 35.3 1.0
C7 D:Q0A401 3.6 38.9 1.0
CA D:GLY271 3.7 27.0 1.0
CG2 D:VAL274 3.7 30.7 1.0
CB D:VAL274 3.9 32.0 1.0
CD1 D:LEU246 4.1 55.1 1.0
CD2 D:LEU290 4.1 42.5 1.0
C6 D:Q0A401 4.1 38.9 1.0
CG D:LEU290 4.2 41.9 1.0
CG1 D:VAL274 4.2 33.5 1.0
N D:GLY271 4.2 26.8 1.0
CE D:MET250 4.2 55.3 1.0
CD1 D:ILE294 4.3 30.5 1.0
CD2 D:PHE270 4.4 31.7 1.0
O D:PHE270 4.5 28.6 1.0
C D:PHE270 4.6 28.3 1.0
CG1 D:ILE294 4.7 35.1 1.0
CE2 D:PHE270 4.7 34.8 1.0
C D:GLY271 4.8 30.5 1.0
O D:GLY271 4.8 30.9 1.0
SD D:MET250 4.9 57.0 1.0
CB D:LEU246 5.0 52.1 1.0

Reference:

K.J.Kump, L.Miao, A.S.A.Mady, N.H.Ansari, U.K.Shrestha, Y.Yang, M.Pal, C.Liao, A.Perdih, F.A.Abulwerdi, K.Chinnaswamy, J.L.Meagher, J.M.Carlson, M.Khanna, J.A.Stuckey, Z.Nikolovska-Coleska. Discovery and Characterization of 2,5-Substituted Benzoic Acid Dual Inhibitors of the Anti-Apoptotic Mcl-1 and Bfl-1 Proteins. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 31971799
DOI: 10.1021/ACS.JMEDCHEM.9B01442
Page generated: Fri Aug 2 02:18:25 2024

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