Sodium in PDB 6lp6: Crystal Structure of Human Dhodh in Complex with Inhibitor 1214

All present enzymatic activity of Crystal Structure of Human Dhodh in Complex with Inhibitor 1214:
1.3.5.2;

The structure of Crystal Structure of Human Dhodh in Complex with Inhibitor 1214, PDB code: 6lp6 was solved by Q.Chen, Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.38 / 1.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.605, 90.605, 123.057, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 17.8

The structure of Crystal Structure of Human Dhodh in Complex with Inhibitor 1214 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1214 (pdb code 6lp6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1214, PDB code: 6lp6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1214


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Dhodh in Complex with Inhibitor 1214 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:28.2 occ:1.00 O A:ACT405 2.6 32.0 1.0 O A:HOH563 2.8 14.5 1.0 HG3 A:GLN165 2.8 30.5 1.0 O A:GLN165 2.8 15.2 1.0 O A:HOH640 2.8 28.4 1.0 HB3 A:GLN168 2.8 17.5 1.0 C A:ACT405 3.2 46.5 1.0 OXT A:ACT405 3.4 44.2 1.0 HG2 A:GLN165 3.4 30.5 1.0 HA A:GLN165 3.5 16.1 1.0 HB2 A:ALA169 3.5 25.2 1.0 H A:ALA169 3.5 20.7 1.0 CG A:GLN165 3.5 25.4 1.0 HG3 A:GLN168 3.7 16.6 1.0 N A:ALA169 3.7 17.2 1.0 CB A:GLN168 3.7 14.6 1.0 C A:GLN165 3.7 20.5 1.0 HG2 A:GLN168 3.8 16.6 1.0 HA A:ALA169 3.8 23.9 1.0 CG A:GLN168 3.9 13.8 1.0 HE21 A:GLN165 4.0 37.3 1.0 CA A:GLN165 4.0 13.4 1.0 CA A:ALA169 4.1 19.9 1.0 C A:GLN168 4.2 17.3 1.0 H3 A:ACT405 4.2 51.6 1.0 CB A:ALA169 4.2 21.0 1.0 HA A:LEU205 4.3 17.2 1.0 CH3 A:ACT405 4.3 43.0 1.0 HB2 A:GLN168 4.4 17.5 1.0 CB A:GLN165 4.4 21.2 1.0 O A:LEU205 4.4 16.3 1.0 CA A:GLN168 4.5 16.3 1.0 HD23 A:LEU205 4.5 25.9 1.0 NE2 A:GLN165 4.6 31.1 1.0 O A:HOH681 4.6 36.2 1.0 CD A:GLN165 4.6 33.2 1.0 H A:GLN168 4.7 21.3 1.0 HB3 A:ALA169 4.8 25.2 1.0 HA A:GLN166 4.8 23.8 1.0 O A:GLN168 4.9 16.1 1.0 HB1 A:ALA169 4.9 25.2 1.0 HB2 A:GLN165 4.9 25.5 1.0 N A:GLN166 4.9 19.4 1.0 O A:HOH643 4.9 14.9 1.0 C A:LEU205 5.0 17.0 1.0 H1 A:ACT405 5.0 51.6 1.0 N A:GLN168 5.0 17.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1214


