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Fluorine in PDB 5fi8: Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bounded with DSM422 (Tetrahydro-2-Naphthyl and 2- Indanyl Triazolopyrimidine)

Enzymatic activity of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bounded with DSM422 (Tetrahydro-2-Naphthyl and 2- Indanyl Triazolopyrimidine)

All present enzymatic activity of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bounded with DSM422 (Tetrahydro-2-Naphthyl and 2- Indanyl Triazolopyrimidine):
1.3.5.2;

Protein crystallography data

The structure of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bounded with DSM422 (Tetrahydro-2-Naphthyl and 2- Indanyl Triazolopyrimidine), PDB code: 5fi8 was solved by X.Deng, S.Kokkonda, D.Tomchick, M.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.50 / 2.32
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 86.147, 86.147, 139.053, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 22.2

Other elements in 5fi8:

The structure of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bounded with DSM422 (Tetrahydro-2-Naphthyl and 2- Indanyl Triazolopyrimidine) also contains other interesting chemical elements:

Bromine (Br) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bounded with DSM422 (Tetrahydro-2-Naphthyl and 2- Indanyl Triazolopyrimidine) (pdb code 5fi8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bounded with DSM422 (Tetrahydro-2-Naphthyl and 2- Indanyl Triazolopyrimidine), PDB code: 5fi8:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5fi8

Go back to Fluorine Binding Sites List in 5fi8
Fluorine binding site 1 out of 2 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bounded with DSM422 (Tetrahydro-2-Naphthyl and 2- Indanyl Triazolopyrimidine)


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 Plasmodium Falciparum Dihydroorotate Dehydrogenase Bounded with DSM422 (Tetrahydro-2-Naphthyl and 2- Indanyl Triazolopyrimidine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:41.5
occ:1.00
 F1 A:5Y51001 0.0 41.5 1.0
C13 A:5Y51001 1.3 27.3 1.0
F2 A:5Y51001 2.2 25.1 1.0
C14 A:5Y51001 2.3 25.8 1.0
C12 A:5Y51001 2.3 19.1 1.0
H143 A:5Y51001 2.6 30.9 1.0
H141 A:5Y51001 2.6 30.9 1.0
N3 A:5Y51001 2.7 22.0 1.0
HG21 A:ILE263 3.1 35.5 1.0
H142 A:5Y51001 3.2 30.9 1.0
HE1 A:TYR528 3.5 31.0 1.0
HD13 A:ILE263 3.5 39.8 1.0
N4 A:5Y51001 3.6 26.7 1.0
HB2 A:HIS185 3.7 37.7 1.0
HG21 A:VAL532 3.7 43.5 1.0
HM71 A:FMN1002 3.8 26.0 1.0
HM73 A:FMN1002 3.9 26.0 1.0
HD13 A:ILE272 4.0 31.6 1.0
CG2 A:ILE263 4.0 29.6 1.0
N2 A:5Y51001 4.0 32.2 1.0
ND1 A:HIS185 4.1 18.0 1.0
HG21 A:ILE272 4.1 31.9 1.0
HG22 A:ILE263 4.2 35.5 1.0
HG22 A:VAL532 4.2 43.5 1.0
HD12 A:ILE263 4.2 39.8 1.0
OH A:TYR528 4.3 24.0 1.0
CD1 A:ILE263 4.3 33.2 1.0
CE1 A:TYR528 4.3 25.8 1.0
C7M A:FMN1002 4.4 21.7 1.0
CG2 A:VAL532 4.4 36.2 1.0
CG A:HIS185 4.4 26.5 1.0
C11 A:5Y51001 4.4 36.8 1.0
HM83 A:FMN1002 4.5 31.2 1.0
CB A:HIS185 4.5 31.4 1.0
HG23 A:ILE263 4.5 35.5 1.0
HN1 A:5Y51001 4.5 39.9 1.0
HA A:GLU182 4.7 34.8 1.0
HB A:ILE263 4.7 37.1 1.0
O A:GLY181 4.7 28.8 1.0
CE1 A:HIS185 4.8 25.9 1.0
CZ A:TYR528 4.8 27.7 1.0
HA3 A:GLY181 4.8 29.6 1.0
HB3 A:HIS185 4.9 37.7 1.0
CB A:ILE263 4.9 30.9 1.0
HG23 A:ILE272 4.9 31.9 1.0
HG23 A:VAL532 4.9 43.5 1.0
HG11 A:VAL532 4.9 66.1 1.0
C A:GLY181 4.9 30.1 1.0
CD1 A:ILE272 4.9 26.3 1.0
CG2 A:ILE272 4.9 26.6 1.0
HD11 A:ILE263 5.0 39.8 1.0
HM72 A:FMN1002 5.0 26.0 1.0
HH A:TYR528 5.0 28.8 1.0
HD3 A:ARG265 5.0 37.3 1.0

