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Fluorine in PDB 6qu7: Crystal Structure of Human Dhodh in Complex with Bay 2402234

Enzymatic activity of Crystal Structure of Human Dhodh in Complex with Bay 2402234

All present enzymatic activity of Crystal Structure of Human Dhodh in Complex with Bay 2402234:
1.3.5.2;

Protein crystallography data

The structure of Crystal Structure of Human Dhodh in Complex with Bay 2402234, PDB code: 6qu7 was solved by A.Friberg, S.Gradl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.29 / 1.52
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.659, 90.659, 122.501, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 17.3

Other elements in 6qu7:

The structure of Crystal Structure of Human Dhodh in Complex with Bay 2402234 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Dhodh in Complex with Bay 2402234 (pdb code 6qu7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of Human Dhodh in Complex with Bay 2402234, PDB code: 6qu7:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 6qu7

Go back to Fluorine Binding Sites List in 6qu7
Fluorine binding site 1 out of 5 in the Crystal Structure of Human Dhodh in Complex with Bay 2402234


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Dhodh in Complex with Bay 2402234 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:22.5
occ:1.00
 F25 A:JJE403 0.0 22.5 1.0
C19 A:JJE403 1.3 23.0 1.0
C20 A:JJE403 2.3 24.4 1.0
C18 A:JJE403 2.4 22.0 1.0
N17 A:JJE403 2.7 19.4 1.0
O2 A:JJE403 2.9 20.6 1.0
C1 A:JJE403 2.9 18.6 1.0
OG1 A:THR63 3.1 20.1 1.0
O A:ALA59 3.3 19.7 1.0
CA A:ALA59 3.6 18.4 1.0
C23 A:JJE403 3.6 24.7 1.0
C21 A:JJE403 3.6 26.1 1.0
CB A:ALA59 3.7 19.3 1.0
C A:ALA59 3.8 18.5 1.0
CB A:PHE62 4.0 22.1 0.5
C15 A:JJE403 4.1 16.7 1.0
C22 A:JJE403 4.1 26.1 1.0
CB A:PHE62 4.1 24.3 0.5
N A:THR63 4.3 20.7 1.0
CE A:MET111 4.4 23.1 1.0
CB A:THR63 4.4 20.0 1.0
CG A:PRO364 4.5 20.3 1.0
CD2 A:LEU68 4.6 33.5 1.0
F5 A:JJE403 4.6 21.5 1.0
CD2 A:PHE62 4.6 24.1 0.5
C9 A:JJE403 4.7 16.2 1.0
CA A:THR63 4.7 20.4 1.0
CG A:PHE62 4.8 23.5 0.5
C A:PHE62 4.8 22.1 0.5
C16 A:JJE403 4.9 17.3 1.0
C A:PHE62 4.9 21.7 0.5
O14 A:JJE403 4.9 18.5 1.0
N A:ALA59 4.9 19.4 1.0
CD2 A:PHE62 4.9 30.0 0.5
CA A:PHE62 5.0 22.2 0.5
CG A:PHE62 5.0 28.0 0.5

Fluorine binding site 2 out of 5 in 6qu7

Go back to Fluorine Binding Sites List in 6qu7
Fluorine binding site 2 out of 5 in the Crystal Structure of Human Dhodh in Complex with Bay 2402234


