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Fluorine in PDB 3sfk: Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM267

Enzymatic activity of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM267

All present enzymatic activity of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM267:
1.3.5.2;

Protein crystallography data

The structure of Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM267, PDB code: 3sfk 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) 50.00 / 2.95
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 86.586, 86.586, 138.167, 90.00, 90.00, 120.00
R / Rfree (%) 22.4 / 28.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM267 (pdb code 3sfk). 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 DSM267, PDB code: 3sfk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 3sfk

Go back to Fluorine Binding Sites List in 3sfk
Fluorine binding site 1 out of 5 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM267


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 DSM267 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:90.8
occ:1.00
 F1 A:D671001 0.0 90.8 1.0
C16 A:D671001 1.3 91.7 1.0
F3 A:D671001 2.1 92.6 1.0
F2 A:D671001 2.2 91.4 1.0
C5 A:D671001 2.3 91.9 1.0
C4 A:D671001 2.7 92.0 1.0
C6 A:D671001 3.6 91.6 1.0
CD1 A:LEU240 3.8 80.5 1.0
CD1 A:LEU197 4.0 79.6 1.0
CE2 A:PHE227 4.1 80.6 1.0
C3 A:D671001 4.1 92.8 1.0
CG1 A:ILE237 4.2 74.5 1.0
CZ A:PHE227 4.3 80.8 1.0
C1 A:D671001 4.7 92.2 1.0
C2 A:D671001 4.9 93.3 1.0

Fluorine binding site 2 out of 5 in 3sfk

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Fluorine binding site 2 out of 5 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM267


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 DSM267 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:91.4
occ:1.00
 F2 A:D671001 0.0 91.4 1.0
C16 A:D671001 1.3 91.7 1.0
F1 A:D671001 2.2 90.8 1.0
F3 A:D671001 2.2 92.6 1.0
C5 A:D671001 2.3 91.9 1.0
C6 A:D671001 2.7 91.6 1.0
CD1 A:LEU240 3.3 80.5 1.0
C4 A:D671001 3.5 92.0 1.0
CD2 A:LEU531 3.6 92.5 1.0
CG A:MET536 3.8 99.7 1.0
C1 A:D671001 4.1 92.2 1.0
CA A:MET536 4.3 0.7 1.0
CB A:LEU531 4.5 94.2 1.0
CB A:MET536 4.5 0.9 1.0
CG A:LEU531 4.5 92.4 1.0
CZ A:PHE227 4.7 80.8 1.0
C3 A:D671001 4.7 92.8 1.0
N A:MET536 4.7 0.8 1.0
CG A:LEU240 4.8 80.3 1.0
O A:GLY535 4.8 0.9 1.0
O A:LEU531 4.8 0.6 1.0
C A:GLY535 4.8 0.8 1.0
C2 A:D671001 4.9 93.3 1.0
SD A:MET536 4.9 98.4 1.0
CE2 A:PHE227 5.0 80.6 1.0
CD1 A:LEU531 5.0 90.5 1.0

Fluorine binding site 3 out of 5 in 3sfk

Go back to Fluorine Binding Sites List in 3sfk
Fluorine binding site 3 out of 5 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM267


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 DSM267 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:92.6
occ:1.00
 F3 A:D671001 0.0 92.6 1.0
C16 A:D671001 1.3 91.7 1.0
F1 A:D671001 2.1 90.8 1.0
F2 A:D671001 2.2 91.4 1.0
C5 A:D671001 2.3 91.9 1.0
C4 A:D671001 3.1 92.0 1.0
C6 A:D671001 3.2 91.6 1.0
CE A:MET536 3.4 0.7 1.0
CG A:MET536 3.5 99.7 1.0
CD1 A:LEU197 3.6 79.6 1.0
SD A:MET536 3.9 98.4 1.0
CD1 A:LEU240 4.2 80.5 1.0
CB A:PHE188 4.3 93.9 1.0
C3 A:D671001 4.3 92.8 1.0
C1 A:D671001 4.4 92.2 1.0
CD1 A:PHE188 4.6 97.6 1.0
CG A:PHE188 4.6 96.3 1.0
CD2 A:LEU197 4.7 83.7 1.0
CB A:MET536 4.7 0.9 1.0
CG A:LEU197 4.8 82.5 1.0
C2 A:D671001 4.9 93.3 1.0

