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Fluorine in PDB 5tbo: Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421

Enzymatic activity of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421

All present enzymatic activity of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421:
1.3.5.2;

Protein crystallography data

The structure of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421, PDB code: 5tbo was solved by X.Deng, M.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.55 / 2.15
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 86.380, 86.380, 138.608, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 21.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421 (pdb code 5tbo). 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 Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421, PDB code: 5tbo:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 5tbo

Go back to Fluorine Binding Sites List in 5tbo
Fluorine binding site 1 out of 5 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421


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 Bound with Inhibitor DSM421 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:94.7
occ:1.00
F4 A:78Z1001 0.0 94.7 1.0
C13 A:78Z1001 1.3 43.8 1.0
F5 A:78Z1001 2.2 33.1 1.0
C14 A:78Z1001 2.3 22.3 1.0
C12 A:78Z1001 2.3 55.2 1.0
H141 A:78Z1001 2.5 26.7 1.0
H143 A:78Z1001 2.6 26.7 1.0
N3 A:78Z1001 2.8 36.5 1.0
HG21 A:ILE263 3.1 32.6 1.0
H142 A:78Z1001 3.2 26.7 1.0
HD11 A:ILE263 3.3 29.9 1.0
HB2 A:HIS185 3.3 26.3 1.0
HE1 A:TYR528 3.4 27.3 1.0
N4 A:78Z1001 3.6 39.6 1.0
HM73 A:FMN1002 3.8 29.7 1.0
OH A:TYR528 3.8 19.8 1.0
HD13 A:ILE263 3.9 29.9 1.0
HM71 A:FMN1002 3.9 29.7 1.0
ND1 A:HIS185 3.9 21.7 1.0
HG23 A:VAL532 4.0 30.4 1.0
CG A:HIS185 4.0 21.6 1.0
CD1 A:ILE263 4.0 24.9 1.0
CB A:HIS185 4.0 21.9 1.0
CG2 A:ILE263 4.1 27.2 1.0
N2 A:78Z1001 4.1 42.5 1.0
CE1 A:TYR528 4.2 22.8 1.0
HA A:GLU182 4.3 31.4 1.0
HG22 A:ILE263 4.3 32.6 1.0
C7M A:FMN1002 4.3 24.7 1.0
HB3 A:HIS185 4.4 26.3 1.0
HH A:TYR528 4.4 23.7 1.0
HD13 A:ILE272 4.5 32.2 1.0
CE1 A:HIS185 4.5 21.6 1.0
O A:GLY181 4.5 23.5 1.0
CZ A:TYR528 4.5 20.1 1.0
C11 A:78Z1001 4.5 60.2 1.0
HG22 A:ILE272 4.6 34.1 1.0
HG23 A:ILE263 4.6 32.6 1.0
HD12 A:ILE263 4.6 29.9 1.0
CD2 A:HIS185 4.6 21.4 1.0
HM82 A:FMN1002 4.6 39.4 1.0
HB A:ILE263 4.7 33.0 1.0
H11 A:78Z1001 4.7 30.7 1.0
C A:GLY181 4.7 24.1 1.0
CG2 A:VAL532 4.8 25.3 1.0
HG22 A:VAL532 4.8 30.4 1.0
HA3 A:GLY181 4.8 29.8 1.0
CB A:ILE263 4.8 27.5 1.0
HE1 A:HIS185 4.9 25.9 1.0
HM72 A:FMN1002 4.9 29.7 1.0
NE2 A:HIS185 4.9 21.3 1.0

Fluorine binding site 2 out of 5 in 5tbo

Go back to Fluorine Binding Sites List in 5tbo
Fluorine binding site 2 out of 5 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421