Fluorine binding site 2 out of 2 in 5fi8

Go back to Fluorine Binding Sites List in 5fi8
Fluorine binding site 2 out of 2 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bounded with DSM422 (Tetrahydro-2-Naphthyl and 2- Indanyl Triazolopyrimidine)


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 Plasmodium Falciparum Dihydroorotate Dehydrogenase Bounded with DSM422 (Tetrahydro-2-Naphthyl and 2- Indanyl Triazolopyrimidine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:25.1
occ:1.00
 F2 A:5Y51001 0.0 25.1 1.0
C13 A:5Y51001 1.3 27.3 1.0
F1 A:5Y51001 2.2 41.5 1.0
C12 A:5Y51001 2.3 19.1 1.0
C14 A:5Y51001 2.3 25.8 1.0
H142 A:5Y51001 2.6 30.9 1.0
H143 A:5Y51001 2.6 30.9 1.0
HG21 A:ILE263 2.7 35.5 1.0
HA3 A:GLY181 2.8 29.6 1.0
N4 A:5Y51001 2.9 26.7 1.0
C A:GLY181 3.1 30.1 1.0
H141 A:5Y51001 3.2 30.9 1.0
HB A:ILE263 3.2 37.1 1.0
HG22 A:ILE263 3.3 35.5 1.0
N3 A:5Y51001 3.4 22.0 1.0
CA A:GLY181 3.4 24.7 1.0
O A:GLY181 3.4 28.8 1.0
CG2 A:ILE263 3.4 29.6 1.0
HD12 A:ILE263 3.5 39.8 1.0
N A:GLU182 3.5 31.8 1.0
HD13 A:ILE263 3.6 39.8 1.0
HA A:GLU182 3.6 34.8 1.0
HA2 A:GLY181 3.6 29.6 1.0
CB A:ILE263 3.8 30.9 1.0
H A:GLU182 3.8 38.1 1.0
HB2 A:HIS185 3.8 37.7 1.0
CD1 A:ILE263 3.9 33.2 1.0
HD3 A:ARG265 4.0 37.3 1.0
C11 A:5Y51001 4.0 36.8 1.0
CA A:GLU182 4.0 29.0 1.0
N2 A:5Y51001 4.2 32.2 1.0
HG23 A:ILE263 4.2 35.5 1.0
HG3 A:ARG265 4.4 46.1 1.0
HB2 A:GLU182 4.4 30.8 1.0
CG1 A:ILE263 4.5 24.9 1.0
N A:GLY181 4.6 26.6 1.0
CB A:HIS185 4.7 31.4 1.0
CD A:ARG265 4.8 31.1 1.0
HD11 A:ILE263 4.8 39.8 1.0
HG21 A:ILE272 4.8 31.9 1.0
H A:GLY181 4.8 31.9 1.0
H A:HIS185 4.8 27.6 1.0
CB A:GLU182 4.8 25.7 1.0
HG23 A:ILE272 4.9 31.9 1.0
O A:HOH1111 4.9 23.5 1.0
HB3 A:HIS185 4.9 37.7 1.0
CG A:ARG265 4.9 38.5 1.0
HG2 A:ARG265 4.9 46.1 1.0
HM71 A:FMN1002 5.0 26.0 1.0

Reference:

S.Kokkonda, X.Deng, K.L.White, J.M.Coteron, M.Marco, L.De Las Heras, J.White, F.El Mazouni, D.R.Tomchick, K.Manjalanagara, K.R.Rudra, G.Chen, J.Morizzi, E.Ryan, W.Kaminsky, D.Leroy, M.S.Martinez-Martinez, M.B.Jimenez-Diaz, S.F.Bazaga, I.Angulo-Barturen, D.Waterson, J.N.Burrows, D.Matthews, S.A.Charman, M.A.Phillips, P.K.Rathod. Tetrahydro-2-Naphthyl and 2-Indanyl Triazolopyrimidines Targeting Plasmodium Falciparum Dihydroorotate Dehydrogenase Display Potent and Selective Antimalarial Activity. J.Med.Chem. V. 59 5416 2016.
ISSN: ISSN 0022-2623
PubMed: 27127993
DOI: 10.1021/ACS.JMEDCHEM.6B00275
Page generated: Thu Aug 1 09:25:14 2024

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