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Fluorine in PDB 5mvc: Crystal Structure of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds

Enzymatic activity of Crystal Structure of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds

All present enzymatic activity of Crystal Structure of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds:
1.3.5.2;

Protein crystallography data

The structure of Crystal Structure of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds, PDB code: 5mvc was solved by P.Goyal, M.Andersson, A.C.Moritzer, S.Sainas, A.C.Pippione, D.Boschi, S.Al-Kadaraghi, M.Lolli, R.Friemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.85 / 1.85
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.190, 91.190, 122.645, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 18.9

Other elements in 5mvc:

The structure of Crystal Structure of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds (pdb code 5mvc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds, PDB code: 5mvc:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5mvc

Go back to Fluorine Binding Sites List in 5mvc
Fluorine binding site 1 out of 4 in the Crystal Structure of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds


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 Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:18.8
occ:1.00
F13 A:Y9B403 0.0 18.8 1.0
C12 A:Y9B403 1.3 17.7 1.0
C14 A:Y9B403 2.3 17.3 1.0
C11 A:Y9B403 2.4 17.7 1.0
F15 A:Y9B403 2.7 20.0 1.0
C27 A:Y9B403 2.9 17.0 1.0
C25 A:Y9B403 3.0 14.0 1.0
CD A:PRO364 3.6 13.5 1.0
C16 A:Y9B403 3.6 21.1 1.0
C19 A:Y9B403 3.6 22.7 1.0
CD1 A:LEU359 3.7 12.1 1.0
CG A:LEU359 3.8 10.7 1.0
CG A:PRO364 3.9 16.5 1.0
CB A:ALA59 4.0 12.7 1.0
C28 A:Y9B403 4.0 17.7 1.0
C17 A:Y9B403 4.1 19.2 1.0
C23 A:Y9B403 4.2 15.3 1.0
O A:LEU359 4.2 12.1 1.0
N A:PRO364 4.3 11.1 1.0
CD2 A:LEU359 4.3 10.7 1.0
CA A:GLY363 4.4 9.2 1.0
C A:GLY363 4.7 10.3 1.0
N03 A:Y9B403 4.8 18.4 1.0
F20 A:Y9B403 4.8 23.9 1.0
O05 A:Y9B403 4.8 15.3 1.0
C A:LEU359 4.9 10.4 1.0
CA A:ALA59 4.9 8.8 1.0
C30 A:Y9B403 5.0 18.8 1.0
CE A:MET111 5.0 12.1 1.0
CE A:MET43 5.0 14.8 1.0

Fluorine binding site 2 out of 4 in 5mvc

Go back to Fluorine Binding Sites List in 5mvc
Fluorine binding site 2 out of 4 in the Crystal Structure of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds


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 Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:20.0
occ:1.00
F15 A:Y9B403 0.0 20.0 1.0
C14 A:Y9B403 1.3 17.3 1.0
C16 A:Y9B403 2.3 21.1 1.0
C12 A:Y9B403 2.3 17.7 1.0
F13 A:Y9B403 2.7 18.8 1.0
O05 A:Y9B403 2.7 15.3 1.0
N03 A:Y9B403 2.8 18.4 1.0
C02 A:Y9B403 2.9 13.9 1.0
O A:LEU359 3.3 12.1 1.0
CA A:THR360 3.5 12.5 1.0
C17 A:Y9B403 3.6 19.2 1.0
C11 A:Y9B403 3.6 17.7 1.0
C A:LEU359 3.7 10.4 1.0
N A:THR360 3.8 9.1 1.0
CG A:LEU359 3.9 10.7 1.0
C19 A:Y9B403 4.1 22.7 1.0
CB A:ALA59 4.1 12.7 1.0
C01 A:Y9B403 4.1 12.8 1.0
CE A:MET43 4.2 14.8 1.0
CB A:THR360 4.4 10.1 1.0
CG2 A:THR360 4.4 12.9 1.0
C A:THR360 4.4 17.1 1.0
O A:HOH510 4.4 18.6 1.0
O A:THR360 4.5 14.9 1.0
CD2 A:LEU359 4.6 10.7 1.0
CB A:LEU359 4.6 9.4 1.0
CD1 A:LEU359 4.6 12.1 1.0
F18 A:Y9B403 4.7 25.5 1.0
CE1 A:PHE98 4.7 14.0 1.0
CA A:LEU359 4.8 13.2 1.0
N10 A:Y9B403 4.9 11.9 1.0
C27 A:Y9B403 4.9 17.0 1.0

