Iron in PDB 6vbn: Crystal Structure of HTDO2 Bound to Inhibitor GNE1

All present enzymatic activity of Crystal Structure of HTDO2 Bound to Inhibitor GNE1:
1.13.11.11;

The structure of Crystal Structure of HTDO2 Bound to Inhibitor GNE1, PDB code: 6vbn 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)	39.37 / 3.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.475, 143.044, 147.236, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.5

The binding sites of Iron atom in the Crystal Structure of HTDO2 Bound to Inhibitor GNE1 (pdb code 6vbn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of HTDO2 Bound to Inhibitor GNE1, PDB code: 6vbn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of HTDO2 Bound to Inhibitor GNE1


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 HTDO2 Bound to Inhibitor GNE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:98.4 occ:1.00 FE A:HEM401 0.0 98.4 1.0 NA A:HEM401 1.9 98.6 1.0 ND A:HEM401 1.9 98.5 1.0 NC A:HEM401 2.0 98.2 1.0 NB A:HEM401 2.0 98.0 1.0 N9 A:QVY402 2.2 90.6 1.0 NE2 A:HIS328 2.3 95.7 1.0 C1D A:HEM401 3.0 98.8 1.0 C4D A:HEM401 3.0 98.8 1.0 C1A A:HEM401 3.0 98.8 1.0 C4C A:HEM401 3.0 98.4 1.0 C4A A:HEM401 3.0 98.6 1.0 C1B A:HEM401 3.0 98.4 1.0 C4B A:HEM401 3.0 98.2 1.0 C1C A:HEM401 3.0 98.0 1.0 C10 A:QVY402 3.1 90.7 1.0 CD2 A:HIS328 3.2 96.1 1.0 C8 A:QVY402 3.3 91.5 1.0 CHA A:HEM401 3.4 99.4 1.0 CHD A:HEM401 3.4 99.2 1.0 CE1 A:HIS328 3.4 95.4 1.0 CHB A:HEM401 3.4 98.9 1.0 CHC A:HEM401 3.4 98.7 1.0 C2A A:HEM401 4.2 99.2 1.0 C3A A:HEM401 4.2 99.1 1.0 C2C A:HEM401 4.2 98.7 1.0 C3C A:HEM401 4.2 98.8 1.0 C2D A:HEM401 4.2 99.2 1.0 C3D A:HEM401 4.3 99.3 1.0 C2B A:HEM401 4.3 98.5 1.0 N11 A:QVY402 4.3 93.4 1.0 C3B A:HEM401 4.3 98.7 1.0 C7 A:QVY402 4.4 93.2 1.0 CG A:HIS328 4.4 94.4 1.0 ND1 A:HIS328 4.5 96.2 1.0 CG1 A:VAL332 4.8 0.3 1.0 H21 A:QVY402 4.9 98.6 1.0 CA A:GLY152 5.0 0.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of HTDO2 Bound to Inhibitor GNE1


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 HTDO2 Bound to Inhibitor GNE1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:0.5 occ:1.00 FE B:HEM401 0.0 0.5 1.0 NA B:HEM401 1.9 0.8 1.0 NC B:HEM401 2.0 0.5 1.0 ND B:HEM401 2.0 0.8 1.0 NB B:HEM401 2.0 0.2 1.0 N9 B:QVY402 2.2 83.5 1.0 NE2 B:HIS328 2.3 85.8 1.0 C1A B:HEM401 3.0 0.0 1.0 C1D B:HEM401 3.0 0.0 1.0 C4A B:HEM401 3.0 0.7 1.0 C4D B:HEM401 3.0 0.1 1.0 C1B B:HEM401 3.0 0.6 1.0 C4C B:HEM401 3.0 0.8 1.0 C4B B:HEM401 3.0 0.5 1.0 C1C B:HEM401 3.0 0.3 1.0 C10 B:QVY402 3.1 84.2 1.0 CE1 B:HIS328 3.2 85.6 1.0 C8 B:QVY402 3.2 83.8 1.0 CD2 B:HIS328 3.3 86.1 1.0 CHB B:HEM401 3.4 0.1 1.0 CHA B:HEM401 3.4 0.5 1.0 CHD B:HEM401 3.4 0.5 1.0 CHC B:HEM401 3.4 1.0 1.0 C2A B:HEM401 4.2 0.4 1.0 C3A B:HEM401 4.2 0.3 1.0 C2C B:HEM401 4.2 1.0 1.0 C3C B:HEM401 4.2 0.0 1.0 C2B B:HEM401 4.3 0.7 1.0 C2D B:HEM401 4.3 0.4 1.0 C3D B:HEM401 4.3 0.5 1.0 N11 B:QVY402 4.3 85.5 1.0 C3B B:HEM401 4.3 0.9 1.0 C7 B:QVY402 4.3 85.1 1.0 ND1 B:HIS328 4.4 86.8 1.0 CG B:HIS328 4.4 85.2 1.0 CA B:GLY152 4.9 0.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure of HTDO2 Bound to Inhibitor GNE1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of HTDO2 Bound to Inhibitor GNE1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:0.4 occ:1.00 FE C:HEM401 0.0 0.4 1.0 NA C:HEM401 1.9 0.7 1.0 ND C:HEM401 1.9 0.5 1.0 NC C:HEM401 2.0 0.4 1.0 NB C:HEM401 2.0 0.2 1.0 N9 C:QVY403 2.2 86.4 1.0 NE2 C:HIS328 2.3 87.6 1.0 C10 C:QVY403 2.9 85.7 1.0 C1D C:HEM401 3.0 0.9 1.0 C1A C:HEM401 3.0 0.9 1.0 C4D C:HEM401 3.0 1.0 1.0 C4A C:HEM401 3.0 0.6 1.0 C4C C:HEM401 3.0 0.6 1.0 C1B C:HEM401 3.0 0.7 1.0 C4B C:HEM401 3.0 0.5 1.0 C1C C:HEM401 3.0 0.3 1.0 CE1 C:HIS328 3.2 87.4 1.0 CD2 C:HIS328 3.3 88.2 1.0 CHA C:HEM401 3.3 0.2 1.0 CHD C:HEM401 3.4 0.3 1.0 C8 C:QVY403 3.4 88.3 1.0 CHB C:HEM401 3.4 0.2 1.0 CHC C:HEM401 3.4 1.0 1.0 C2A C:HEM401 4.1 0.3 1.0 N11 C:QVY403 4.2 88.8 1.0 C3A C:HEM401 4.2 0.2 1.0 C3C C:HEM401 4.2 0.9 1.0 C2D C:HEM401 4.2 0.4 1.0 C2C C:HEM401 4.2 0.8 1.0 C3D C:HEM401 4.2 0.4 1.0 C2B C:HEM401 4.3 0.7 1.0 C3B C:HEM401 4.3 0.9 1.0 ND1 C:HIS328 4.4 88.7 1.0 CG C:HIS328 4.4 87.5 1.0 C7 C:QVY403 4.4 88.8 1.0 H21 C:QVY403 4.7 1.0 1.0 CA C:GLY152 4.8 0.2 1.0