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Dhodh in Complex with Bay 2402234 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:21.5
occ:1.00
 F5 A:JJE403 0.0 21.5 1.0
C7 A:JJE403 1.3 21.6 1.0
F4 A:JJE403 2.1 22.2 1.0
F6 A:JJE403 2.2 23.4 1.0
C8 A:JJE403 2.3 19.9 1.0
O14 A:JJE403 2.7 18.5 1.0
N A:ALA59 3.2 19.4 1.0
CA A:ALA59 3.4 18.4 1.0
N17 A:JJE403 3.5 19.4 1.0
O A:ALA55 3.6 18.4 1.0
C16 A:JJE403 3.6 17.3 1.0
CD2 A:PHE62 3.6 30.0 0.5
C3 A:JJE403 3.6 21.4 1.0
C A:LEU58 3.6 20.1 0.5
C A:LEU58 3.6 20.4 0.5
CB A:ALA59 3.6 19.3 1.0
CB A:LEU58 3.7 23.1 0.5
CB A:LEU58 3.8 21.5 0.5
CE2 A:PHE62 3.8 31.4 0.5
CD2 A:PHE62 3.8 24.1 0.5
CE2 A:PHE62 3.8 25.6 0.5
CG A:LEU58 4.1 25.6 0.5
O A:LEU58 4.1 20.4 0.5
C18 A:JJE403 4.1 22.0 1.0
O A:LEU58 4.1 20.7 0.5
CA A:LEU58 4.3 21.7 0.5
C15 A:JJE403 4.3 16.7 1.0
CA A:LEU58 4.3 21.0 0.5
C1 A:JJE403 4.3 18.6 1.0
C13 A:JJE403 4.3 16.7 1.0
CD2 A:LEU58 4.5 26.4 0.5
F25 A:JJE403 4.6 22.5 1.0
C19 A:JJE403 4.6 23.0 1.0
C A:ALA55 4.6 18.8 1.0
CG A:PHE62 4.7 23.5 0.5
CZ A:PHE62 4.7 26.1 0.5
C23 A:JJE403 4.8 24.7 1.0
C A:ALA59 4.8 18.5 1.0
CG A:PHE62 4.8 28.0 0.5
CL A:JJE403 5.0 27.6 1.0

Fluorine binding site 3 out of 5 in 6qu7

Go back to Fluorine Binding Sites List in 6qu7
Fluorine binding site 3 out of 5 in the Crystal Structure of Human Dhodh in Complex with Bay 2402234


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Dhodh in Complex with Bay 2402234 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:23.4
occ:1.00
 F6 A:JJE403 0.0 23.4 1.0
C7 A:JJE403 1.3 21.6 1.0
F4 A:JJE403 2.1 22.2 1.0
F5 A:JJE403 2.2 21.5 1.0
C8 A:JJE403 2.3 19.9 1.0
C3 A:JJE403 2.8 21.4 1.0
CD1 A:LEU50 3.4 29.1 1.0
O14 A:JJE403 3.5 18.5 1.0
CD2 A:LEU58 3.6 26.4 0.5
CB A:LEU58 3.7 23.1 0.5
CB A:LEU58 3.8 21.5 0.5
CG A:LEU58 3.9 25.6 0.5
O A:ALA55 3.9 18.4 1.0
CD1 A:LEU58 4.0 23.6 0.5
CA A:ALA55 4.3 19.0 1.0
CE2 A:PHE62 4.3 31.4 0.5
CE2 A:PHE62 4.4 25.6 0.5
CD1 A:LEU46 4.5 30.7 1.0
CG A:LEU58 4.6 22.9 0.5
C A:ALA55 4.6 18.8 1.0
C16 A:JJE403 4.6 17.3 1.0
CB A:ALA55 4.6 20.0 1.0
N A:ALA59 4.7 19.4 1.0
CB A:LEU46 4.8 27.9 1.0
CD2 A:PHE62 4.8 30.0 0.5
C A:LEU58 4.9 20.1 0.5
CA A:LEU58 4.9 21.7 0.5
C A:LEU58 4.9 20.4 0.5
CA A:LEU58 4.9 21.0 0.5
CG A:LEU50 4.9 28.9 1.0

Fluorine binding site 4 out of 5 in 6qu7

Go back to Fluorine Binding Sites List in 6qu7
Fluorine binding site 4 out of 5 in the Crystal Structure of Human Dhodh in Complex with Bay 2402234


