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Fluorine in PDB 6fmd: Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold

Enzymatic activity of Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold

All present enzymatic activity of Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold:
1.3.5.2;

Protein crystallography data

The structure of Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold, PDB code: 6fmd was solved by P.Goyal, M.Jarva, M.Andersson, M.L.Lolli, R.Friemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.32 / 1.58
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.441, 90.441, 122.446, 90.00, 90.00, 120.00
R / Rfree (%) 13.7 / 16

Other elements in 6fmd:

The structure of Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold (pdb code 6fmd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold, PDB code: 6fmd:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6fmd

Go back to Fluorine Binding Sites List in 6fmd
Fluorine binding site 1 out of 4 in the Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:21.5
occ:1.00
 F16 A:DUH401 0.0 21.5 1.0
C12 A:DUH401 1.3 20.6 1.0
C13 A:DUH401 2.4 20.9 1.0
C11 A:DUH401 2.4 20.2 1.0
O23 A:DUH401 2.7 18.3 1.0
F17 A:DUH401 2.7 22.6 1.0
N20 A:DUH401 2.8 18.8 1.0
C22 A:DUH401 3.0 17.5 1.0
O A:LEU359 3.3 18.4 1.0
CA A:THR360 3.4 19.3 1.0
C10 A:DUH401 3.6 21.9 1.0
C14 A:DUH401 3.7 23.0 1.0
C A:LEU359 3.7 16.4 1.0
N A:THR360 3.8 17.9 1.0
CG A:LEU359 3.9 19.1 1.0
CB A:ALA59 4.1 18.9 1.0
C15 A:DUH401 4.1 22.5 1.0
C25 A:DUH401 4.1 16.8 1.0
CG2 A:THR360 4.2 18.9 1.0
CB A:THR360 4.2 19.1 1.0
CE A:MET43 4.2 28.0 1.0
C A:THR360 4.3 19.5 1.0
O A:THR360 4.4 24.1 1.0
CD2 A:LEU359 4.4 19.5 1.0
CE1 A:PHE98 4.4 19.0 1.0
CB A:LEU359 4.6 18.3 1.0
CD1 A:LEU359 4.7 21.4 1.0
F19 A:DUH401 4.8 26.5 1.0
CA A:LEU359 4.8 16.5 1.0
C29 A:DUH401 4.8 16.7 1.0
C4 A:DUH401 4.9 22.5 1.0
C26 A:DUH401 4.9 17.5 1.0

Fluorine binding site 2 out of 4 in 6fmd

Go back to Fluorine Binding Sites List in 6fmd
Fluorine binding site 2 out of 4 in the Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:22.6
occ:1.00
 F17 A:DUH401 0.0 22.6 1.0
C11 A:DUH401 1.3 20.2 1.0
C10 A:DUH401 2.3 21.9 1.0
C12 A:DUH401 2.4 20.6 1.0
F16 A:DUH401 2.7 21.5 1.0
C4 A:DUH401 2.8 22.5 1.0
C3 A:DUH401 3.0 23.1 1.0
C13 A:DUH401 3.6 20.9 1.0
CD A:PRO364 3.7 23.3 1.0
C15 A:DUH401 3.7 22.5 1.0
CD1 A:LEU359 3.7 21.4 1.0
CG A:LEU359 3.8 19.1 1.0
CG A:PRO364 4.0 23.0 1.0
C5 A:DUH401 4.0 23.3 1.0
CB A:ALA59 4.1 18.9 1.0
O A:LEU359 4.1 18.4 1.0
C14 A:DUH401 4.1 23.0 1.0
CD2 A:LEU359 4.2 19.5 1.0
C2 A:DUH401 4.3 24.1 1.0
N A:PRO364 4.4 21.3 1.0
CA A:GLY363 4.4 20.9 1.0
C A:GLY363 4.7 21.1 1.0
CE A:MET111 4.7 27.6 1.0
CE A:MET43 4.7 28.0 1.0
F18 A:DUH401 4.8 29.8 1.0
N20 A:DUH401 4.8 18.8 1.0
O23 A:DUH401 4.8 18.3 1.0
C A:LEU359 4.8 16.4 1.0
C6 A:DUH401 4.9 26.1 1.0
CZ A:PHE98 5.0 20.6 1.0
CA A:ALA59 5.0 19.5 1.0

