Fluorine in PDB 6e40: Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat

Enzymatic activity of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat

All present enzymatic activity of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat:
1.13.11.52;

Protein crystallography data

The structure of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat, PDB code: 6e40 was solved by S.Luo, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.86 / 2.31
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.367, 200.144, 114.741, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.4

Other elements in 6e40:

The structure of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat also contains other interesting chemical elements:

Bromine (Br) 3 atoms
Iron (Fe) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat (pdb code 6e40). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat, PDB code: 6e40:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6e40

Go back to Fluorine Binding Sites List in 6e40
Fluorine binding site 1 out of 3 in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat


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 the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:68.5
occ:1.00
F7 A:BBJ502 0.0 68.5 1.0
C3 A:BBJ502 1.4 67.9 1.0
C4 A:BBJ502 2.4 61.2 1.0
C2 A:BBJ502 2.4 66.8 1.0
CG2 A:VAL130 3.0 46.0 1.0
BR8 A:BBJ502 3.1 78.4 1.0
SG A:CYS129 3.1 44.6 1.0
CE1 A:PHE164 3.2 43.2 1.0
CD1 A:PHE164 3.5 43.4 1.0
C5 A:BBJ502 3.7 61.5 1.0
C1 A:BBJ502 3.7 63.6 1.0
CE2 A:PHE163 4.1 51.0 1.0
C6 A:BBJ502 4.2 67.0 1.0
CB A:VAL130 4.2 45.7 1.0
CD1 A:TYR126 4.3 55.5 1.0
CB A:CYS129 4.4 39.3 1.0
CZ A:PHE164 4.4 40.1 1.0
CD2 A:PHE163 4.5 47.6 1.0
CA A:TYR126 4.5 44.1 1.0
N A:VAL130 4.6 46.9 1.0
C A:CYS129 4.6 48.5 1.0
CD1 A:LEU234 4.7 47.4 1.0
O A:CYS129 4.8 44.2 1.0
CG A:PHE164 4.8 40.7 1.0
CE1 A:TYR126 4.8 53.2 1.0
O A:TYR126 4.8 43.0 1.0
CA A:VAL130 4.9 45.1 1.0
CZ A:PHE163 4.9 55.2 1.0

Fluorine binding site 2 out of 3 in 6e40

Go back to Fluorine Binding Sites List in 6e40
Fluorine binding site 2 out of 3 in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat


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 the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:66.1
occ:1.00
F7 B:BBJ502 0.0 66.1 1.0
C3 B:BBJ502 1.4 64.3 1.0
C4 B:BBJ502 2.4 56.6 1.0
C2 B:BBJ502 2.4 59.2 1.0
CG2 B:VAL130 2.9 38.4 1.0
BR8 B:BBJ502 3.1 72.3 1.0
CD1 B:PHE164 3.3 39.8 1.0
CE1 B:PHE164 3.3 42.2 1.0
SG B:CYS129 3.6 45.0 1.0
C5 B:BBJ502 3.7 56.3 1.0
C1 B:BBJ502 3.7 54.0 1.0
CE2 B:PHE163 3.8 47.6 1.0
C6 B:BBJ502 4.2 59.9 1.0
CD2 B:PHE163 4.2 46.1 1.0
CB B:VAL130 4.3 43.5 1.0
CD1 B:TYR126 4.4 46.8 1.0
CG B:PHE164 4.6 41.3 1.0
CZ B:PHE164 4.7 42.1 1.0
N B:VAL130 4.7 38.9 1.0
CZ B:PHE163 4.7 51.5 1.0
C B:CYS129 4.7 42.5 1.0
O B:CYS129 4.8 44.2 1.0
CE1 B:TYR126 4.8 50.3 1.0
CD1 B:LEU234 4.8 52.8 1.0
CB B:CYS129 4.9 41.5 1.0
OG B:SER167 4.9 45.2 1.0
CA B:VAL130 5.0 40.0 1.0
CA B:PHE164 5.0 39.3 1.0

Fluorine binding site 3 out of 3 in 6e40

Go back to Fluorine Binding Sites List in 6e40
Fluorine binding site 3 out of 3 in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat


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 the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:63.0
occ:1.00
F7 D:BBJ502 0.0 63.0 1.0
C3 D:BBJ502 1.4 59.5 1.0
C2 D:BBJ502 2.4 58.2 1.0
C4 D:BBJ502 2.4 56.8 1.0
CG2 D:VAL130 2.9 41.7 1.0
BR8 D:BBJ502 3.1 67.4 1.0
CD1 D:PHE164 3.1 39.1 1.0
CE1 D:PHE164 3.1 43.1 1.0
SG D:CYS129 3.6 43.3 1.0
C5 D:BBJ502 3.7 50.8 1.0
C1 D:BBJ502 3.7 52.7 1.0
CE2 D:PHE163 4.1 47.7 1.0
C6 D:BBJ502 4.2 55.7 1.0
CB D:VAL130 4.3 46.0 1.0
CD2 D:PHE163 4.4 45.1 1.0
CD1 D:TYR126 4.5 46.4 1.0
CG D:PHE164 4.5 37.4 1.0
CZ D:PHE164 4.5 42.2 1.0
N D:VAL130 4.6 42.4 1.0
C D:CYS129 4.6 45.0 1.0
CD1 D:LEU234 4.6 48.7 1.0
O D:CYS129 4.6 45.2 1.0
CB D:CYS129 4.8 39.4 1.0
CE1 D:TYR126 4.9 50.8 1.0
CA D:VAL130 4.9 45.1 1.0
CA D:TYR126 4.9 40.9 1.0

Reference:

S.Luo, K.Xu, S.Xiang, J.Chen, C.Chen, C.Guo, Y.Tong, L.Tong. High-Resolution Structures of Inhibitor Complexes of Human Indoleamine 2,3-Dioxygenase 1 in A New Crystal Form. Acta Crystallogr F Struct V. 74 717 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30387777
DOI: 10.1107/S2053230X18012955
Page generated: Sun Dec 13 12:48:46 2020

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