Fluorine binding site 3 out of 4 in 5mvc

Go back to Fluorine Binding Sites List in 5mvc
Fluorine binding site 3 out of 4 in the Crystal Structure of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds


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 Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:25.5
occ:1.00
F18 A:Y9B403 0.0 25.5 1.0
C17 A:Y9B403 1.3 19.2 1.0
C16 A:Y9B403 2.3 21.1 1.0
C19 A:Y9B403 2.4 22.7 1.0
N03 A:Y9B403 2.7 18.4 1.0
F20 A:Y9B403 2.7 23.9 1.0
O A:ALA55 3.5 12.9 1.0
CB A:ALA55 3.6 9.8 1.0
C14 A:Y9B403 3.6 17.3 1.0
C11 A:Y9B403 3.6 17.7 1.0
C02 A:Y9B403 3.8 13.9 1.0
CD1 A:LEU46 3.9 30.8 1.0
C A:ALA55 4.0 12.4 1.0
CA A:ALA55 4.0 10.4 1.0
C12 A:Y9B403 4.1 17.7 1.0
O07 A:Y9B403 4.1 15.1 1.0
O05 A:Y9B403 4.4 15.3 1.0
CE A:MET43 4.4 14.8 1.0
CB A:LEU46 4.5 26.5 1.0
F15 A:Y9B403 4.7 20.0 1.0
CB A:ALA59 4.7 12.7 1.0
CG A:LEU46 4.7 36.5 1.0
C01 A:Y9B403 4.7 12.8 1.0
C06 A:Y9B403 4.8 12.8 1.0
SD A:MET43 4.9 17.7 1.0
C27 A:Y9B403 4.9 17.0 1.0
N A:ALA59 5.0 12.9 1.0

Fluorine binding site 4 out of 4 in 5mvc

Go back to Fluorine Binding Sites List in 5mvc
Fluorine binding site 4 out of 4 in the Crystal Structure of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds


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 Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:23.9
occ:1.00
F20 A:Y9B403 0.0 23.9 1.0
C19 A:Y9B403 1.3 22.7 1.0
C17 A:Y9B403 2.3 19.2 1.0
C11 A:Y9B403 2.4 17.7 1.0
F18 A:Y9B403 2.7 25.5 1.0
C27 A:Y9B403 2.8 17.0 1.0
C28 A:Y9B403 3.0 17.7 1.0
CD1 A:LEU46 3.3 30.8 1.0
C16 A:Y9B403 3.6 21.1 1.0
C12 A:Y9B403 3.6 17.7 1.0
C25 A:Y9B403 3.9 14.0 1.0
C14 A:Y9B403 4.1 17.3 1.0
C30 A:Y9B403 4.1 18.8 1.0
CA A:ALA59 4.6 8.8 1.0
CB A:ALA59 4.6 12.7 1.0
CG A:LEU46 4.6 36.5 1.0
SD A:MET43 4.7 17.7 1.0
N03 A:Y9B403 4.7 18.4 1.0
N A:ALA59 4.8 12.9 1.0
F13 A:Y9B403 4.8 18.8 1.0
C23 A:Y9B403 4.8 15.3 1.0
CD2 A:LEU58 4.8 26.6 1.0
O A:ALA55 4.9 12.9 1.0
C21 A:Y9B403 4.9 13.2 1.0
CD2 A:LEU46 4.9 34.5 1.0
CG A:LEU58 5.0 26.4 1.0

Reference:

S.Sainas, A.C.Pippione, M.Giorgis, E.Lupino, P.Goyal, C.Ramondetti, B.Buccinna, M.Piccinini, R.C.Braga, C.H.Andrade, M.Andersson, A.C.Moritzer, R.Friemann, S.Mensa, S.Al-Kadaraghi, D.Boschi, M.L.Lolli. Design, Synthesis, Biological Evaluation and X-Ray Structural Studies of Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on Hydroxylated Azole Scaffolds. Eur J Med Chem V. 129 287 2017.
ISSN: ISSN 1768-3254
PubMed: 28235702
DOI: 10.1016/J.EJMECH.2017.02.017
Page generated: Thu Aug 1 11:51:35 2024

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