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 Bound with Inhibitor DSM421 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:33.1
occ:1.00
F5 A:78Z1001 0.0 33.1 1.0
C13 A:78Z1001 1.3 43.8 1.0
F4 A:78Z1001 2.2 94.7 1.0
C14 A:78Z1001 2.3 22.3 1.0
C12 A:78Z1001 2.3 55.2 1.0
H142 A:78Z1001 2.5 26.7 1.0
H141 A:78Z1001 2.6 26.7 1.0
HG21 A:ILE263 2.6 32.6 1.0
HA3 A:GLY181 2.7 29.8 1.0
N4 A:78Z1001 3.0 39.6 1.0
C A:GLY181 3.1 24.1 1.0
HB A:ILE263 3.1 33.0 1.0
H143 A:78Z1001 3.2 26.7 1.0
HG22 A:ILE263 3.2 32.6 1.0
CG2 A:ILE263 3.2 27.2 1.0
HD13 A:ILE263 3.3 29.9 1.0
CA A:GLY181 3.3 24.9 1.0
HD11 A:ILE263 3.4 29.9 1.0
N A:GLU182 3.4 26.7 1.0
O A:GLY181 3.4 23.5 1.0
N3 A:78Z1001 3.5 36.5 1.0
HA A:GLU182 3.5 31.4 1.0
HA2 A:GLY181 3.6 29.8 1.0
CB A:ILE263 3.6 27.5 1.0
H A:GLU182 3.6 32.0 1.0
CD1 A:ILE263 3.7 24.9 1.0
HD3 A:ARG265 3.8 44.6 1.0
HB2 A:HIS185 3.8 26.3 1.0
CA A:GLU182 4.0 26.2 1.0
HG23 A:ILE263 4.1 32.6 1.0
C11 A:78Z1001 4.2 60.2 1.0
CG1 A:ILE263 4.3 26.4 1.0
HB2 A:GLU182 4.3 32.0 1.0
HG3 A:ARG265 4.3 44.6 1.0
N2 A:78Z1001 4.4 42.5 1.0
CD A:ARG265 4.6 37.2 1.0
N A:GLY181 4.6 25.5 1.0
HD12 A:ILE263 4.6 29.9 1.0
CB A:HIS185 4.7 21.9 1.0
HG2 A:ARG265 4.7 44.6 1.0
H A:GLY181 4.8 30.6 1.0
CB A:GLU182 4.8 26.7 1.0
CG A:ARG265 4.8 37.2 1.0
HB3 A:HIS185 4.8 26.3 1.0
HG22 A:ILE272 4.8 34.1 1.0
H A:HIS185 4.9 26.7 1.0
HG13 A:ILE263 4.9 31.7 1.0
HM71 A:FMN1002 4.9 29.7 1.0
HG23 A:VAL532 4.9 30.4 1.0
HG12 A:ILE263 4.9 31.7 1.0
HG21 A:ILE272 4.9 34.1 1.0
CA A:ILE263 4.9 29.2 1.0
O A:HOH1139 5.0 18.9 1.0
C A:ILE263 5.0 30.4 1.0

Fluorine binding site 3 out of 5 in 5tbo

Go back to Fluorine Binding Sites List in 5tbo
Fluorine binding site 3 out of 5 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421