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Dhodh in Complex with Bay 2402234 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:22.2
occ:1.00
 F4 A:JJE403 0.0 22.2 1.0
C7 A:JJE403 1.3 21.6 1.0
F5 A:JJE403 2.1 21.5 1.0
F6 A:JJE403 2.1 23.4 1.0
C8 A:JJE403 2.3 19.9 1.0
O14 A:JJE403 2.6 18.5 1.0
C3 A:JJE403 2.8 21.4 1.0
CD1 A:LEU46 3.4 30.7 1.0
N17 A:JJE403 3.5 19.4 1.0
CL A:JJE403 3.6 27.6 1.0
C16 A:JJE403 4.0 17.3 1.0
C18 A:JJE403 4.0 22.0 1.0
CE2 A:PHE62 4.0 25.6 0.5
C23 A:JJE403 4.0 24.7 1.0
CD2 A:PHE62 4.3 24.1 0.5
CE2 A:PHE62 4.5 31.4 0.5
CG A:LEU46 4.6 30.1 1.0
C1 A:JJE403 4.6 18.6 1.0
CD2 A:PHE62 4.6 30.0 0.5
CB A:LEU46 4.6 27.9 1.0
C15 A:JJE403 4.7 16.7 1.0
C13 A:JJE403 4.9 16.7 1.0
C19 A:JJE403 5.0 23.0 1.0

Fluorine binding site 5 out of 5 in 6qu7

Go back to Fluorine Binding Sites List in 6qu7
Fluorine binding site 5 out of 5 in the Crystal Structure of Human Dhodh in Complex with Bay 2402234


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Dhodh in Complex with Bay 2402234 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:17.0
occ:1.00
 F10 A:JJE403 0.0 17.0 1.0
C11 A:JJE403 1.3 15.8 1.0
C9 A:JJE403 2.3 16.2 1.0
C12 A:JJE403 2.4 15.7 1.0
O31 A:JJE403 2.6 16.0 1.0
N26 A:JJE403 2.8 17.6 1.0
C27 A:JJE403 2.9 17.4 1.0
CG2 A:THR360 3.5 20.0 1.0
CE1 A:TYR356 3.5 14.1 1.0
C13 A:JJE403 3.6 16.7 1.0
C15 A:JJE403 3.6 16.7 1.0
CE1 A:PHE98 3.6 17.9 1.0
CD1 A:PHE98 3.8 16.8 1.0
CD2 A:LEU359 3.8 21.7 1.0
N30 A:JJE403 3.9 17.4 1.0
N A:THR360 4.0 18.3 1.0
CG A:LEU359 4.0 20.9 1.0
CA A:THR360 4.1 19.3 1.0
CB A:LEU359 4.1 18.8 1.0
C16 A:JJE403 4.1 17.3 1.0
N28 A:JJE403 4.1 16.9 1.0
C A:LEU359 4.1 18.5 1.0
CD1 A:TYR356 4.1 14.3 1.0
CB A:THR360 4.3 19.9 1.0
O A:LEU359 4.4 19.4 1.0
CZ A:TYR356 4.6 13.8 1.0
C29 A:JJE403 4.6 17.2 1.0
OH A:TYR356 4.6 15.7 1.0
CA A:LEU359 4.8 17.2 1.0
CB A:ALA59 4.8 19.3 1.0
CZ A:PHE98 4.8 18.8 1.0
C1 A:JJE403 4.9 18.6 1.0
O A:TYR356 4.9 15.1 1.0
CG A:PHE98 5.0 14.9 1.0
O2 A:JJE403 5.0 20.6 1.0

Reference:

S.Christian, C.Merz, L.Evans, S.Gradl, H.Seidel, A.Friberg, A.Eheim, P.Lejeune, K.Brzezinka, K.Zimmermann, S.Ferrara, H.Meyer, R.Lesche, D.Stoeckigt, M.Bauser, A.Haegebarth, D.B.Sykes, D.T.Scadden, J.A.Losman, A.Janzer. The Novel Dihydroorotate Dehydrogenase (Dhodh) Inhibitor Bay 2402234 Triggers Differentiation and Is Effective in the Treatment of Myeloid Malignancies. Leukemia V. 33 2403 2019.
ISSN: ESSN 1476-5551
PubMed: 30940908
DOI: 10.1038/S41375-019-0461-5
Page generated: Fri Aug 2 01:01:14 2024

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