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Dhodh in Complex with Inhibitor 1214 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na413 b:34.9 occ:1.00 H A:GLN263 2.2 19.5 1.0 H3 A:ACT408 2.3 58.8 1.0 HB A:THR261 2.5 24.5 1.0 H1 A:ACT408 2.6 58.8 1.0 CH3 A:ACT408 2.8 49.0 1.0 HB2 A:GLN263 2.9 29.9 1.0 O A:ACT411 2.9 54.2 1.0 N A:GLN263 3.1 16.3 1.0 HB2 A:SER262 3.1 33.3 1.0 H A:SER262 3.2 24.7 1.0 HB3 A:GLN263 3.2 29.9 1.0 C A:ACT408 3.3 58.5 1.0 CB A:THR261 3.4 20.4 1.0 CB A:GLN263 3.4 24.9 1.0 N A:SER262 3.5 20.6 1.0 HG1 A:THR261 3.6 28.3 1.0 O A:ACT408 3.6 38.3 1.0 OG1 A:THR261 3.7 23.6 1.0 C A:ACT411 3.8 38.1 1.0 H2 A:ACT408 3.8 58.8 1.0 CA A:GLN263 3.8 21.0 1.0 CB A:SER262 3.9 27.7 1.0 C A:SER262 4.0 15.4 1.0 CA A:SER262 4.0 18.4 1.0 OXT A:ACT408 4.1 76.5 1.0 C A:THR261 4.1 23.8 1.0 HG21 A:THR261 4.2 31.1 1.0 CA A:THR261 4.3 21.9 1.0 HA A:GLN263 4.3 25.2 1.0 CG2 A:THR261 4.3 26.0 1.0 CH3 A:ACT411 4.4 21.6 1.0 HA A:THR261 4.4 26.2 1.0 H A:ASP264 4.5 21.4 1.0 HB3 A:SER262 4.5 33.3 1.0 HG22 A:THR261 4.5 31.1 1.0 OXT A:ACT411 4.6 67.4 1.0 OG A:SER262 4.8 36.5 1.0 CG A:GLN263 4.8 27.7 1.0 HG2 A:GLN263 4.9 33.3 1.0 HA A:SER262 5.0 22.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1214


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human Dhodh in Complex with Inhibitor 1214 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na414 b:51.9 occ:1.00 O A:HOH697 2.4 49.8 1.0 O A:HOH516 2.8 34.1 1.0 H1 A:ACT405 3.3 51.6 1.0 O A:HOH547 3.4 15.8 1.0 HA A:ASP207 3.5 13.2 1.0 O A:ARG249 3.5 18.2 1.0 HA A:PRO250 3.5 20.3 1.0 H A:ARG249 3.9 20.5 1.0 O A:ALA206 3.9 17.2 1.0 O A:VAL247 3.9 26.1 1.0 C A:ARG249 3.9 17.9 1.0 HE1 A:HIS86 4.1 35.1 1.0 O A:HOH681 4.1 36.2 1.0 N A:ARG249 4.2 17.1 1.0 OD1 A:ASP207 4.2 19.0 1.0 NE2 A:HIS86 4.3 22.4 1.0 CA A:PRO250 4.3 16.9 1.0 HA A:HIS248 4.3 20.8 1.0 CH3 A:ACT405 4.4 43.0 1.0 N A:PRO250 4.4 15.0 1.0 CA A:ASP207 4.4 11.0 1.0 CE1 A:HIS86 4.5 29.3 1.0 C A:VAL247 4.6 27.1 1.0 O A:ASP207 4.6 13.6 1.0 HB3 A:PRO250 4.6 19.4 1.0 C A:HIS248 4.6 15.5 1.0 H3 A:ACT405 4.7 51.6 1.0 CA A:ARG249 4.7 16.1 1.0 H2 A:ACT405 4.8 51.6 1.0 C A:ALA206 4.8 14.9 1.0 CA A:HIS248 4.8 17.3 1.0 C A:ASP207 5.0 12.0 1.0 N A:HIS248 5.0 19.5 1.0

Z.Zuo, X.Liu, X.Qian, T.Zeng, N.Sang, H.Liu, Y.Zhou, L.Tao, X.Zhou, N.Su, Y.Yu, Q.Chen, Y.Luo, Y.Zhao. Bifunctional Naphtho[2,3- D ][1,2,3]Triazole-4,9-Dione Compounds Exhibit Antitumor Effects in Vitro and in Vivo By Inhibiting Dihydroorotate Dehydrogenase and Inducing Reactive Oxygen Species Production. J.Med.Chem. V. 63 7633 2020.
ISSN: ISSN 0022-2623
PubMed: 32496056
DOI: 10.1021/ACS.JMEDCHEM.0C00512