Iron in PDB 6o3i: Crystal Structure of Human IDO1 Bound to Navoximod (Nlg-919)

All present enzymatic activity of Crystal Structure of Human IDO1 Bound to Navoximod (Nlg-919):
1.13.11.52;

The structure of Crystal Structure of Human IDO1 Bound to Navoximod (Nlg-919), PDB code: 6o3i was solved by S.F.Harris, A.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.17 / 2.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.062, 90.224, 130.237, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 26.4

The structure of Crystal Structure of Human IDO1 Bound to Navoximod (Nlg-919) also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Iron atom in the Crystal Structure of Human IDO1 Bound to Navoximod (Nlg-919) (pdb code 6o3i). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Human IDO1 Bound to Navoximod (Nlg-919), PDB code: 6o3i:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Human IDO1 Bound to Navoximod (Nlg-919)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Human IDO1 Bound to Navoximod (Nlg-919) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:49.7 occ:1.00 FE A:HEM501 0.0 49.7 1.0 ND A:HEM501 2.0 49.8 1.0 NC A:HEM501 2.0 49.5 1.0 NB A:HEM501 2.0 49.3 1.0 NA A:HEM501 2.0 49.9 1.0 NE2 A:HIS346 2.1 48.9 1.0 N10 A:LKP502 2.1 47.4 1.0 C1D A:HEM501 2.9 50.1 1.0 C4D A:HEM501 3.0 50.0 1.0 C9 A:LKP502 3.0 47.5 1.0 C4B A:HEM501 3.0 49.6 1.0 C4C A:HEM501 3.0 49.8 1.0 C1B A:HEM501 3.0 49.7 1.0 CE1 A:HIS346 3.0 48.9 1.0 C1C A:HEM501 3.0 49.4 1.0 C4A A:HEM501 3.0 49.8 1.0 C1A A:HEM501 3.1 50.1 1.0 CD2 A:HIS346 3.1 49.5 1.0 C11 A:LKP502 3.3 48.4 1.0 CHD A:HEM501 3.3 50.5 1.0 CHA A:HEM501 3.4 50.5 1.0 CHC A:HEM501 3.4 50.2 1.0 CHB A:HEM501 3.4 50.2 1.0 ND1 A:HIS346 4.2 50.3 1.0 CG A:HIS346 4.2 49.3 1.0 C3D A:HEM501 4.2 50.7 1.0 C2D A:HEM501 4.2 50.4 1.0 C2C A:HEM501 4.2 50.0 1.0 C3C A:HEM501 4.2 50.1 1.0 N8 A:LKP502 4.2 46.1 1.0 C2A A:HEM501 4.3 50.6 1.0 C3A A:HEM501 4.3 50.4 1.0 C2B A:HEM501 4.3 49.8 1.0 C3B A:HEM501 4.3 50.0 1.0 C7 A:LKP502 4.4 47.5 1.0 CB A:ALA264 4.5 48.0 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Human IDO1 Bound to Navoximod (Nlg-919)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Human IDO1 Bound to Navoximod (Nlg-919) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:56.4 occ:1.00 FE B:HEM501 0.0 56.4 1.0 NA B:HEM501 1.9 56.6 1.0 N10 B:LKP502 1.9 45.5 1.0 NC B:HEM501 2.0 56.3 1.0 ND B:HEM501 2.0 56.5 1.0 NB B:HEM501 2.0 56.2 1.0 NE2 B:HIS346 2.2 61.7 1.0 C9 B:LKP502 2.8 45.2 1.0 C4A B:HEM501 3.0 56.6 1.0 C1D B:HEM501 3.0 56.8 1.0 C4D B:HEM501 3.0 56.8 1.0 C4C B:HEM501 3.0 56.5 1.0 C1C B:HEM501 3.0 56.2 1.0 C1A B:HEM501 3.0 56.8 1.0 C1B B:HEM501 3.0 56.6 1.0 C4B B:HEM501 3.1 56.5 1.0 C11 B:LKP502 3.1 45.5 1.0 CE1 B:HIS346 3.1 61.5 1.0 CD2 B:HIS346 3.3 61.9 1.0 CHB B:HEM501 3.4 57.0 1.0 CHA B:HEM501 3.4 57.2 1.0 CHD B:HEM501 3.4 57.2 1.0 CHC B:HEM501 3.4 56.9 1.0 N8 B:LKP502 4.1 46.2 1.0 C7 B:LKP502 4.2 46.1 1.0 C3A B:HEM501 4.2 57.1 1.0 C2A B:HEM501 4.2 57.2 1.0 C2C B:HEM501 4.2 56.8 1.0 C3C B:HEM501 4.2 56.8 1.0 CB B:ALA264 4.3 53.3 1.0 C3D B:HEM501 4.3 57.2 1.0 ND1 B:HIS346 4.3 62.5 1.0 C2D B:HEM501 4.3 57.2 1.0 C2B B:HEM501 4.3 56.7 1.0 C3B B:HEM501 4.3 57.0 1.0 CG B:HIS346 4.4 60.9 1.0

S.Kumar, J.P.Waldo, F.A.Jaipuri, A.Marcinowicz, C.Van Allen, J.Adams, T.Kesharwani, X.Zhang, R.Metz, A.J.Oh, S.F.Harris, M.R.Mautino. Discovery of Clinical Candidate (1R,4R)-4-((R)-2-((S)-6-Fluoro-5H-Imidazo[5, 1-A]Isoindol-5-Yl)-1-Hydroxyethyl)Cyclohexan-1-Ol (Navoximod), A Potent and Selective Inhibitor of Indoleamine 2,3-Dioxygenase 1. J.Med.Chem. V. 62 6705 2019.
ISSN: ISSN 0022-2623
PubMed: 31264862
DOI: 10.1021/ACS.JMEDCHEM.9B00662