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Fluorine in PDB 3s9y: Crystal Structure of P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump

Enzymatic activity of Crystal Structure of P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump

All present enzymatic activity of Crystal Structure of P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump:
4.1.1.23;

Protein crystallography data

The structure of Crystal Structure of P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump, PDB code: 3s9y was solved by Y.Liu, L.P.Kotra, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.99 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.592, 82.905, 91.730, 90.00, 90.93, 90.00
R / Rfree (%) 16.3 / 20.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump (pdb code 3s9y). 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 P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump, PDB code: 3s9y:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3s9y

Go back to Fluorine Binding Sites List in 3s9y
Fluorine binding site 1 out of 4 in the Crystal Structure of P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump


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 P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F324

b:8.9
occ:1.00
 F24 A:FNU324 0.0 8.9 1.0
C5 A:FNU324 1.4 7.4 1.0
C4 A:FNU324 2.4 10.0 1.0
C6 A:FNU324 2.4 7.4 1.0
N3 A:FNU324 2.8 7.1 1.0
O4 A:FNU324 2.8 9.3 1.0
CG1 A:VAL240 3.3 7.4 1.0
CE A:LYS138 3.5 10.9 1.0
CD2 A:LEU191 3.6 10.6 1.0
N2 A:FNU324 3.6 7.6 1.0
CG2 A:THR194 3.6 9.0 1.0
N1 A:FNU324 3.6 7.5 1.0
C2 A:FNU324 4.1 10.4 1.0
NZ A:LYS138 4.2 11.7 1.0
CB A:THR194 4.3 9.7 1.0
O A:HOH378 4.3 13.7 1.0
CB A:VAL240 4.3 5.7 1.0
CG A:PRO264 4.4 8.7 1.0
CE B:MET168 4.6 14.2 1.0
CD A:LYS138 4.8 8.4 1.0
CG2 A:VAL240 4.8 6.7 1.0
CA A:THR194 4.8 9.1 1.0
C1' A:FNU324 4.8 8.1 1.0
CG A:LEU191 4.8 7.3 1.0

Fluorine binding site 2 out of 4 in 3s9y

Go back to Fluorine Binding Sites List in 3s9y
Fluorine binding site 2 out of 4 in the Crystal Structure of P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump


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 P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F324

b:9.7
occ:1.00
 F24 B:FNU324 0.0 9.7 1.0
C5 B:FNU324 1.4 8.4 1.0
C4 B:FNU324 2.4 7.1 1.0
C6 B:FNU324 2.4 10.3 1.0
N3 B:FNU324 2.8 5.1 1.0
O4 B:FNU324 2.8 7.1 1.0
CG1 B:VAL240 3.4 7.0 1.0
CD2 B:LEU191 3.6 9.2 1.0
CE B:LYS138 3.6 10.6 1.0
N2 B:FNU324 3.6 8.0 1.0
N1 B:FNU324 3.7 8.4 1.0
CG2 B:THR194 3.7 8.8 1.0
C2 B:FNU324 4.1 8.4 1.0
NZ B:LYS138 4.2 10.8 1.0
CB B:VAL240 4.3 5.3 1.0
CE A:MET168 4.3 12.4 1.0
O B:HOH385 4.3 16.0 1.0
CB B:THR194 4.4 7.5 1.0
CG B:PRO264 4.4 8.0 1.0
CG2 B:VAL240 4.7 6.3 1.0
CG B:LEU191 4.8 7.3 1.0
CD B:LYS138 4.8 7.8 1.0
C1' B:FNU324 4.8 6.6 1.0
CA B:THR194 4.9 7.4 1.0
CD1 B:LEU191 5.0 8.6 1.0
SD A:MET168 5.0 10.8 1.0

Fluorine binding site 3 out of 4 in 3s9y

Go back to Fluorine Binding Sites List in 3s9y
Fluorine binding site 3 out of 4 in the Crystal Structure of P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump


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 P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F324

b:12.3
occ:1.00
 F24 C:FNU324 0.0 12.3 1.0
C5 C:FNU324 1.4 10.6 1.0
C6 C:FNU324 2.4 10.3 1.0
C4 C:FNU324 2.4 10.0 1.0
N3 C:FNU324 2.7 8.4 1.0
O4 C:FNU324 2.8 10.0 1.0
CG1 C:VAL240 3.3 8.7 1.0
CE C:LYS138 3.5 9.7 1.0
N2 C:FNU324 3.6 10.4 1.0
N1 C:FNU324 3.6 11.4 1.0
CD2 C:LEU191 3.6 11.8 1.0
CG2 C:THR194 3.7 10.0 1.0
CE D:MET168 4.1 18.1 1.0
C2 C:FNU324 4.1 10.0 1.0
NZ C:LYS138 4.2 10.4 1.0
CB C:VAL240 4.3 7.9 1.0
O C:HOH353 4.3 16.3 1.0
CB C:THR194 4.4 9.1 1.0
CG C:PRO264 4.4 9.4 1.0
CG2 C:VAL240 4.8 9.3 1.0
CD C:LYS138 4.8 10.0 1.0
C1' C:FNU324 4.8 10.0 1.0
CG C:LEU191 4.8 9.8 1.0
CA C:THR194 4.8 9.1 1.0

Fluorine binding site 4 out of 4 in 3s9y

Go back to Fluorine Binding Sites List in 3s9y
Fluorine binding site 4 out of 4 in the Crystal Structure of P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump


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 P. Falciparum Orotidine 5'-Monophosphate Decarboxylase Complexed with 5-Fluoro-6-Amino-Ump in Space Group P21, Produced From 5-Fluoro-6-Azido-Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F324

b:11.3
occ:1.00
 F24 D:FNU324 0.0 11.3 1.0
C5 D:FNU324 1.4 10.7 1.0
C4 D:FNU324 2.4 8.4 1.0
C6 D:FNU324 2.4 10.0 1.0
O4 D:FNU324 2.7 11.0 1.0
N3 D:FNU324 2.8 10.0 1.0
CG1 D:VAL240 3.3 9.0 1.0
CE D:LYS138 3.5 11.3 1.0
CG2 D:THR194 3.5 10.8 1.0
N2 D:FNU324 3.6 8.9 1.0
N1 D:FNU324 3.6 11.6 1.0
CD2 D:LEU191 3.7 11.4 1.0
C2 D:FNU324 4.1 9.0 1.0
NZ D:LYS138 4.2 12.4 1.0
CB D:THR194 4.3 9.6 1.0
CB D:VAL240 4.3 10.3 1.0
O D:HOH346 4.4 18.4 1.0
CG D:PRO264 4.4 11.7 1.0
CE C:MET168 4.5 13.7 1.0
CA D:THR194 4.8 9.7 1.0
CD D:LYS138 4.8 10.6 1.0
CG2 D:VAL240 4.8 11.4 1.0
C1' D:FNU324 4.9 10.1 1.0
CG D:LEU191 4.9 10.9 1.0

Reference:

A.M.Bello, D.Konforte, E.Poduch, C.Furlonger, L.Wei, Y.Liu, M.Lewis, E.F.Pai, C.J.Paige, L.P.Kotra. Structure-Activity Relationships of Orotidine-5'-Monophosphate Decarboxylase Inhibitors As Anticancer Agents. J.Med.Chem. V. 52 1648 2009.
ISSN: ISSN 0022-2623
PubMed: 19260677
DOI: 10.1021/JM801224T
Page generated: Mon Jul 14 19:16:18 2025

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