Fluorine binding site 3 out of 4 in 6fmd

Go back to Fluorine Binding Sites List in 6fmd
Fluorine binding site 3 out of 4 in the Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:29.8
occ:1.00
 F18 A:DUH401 0.0 29.8 1.0
C15 A:DUH401 1.3 22.5 1.0
C14 A:DUH401 2.3 23.0 1.0
C10 A:DUH401 2.4 21.9 1.0
F19 A:DUH401 2.7 26.5 1.0
C4 A:DUH401 2.8 22.5 1.0
C5 A:DUH401 3.0 23.3 1.0
CD1 A:LEU46 3.1 37.5 1.0
C13 A:DUH401 3.6 20.9 1.0
C11 A:DUH401 3.6 20.2 1.0
C3 A:DUH401 3.8 23.1 1.0
CD2 A:PHE62 4.0 37.3 1.0
C6 A:DUH401 4.1 26.1 1.0
CE2 A:PHE62 4.1 43.3 1.0
C12 A:DUH401 4.1 20.6 1.0
CG A:LEU46 4.5 36.5 1.0
CA A:ALA59 4.6 19.5 1.0
CB A:ALA59 4.6 18.9 1.0
SD A:MET43 4.7 28.2 1.0
CD2 A:LEU58 4.7 38.8 1.0
N A:ALA59 4.7 20.4 1.0
F17 A:DUH401 4.8 22.6 1.0
N20 A:DUH401 4.8 18.8 1.0
C2 A:DUH401 4.8 24.1 1.0
CB A:LEU46 4.9 31.1 1.0
C7 A:DUH401 4.9 23.5 1.0
CE A:MET43 4.9 28.0 1.0
CD2 A:LEU46 5.0 39.5 1.0

Fluorine binding site 4 out of 4 in 6fmd

Go back to Fluorine Binding Sites List in 6fmd
Fluorine binding site 4 out of 4 in the Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Targeting Myeloid Differentiation Using Potent Human Dihydroorotate Dehydrogenase (Hdhodh) Inhibitors Based on 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:26.5
occ:1.00
 F19 A:DUH401 0.0 26.5 1.0
C14 A:DUH401 1.3 23.0 1.0
C15 A:DUH401 2.3 22.5 1.0
C13 A:DUH401 2.4 20.9 1.0
F18 A:DUH401 2.7 29.8 1.0
N20 A:DUH401 2.8 18.8 1.0
CB A:ALA55 3.5 21.1 1.0
C12 A:DUH401 3.6 20.6 1.0
O A:ALA55 3.7 18.5 1.0
C10 A:DUH401 3.7 21.9 1.0
C22 A:DUH401 3.9 17.5 1.0
CA A:ALA55 4.0 19.9 1.0
CD1 A:LEU46 4.0 37.5 1.0
C A:ALA55 4.1 19.4 1.0
C11 A:DUH401 4.2 20.2 1.0
CB A:LEU46 4.2 31.1 1.0
O34 A:DUH401 4.3 19.0 1.0
O23 A:DUH401 4.4 18.3 1.0
CE A:MET43 4.5 28.0 1.0
CB A:ALA59 4.6 18.9 1.0
CG A:LEU46 4.7 36.5 1.0
F16 A:DUH401 4.8 21.5 1.0
C25 A:DUH401 4.8 16.8 1.0
C4 A:DUH401 4.9 22.5 1.0
N A:ALA59 4.9 20.4 1.0
C26 A:DUH401 4.9 17.5 1.0

Reference:

S.Sainas, A.C.Pippione, E.Lupino, M.Giorgis, P.Circosta, V.Gaidano, P.Goyal, D.Bonanni, B.Rolando, A.Cignetti, A.Ducime, M.Andersson, M.Jarva, R.Friemann, M.Piccinini, C.Ramondetti, B.Buccinna, S.Al-Karadaghi, D.Boschi, G.Saglio, M.L.Lolli. Targeting Myeloid Differentiation Using Potent 2-Hydroxypyrazolo[1,5- A]Pyridine Scaffold-Based Human Dihydroorotate Dehydrogenase Inhibitors. J. Med. Chem. V. 61 6034 2018.
ISSN: ISSN 1520-4804
PubMed: 29939742
DOI: 10.1021/ACS.JMEDCHEM.8B00373
Page generated: Thu Aug 1 20:07:29 2024

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