Iron in PDB 9esd: Holo Tdo with A Bound Inhibitor

All present enzymatic activity of Holo Tdo with A Bound Inhibitor:
1.13.11.11;

The structure of Holo Tdo with A Bound Inhibitor, PDB code: 9esd was solved by M.Wicki, A.Mac Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.05 / 2.10
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	143.736, 143.736, 141.218, 90, 90, 120
R / Rfree (%)	23.3 / 25.5

The binding sites of Iron atom in the Holo Tdo with A Bound Inhibitor (pdb code 9esd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Holo Tdo with A Bound Inhibitor, PDB code: 9esd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Holo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Holo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:44.5 occ:1.00 FE A:HEM401 0.0 44.5 1.0 ND A:HEM401 2.0 44.5 1.0 NB A:HEM401 2.1 44.8 1.0 NA A:HEM401 2.1 45.4 1.0 NC A:HEM401 2.1 44.2 1.0 NE2 A:HIS312 2.2 43.9 1.0 NAP A:5PK402 2.2 55.0 1.0 CE1 A:HIS312 3.0 43.0 1.0 C1D A:HEM401 3.0 44.4 1.0 C1B A:HEM401 3.1 45.2 1.0 C4C A:HEM401 3.1 44.0 1.0 C4A A:HEM401 3.1 45.5 1.0 C1A A:HEM401 3.1 46.0 1.0 CAQ A:5PK402 3.1 55.4 1.0 C4D A:HEM401 3.1 44.7 1.0 C1C A:HEM401 3.1 44.5 1.0 C4B A:HEM401 3.1 45.0 1.0 CAO A:5PK402 3.2 55.2 1.0 CD2 A:HIS312 3.3 42.5 1.0 CHD A:HEM401 3.4 44.1 1.0 CHB A:HEM401 3.4 45.4 1.0 CHA A:HEM401 3.5 45.0 1.0 CHC A:HEM401 3.5 44.6 1.0 ND1 A:HIS312 4.2 42.6 1.0 NAN A:5PK402 4.2 55.8 1.0 C2D A:HEM401 4.3 44.7 1.0 C3C A:HEM401 4.3 44.0 1.0 CAM A:5PK402 4.3 55.5 1.0 C3D A:HEM401 4.3 44.9 1.0 C2A A:HEM401 4.3 46.9 1.0 C3A A:HEM401 4.3 46.1 1.0 C3B A:HEM401 4.3 45.0 1.0 C2B A:HEM401 4.3 45.2 1.0 C2C A:HEM401 4.3 44.3 1.0 CG A:HIS312 4.3 41.4 1.0 CG2 A:VAL316 4.7 44.6 1.0

Iron binding site 2 out of 4 in the Holo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Holo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:43.2 occ:1.00 FE B:HEM401 0.0 43.2 1.0 ND B:HEM401 2.0 43.4 1.0 NB B:HEM401 2.0 43.5 1.0 NA B:HEM401 2.1 45.0 1.0 NC B:HEM401 2.1 43.0 1.0 NAP B:5PK402 2.1 50.5 1.0 NE2 B:HIS312 2.1 45.4 1.0 CAQ B:5PK402 2.7 50.6 1.0 CE1 B:HIS312 3.0 45.6 1.0 C1D B:HEM401 3.0 43.4 1.0 C1B B:HEM401 3.1 43.8 1.0 C1A B:HEM401 3.1 45.5 1.0 C4C B:HEM401 3.1 42.8 1.0 C4D B:HEM401 3.1 43.9 1.0 C4A B:HEM401 3.1 45.0 1.0 C1C B:HEM401 3.1 42.8 1.0 C4B B:HEM401 3.1 43.5 1.0 CD2 B:HIS312 3.3 44.0 1.0 CAO B:5PK402 3.3 50.5 1.0 CHD B:HEM401 3.4 43.0 1.0 CHB B:HEM401 3.4 44.3 1.0 CHA B:HEM401 3.4 44.6 1.0 CHC B:HEM401 3.5 43.1 1.0 NAN B:5PK402 3.9 51.1 1.0 ND1 B:HIS312 4.2 45.0 1.0 CAM B:5PK402 4.2 50.9 1.0 CG B:HIS312 4.3 42.9 1.0 C2D B:HEM401 4.3 43.7 1.0 C3C B:HEM401 4.3 42.6 1.0 C3B B:HEM401 4.3 43.9 1.0 C3D B:HEM401 4.3 43.7 1.0 C2B B:HEM401 4.3 43.3 1.0 C2A B:HEM401 4.3 46.5 1.0 C3A B:HEM401 4.3 45.3 1.0 C2C B:HEM401 4.3 42.5 1.0 CG2 B:VAL316 4.6 41.8 1.0