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 Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:24.3
occ:1.00
F1 A:78Z1001 0.0 24.3 1.0
C16 A:78Z1001 1.3 22.8 1.0
F2 A:78Z1001 2.2 17.7 1.0
F3 A:78Z1001 2.2 19.7 1.0
C5 A:78Z1001 2.3 52.2 1.0
H41 A:78Z1001 2.4 58.0 1.0
HD22 A:LEU531 2.6 34.4 1.0
HG2 A:MET536 2.7 41.2 1.0
C4 A:78Z1001 2.7 48.3 1.0
HD11 A:LEU240 2.9 22.9 1.0
HD13 A:LEU240 3.0 22.9 1.0
HA A:MET536 3.1 39.1 1.0
HG3 A:MET536 3.1 41.2 1.0
CD1 A:LEU240 3.3 19.0 1.0
CG A:MET536 3.3 34.4 1.0
CD2 A:LEU531 3.4 28.7 1.0
HD23 A:LEU531 3.5 34.4 1.0
N6 A:78Z1001 3.6 23.2 1.0
HD12 A:LEU240 3.6 22.9 1.0
HB3 A:LEU531 3.8 25.6 1.0
HD21 A:LEU531 3.9 34.4 1.0
CA A:MET536 3.9 32.6 1.0
HE1 A:MET536 4.0 56.1 1.0
C3 A:78Z1001 4.1 27.1 1.0
CB A:MET536 4.2 32.1 1.0
N A:MET536 4.3 32.1 1.0
HZ A:PHE227 4.3 23.2 1.0
C A:GLY535 4.5 29.1 1.0
HD13 A:LEU531 4.5 27.0 1.0
CG A:LEU531 4.5 21.1 1.0
HB3 A:MET536 4.6 38.5 1.0
O A:GLY535 4.6 30.1 1.0
CB A:LEU531 4.6 21.4 1.0
HD21 A:LEU240 4.6 20.8 1.0
HD11 A:LEU197 4.6 25.8 1.0
H A:MET536 4.6 38.5 1.0
C1 A:78Z1001 4.7 28.3 1.0
CE A:MET536 4.7 46.8 1.0
CG A:LEU240 4.7 17.0 1.0
HD22 A:LEU240 4.7 20.8 1.0
SD A:MET536 4.7 33.8 1.0
H31 A:78Z1001 4.7 32.6 1.0
HE2 A:MET536 4.7 56.1 1.0
HA2 A:GLY535 4.8 34.6 1.0
O A:LEU531 4.9 20.8 1.0
CD2 A:LEU240 4.9 17.3 1.0
C2 A:78Z1001 4.9 29.9 1.0
HE1 A:PHE227 4.9 23.4 1.0
HD12 A:LEU172 5.0 41.8 1.0
HB2 A:MET536 5.0 38.5 1.0
HA A:LEU531 5.0 27.0 1.0

Fluorine binding site 4 out of 5 in 5tbo

Go back to Fluorine Binding Sites List in 5tbo
Fluorine binding site 4 out of 5 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421


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 Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:17.7
occ:1.00
F2 A:78Z1001 0.0 17.7 1.0
C16 A:78Z1001 1.3 22.8 1.0
F3 A:78Z1001 2.2 19.7 1.0
F1 A:78Z1001 2.2 24.3 1.0
C5 A:78Z1001 2.3 52.2 1.0
HE1 A:MET536 2.8 56.1 1.0
N6 A:78Z1001 2.9 23.2 1.0
HD11 A:LEU197 3.0 25.8 1.0
HG2 A:MET536 3.0 41.2 1.0
HD11 A:LEU240 3.1 22.9 1.0
HB3 A:PHE188 3.3 25.3 1.0
C4 A:78Z1001 3.4 48.3 1.0
HD12 A:LEU197 3.5 25.8 1.0
H41 A:78Z1001 3.6 58.0 1.0
HG3 A:MET536 3.6 41.2 1.0
CG A:MET536 3.7 34.4 1.0
CD1 A:LEU197 3.7 21.5 1.0
CE A:MET536 3.7 46.8 1.0
CD1 A:LEU240 4.0 19.0 1.0
HE2 A:MET536 4.1 56.1 1.0
C1 A:78Z1001 4.1 28.3 1.0
HD13 A:LEU240 4.1 22.9 1.0
HD22 A:LEU197 4.2 35.3 1.0
HD1 A:PHE188 4.2 28.6 1.0
SD A:MET536 4.2 33.8 1.0
HD13 A:LEU197 4.2 25.8 1.0
CB A:PHE188 4.2 21.1 1.0
HE3 A:MET536 4.3 56.1 1.0
HD12 A:LEU240 4.4 22.9 1.0
HD21 A:LEU240 4.5 20.8 1.0
C3 A:78Z1001 4.5 27.1 1.0
HD21 A:LEU197 4.6 35.3 1.0
HD22 A:LEU531 4.6 34.4 1.0
CD1 A:PHE188 4.6 23.8 1.0
HB2 A:PHE188 4.6 25.3 1.0
CG A:PHE188 4.7 21.8 1.0
CD2 A:LEU197 4.7 29.4 1.0
HA A:MET536 4.7 39.1 1.0
H12 A:78Z1001 4.7 34.0 1.0
CG A:LEU197 4.8 23.4 1.0
HG12 A:ILE237 4.8 19.2 1.0
HE1 A:PHE227 4.8 23.4 1.0
O A:PHE188 4.8 19.9 1.0
C2 A:78Z1001 4.8 29.9 1.0
HZ A:PHE227 4.9 23.2 1.0