Iron binding site 4 out of 4 in the Crystal Structure of HTDO2 Bound to Inhibitor GNE1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of HTDO2 Bound to Inhibitor GNE1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:0.4 occ:1.00 FE D:HEM401 0.0 0.4 1.0 NA D:HEM401 1.9 0.7 1.0 ND D:HEM401 2.0 0.5 1.0 NC D:HEM401 2.0 0.3 1.0 NB D:HEM401 2.0 0.1 1.0 N9 C:QVY402 2.2 0.5 1.0 NE2 D:HIS328 2.4 0.9 1.0 C10 C:QVY402 2.8 0.7 1.0 C1D D:HEM401 3.0 0.7 1.0 C1A D:HEM401 3.0 0.8 1.0 C4D D:HEM401 3.0 0.9 1.0 C4C D:HEM401 3.0 0.5 1.0 C4A D:HEM401 3.0 0.7 1.0 C1B D:HEM401 3.0 0.5 1.0 C4B D:HEM401 3.0 0.4 1.0 C1C D:HEM401 3.0 0.3 1.0 CE1 D:HIS328 3.3 0.6 1.0 CHD D:HEM401 3.4 0.2 1.0 CHA D:HEM401 3.4 0.2 1.0 CHB D:HEM401 3.4 0.9 1.0 CD2 D:HIS328 3.4 0.2 1.0 CHC D:HEM401 3.4 0.9 1.0 C8 C:QVY402 3.5 0.6 1.0 N11 C:QVY402 4.1 0.6 1.0 C2A D:HEM401 4.2 0.3 1.0 C3A D:HEM401 4.2 0.2 1.0 C3C D:HEM401 4.2 0.9 1.0 C2C D:HEM401 4.2 0.8 1.0 C2D D:HEM401 4.2 0.3 1.0 C2B D:HEM401 4.3 0.7 1.0 C3D D:HEM401 4.3 0.3 1.0 C3B D:HEM401 4.3 0.8 1.0 C7 C:QVY402 4.5 0.1 1.0 ND1 D:HIS328 4.5 0.4 1.0 CG D:HIS328 4.5 0.7 1.0 CA D:GLY152 4.6 0.4 1.0 H21 C:QVY402 4.7 0.3 1.0 CG1 D:VAL332 4.8 0.4 1.0

B.T.Parr, R.Pastor, B.D.Sellers, Z.Pei, F.A.Jaipuri, G.M.Castanedo, L.Gazzard, S.Kumar, X.Li, W.Liu, R.Mendonca, R.K.Pavana, H.Potturi, C.Shao, V.Velvadapu, J.P.Waldo, G.Wu, P.W.Yuen, Z.Zhang, Y.Zhang, S.F.Harris, A.J.Oh, A.Dipasquale, K.Dement, H.La, L.Goon, A.Gustafson, E.C.Vanderporten, M.R.Mautino, Y.Liu. Implementation of the Cyp Index For the Design of Selective Tryptophan-2,3-Dioxygenase Inhibitors. Acs Med.Chem.Lett. V. 11 541 2020.
ISSN: ISSN 1948-5875
PubMed: 32292562
DOI: 10.1021/ACSMEDCHEMLETT.0C00004