Iron binding site 3 out of 4 in the Holo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Holo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:42.3 occ:1.00 FE C:HEM401 0.0 42.3 1.0 ND C:HEM401 2.0 42.1 1.0 NA C:HEM401 2.0 43.4 1.0 NB C:HEM401 2.1 42.4 1.0 NC C:HEM401 2.1 41.7 1.0 NAP C:5PK402 2.1 54.3 1.0 NE2 C:HIS312 2.1 43.0 1.0 CAQ C:5PK402 2.7 54.2 1.0 CE1 C:HIS312 3.0 42.7 1.0 C1B C:HEM401 3.1 42.8 1.0 C1A C:HEM401 3.1 43.6 1.0 C1D C:HEM401 3.1 42.0 1.0 C4D C:HEM401 3.1 42.6 1.0 C4A C:HEM401 3.1 43.5 1.0 C4C C:HEM401 3.1 41.4 1.0 C1C C:HEM401 3.1 41.4 1.0 C4B C:HEM401 3.1 42.1 1.0 CD2 C:HIS312 3.3 41.6 1.0 CAO C:5PK402 3.3 54.3 1.0 CHB C:HEM401 3.4 43.2 1.0 CHD C:HEM401 3.4 41.6 1.0 CHA C:HEM401 3.4 43.1 1.0 CHC C:HEM401 3.5 41.4 1.0 NAN C:5PK402 4.0 54.8 1.0 ND1 C:HIS312 4.2 42.1 1.0 CAM C:5PK402 4.3 54.5 1.0 C3C C:HEM401 4.3 40.8 1.0 CG C:HIS312 4.3 40.7 1.0 C2A C:HEM401 4.3 45.0 1.0 C2D C:HEM401 4.3 42.2 1.0 C3D C:HEM401 4.3 42.5 1.0 C2B C:HEM401 4.3 42.3 1.0 C3B C:HEM401 4.3 41.9 1.0 C3A C:HEM401 4.3 44.2 1.0 C2C C:HEM401 4.3 40.8 1.0 CG2 C:VAL316 4.6 41.5 1.0

Iron binding site 4 out of 4 in the Holo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Holo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:43.5 occ:1.00 FE D:HEM401 0.0 43.5 1.0 ND D:HEM401 2.0 44.4 1.0 NB D:HEM401 2.1 43.2 1.0 NA D:HEM401 2.1 44.4 1.0 NC D:HEM401 2.1 43.5 1.0 NE2 D:HIS312 2.1 45.1 1.0 NAP D:5PK402 2.2 53.1 1.0 CAQ D:5PK402 2.7 53.2 1.0 CE1 D:HIS312 2.9 45.1 1.0 C1D D:HEM401 3.0 45.0 1.0 C1B D:HEM401 3.1 43.2 1.0 C4C D:HEM401 3.1 43.8 1.0 C1A D:HEM401 3.1 44.8 1.0 C4A D:HEM401 3.1 44.0 1.0 C4D D:HEM401 3.1 44.6 1.0 C1C D:HEM401 3.1 43.1 1.0 C4B D:HEM401 3.1 43.0 1.0 CD2 D:HIS312 3.2 44.1 1.0 CHD D:HEM401 3.4 44.5 1.0 CHB D:HEM401 3.4 43.4 1.0 CAO D:5PK402 3.4 53.0 1.0 CHA D:HEM401 3.4 44.4 1.0 CHC D:HEM401 3.5 42.6 1.0 NAN D:5PK402 4.0 53.2 1.0 ND1 D:HIS312 4.1 45.1 1.0 CG D:HIS312 4.3 43.5 1.0 C2D D:HEM401 4.3 45.3 1.0 C3C D:HEM401 4.3 43.7 1.0 C3D D:HEM401 4.3 45.3 1.0 C3B D:HEM401 4.3 43.0 1.0 C3A D:HEM401 4.3 44.5 1.0 C2A D:HEM401 4.3 45.9 1.0 C2B D:HEM401 4.3 42.6 1.0 CAM D:5PK402 4.3 52.8 1.0 C2C D:HEM401 4.3 43.9 1.0 CG2 D:VAL316 4.6 38.7 1.0

S.Cren, C.Lotz, A.Mac Sweeney, R.Lange, T.Kimmerlin. Sar and Cellular Potency Optimization of Novel Heme-Binding IDO1 Inhibitors To Be Published.