Fluorine binding site 4 out of 5 in 3sfk

Go back to Fluorine Binding Sites List in 3sfk
Fluorine binding site 4 out of 5 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM267


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 DSM267 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:96.7
occ:1.00
 F4 A:D671001 0.0 96.7 1.0
C13 A:D671001 1.3 95.9 1.0
F5 A:D671001 2.1 95.9 1.0
C14 A:D671001 2.3 95.0 1.0
C12 A:D671001 2.3 96.4 1.0
N3 A:D671001 2.7 96.6 1.0
N4 A:D671001 3.6 96.7 1.0
OH A:TYR528 3.7 94.3 1.0
CG2 A:ILE263 3.9 0.8 1.0
CD1 A:ILE263 4.0 0.8 1.0
ND1 A:HIS185 4.0 96.4 1.0
N2 A:D671001 4.0 96.6 1.0
C7M A:FMN1002 4.1 81.2 1.0
CG A:HIS185 4.2 96.3 1.0
CE2 A:TYR528 4.2 95.3 1.0
CB A:HIS185 4.3 97.0 1.0
O A:GLY181 4.4 0.4 1.0
C11 A:D671001 4.4 97.0 1.0
CZ A:TYR528 4.5 93.5 1.0
CE1 A:HIS185 4.6 96.6 1.0
CB A:ILE263 4.7 0.5 1.0
C A:GLY181 4.7 0.4 1.0
CD2 A:HIS185 4.8 95.7 1.0
CG2 A:VAL532 4.9 0.5 1.0
CG1 A:ILE263 4.9 1.0 1.0

Fluorine binding site 5 out of 5 in 3sfk

Go back to Fluorine Binding Sites List in 3sfk
Fluorine binding site 5 out of 5 in the Crystal Structure of Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound with Inhibitor DSM267


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 DSM267 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:95.9
occ:1.00
 F5 A:D671001 0.0 95.9 1.0
C13 A:D671001 1.3 95.9 1.0
F4 A:D671001 2.1 96.7 1.0
C12 A:D671001 2.3 96.4 1.0
C14 A:D671001 2.3 95.0 1.0
N4 A:D671001 2.9 96.7 1.0
C A:GLY181 3.2 0.4 1.0
CG2 A:ILE263 3.2 0.8 1.0
O A:GLY181 3.3 0.4 1.0
CA A:GLY181 3.4 0.2 1.0
N3 A:D671001 3.4 96.6 1.0
CB A:ILE263 3.6 0.5 1.0
N A:GLU182 3.6 0.8 1.0
CD1 A:ILE263 3.9 0.8 1.0
C11 A:D671001 4.1 97.0 1.0
CD A:ARG265 4.2 0.6 1.0
CA A:GLU182 4.2 0.1 1.0
N2 A:D671001 4.3 96.6 1.0
CG1 A:ILE263 4.3 1.0 1.0
CG A:ARG265 4.4 0.7 1.0
N A:GLY181 4.7 0.8 1.0
C A:ILE263 4.8 0.7 1.0
NE A:ARG265 4.8 0.5 1.0
CA A:ILE263 4.8 0.8 1.0
CB A:GLU182 4.9 0.3 1.0
O A:ILE263 4.9 0.1 1.0
CB A:HIS185 4.9 97.0 1.0

Reference:

J.M.Coteron, M.Marco, J.Esquivias, X.Deng, K.L.White, J.White, M.Koltun, F.El Mazouni, S.Kokkonda, K.Katneni, R.Bhamidipati, D.M.Shackleford, I.Angulo-Barturen, S.B.Ferrer, M.B.Jimenez-Diaz, F.J.Gamo, E.J.Goldsmith, W.N.Charman, I.Bathurst, D.Floyd, D.Matthews, J.N.Burrows, P.K.Rathod, S.A.Charman, M.A.Phillips. Structure-Guided Lead Optimization of Triazolopyrimidine-Ring Substituents Identifies Potent Plasmodium Falciparum Dihydroorotate Dehydrogenase Inhibitors with Clinical Candidate Potential. J.Med.Chem. V. 54 5540 2011.
ISSN: ISSN 0022-2623
PubMed: 21696174
DOI: 10.1021/JM200592F
Page generated: Wed Jul 31 22:32:24 2024

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