Fluorine binding site 5 out of 5 in 5tbo

Go back to Fluorine Binding Sites List in 5tbo
Fluorine binding site 5 out of 5 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421


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 Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM421 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:19.7
occ:1.00
F3 A:78Z1001 0.0 19.7 1.0
C16 A:78Z1001 1.3 22.8 1.0
F2 A:78Z1001 2.2 17.7 1.0
F1 A:78Z1001 2.2 24.3 1.0
C5 A:78Z1001 2.3 52.2 1.0
N6 A:78Z1001 2.8 23.2 1.0
HD11 A:LEU240 2.8 22.9 1.0
HG12 A:ILE237 3.1 19.2 1.0
HE1 A:PHE227 3.1 23.4 1.0
HD12 A:LEU240 3.2 22.9 1.0
HD22 A:LEU531 3.3 34.4 1.0
CD1 A:LEU240 3.4 19.0 1.0
C4 A:78Z1001 3.5 48.3 1.0
HZ A:PHE227 3.5 23.2 1.0
HD13 A:LEU240 3.6 22.9 1.0
H41 A:78Z1001 3.7 58.0 1.0
CE1 A:PHE227 3.8 19.5 1.0
CZ A:PHE227 4.0 19.4 1.0
C1 A:78Z1001 4.0 28.3 1.0
HD13 A:LEU531 4.1 27.0 1.0
CG1 A:ILE237 4.1 16.0 1.0
HG23 A:ILE237 4.2 19.4 1.0
HD11 A:LEU197 4.2 25.8 1.0
HA A:ILE237 4.3 18.6 1.0
HG2 A:MET536 4.3 41.2 1.0
CD2 A:LEU531 4.3 28.7 1.0
HG13 A:ILE237 4.3 19.2 1.0
HB3 A:LEU531 4.4 25.6 1.0
HD21 A:LEU531 4.5 34.4 1.0
HD11 A:ILE237 4.5 19.5 1.0
C3 A:78Z1001 4.6 27.1 1.0
H12 A:78Z1001 4.6 34.0 1.0
HB3 A:PHE188 4.7 25.3 1.0
CD1 A:ILE237 4.8 16.3 1.0
CG A:LEU240 4.8 17.0 1.0
HD12 A:LEU197 4.8 25.8 1.0
HD13 A:ILE237 4.8 19.5 1.0
C2 A:78Z1001 4.8 29.9 1.0
HD23 A:LEU531 4.8 34.4 1.0
CD1 A:LEU531 4.9 22.5 1.0
CD1 A:LEU197 4.9 21.5 1.0
HG A:LEU240 4.9 20.4 1.0
CB A:ILE237 4.9 15.7 1.0
HE1 A:MET536 4.9 56.1 1.0
CG2 A:ILE237 5.0 16.1 1.0
CD1 A:PHE227 5.0 18.5 1.0

Reference:

M.A.Phillips, K.L.White, S.Kokkonda, X.Deng, J.White, F.El Mazouni, K.Marsh, D.R.Tomchick, K.Manjalanagara, K.R.Rudra, G.Wirjanata, R.Noviyanti, R.N.Price, J.Marfurt, D.M.Shackleford, F.C.Chiu, M.Campbell, M.B.Jimenez-Diaz, S.F.Bazaga, I.Angulo-Barturen, M.S.Martinez, M.Lafuente-Monasterio, W.Kaminsky, K.Silue, A.M.Zeeman, C.Kocken, D.Leroy, B.Blasco, E.Rossignol, T.Rueckle, D.Matthews, J.N.Burrows, D.Waterson, M.J.Palmer, P.K.Rathod, S.A.Charman. A Triazolopyrimidine-Based Dihydroorotate Dehydrogenase Inhibitor with Improved Drug-Like Properties For Treatment and Prevention of Malaria. Acs Infect Dis V. 2 945 2016.
ISSN: ESSN 2373-8227
PubMed: 27641613
DOI: 10.1021/ACSINFECDIS.6B00144
Page generated: Tue Jul 15 07:51:31 2025

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