Chlorine in PDB 8tm7: Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A3

All present enzymatic activity of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A3:
2.4.2.12;

The structure of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A3, PDB code: 8tm7 was solved by K.M.Ratia, G.R.Thatcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.47 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.56, 106.864, 83.222, 90, 96.71, 90
R / Rfree (%)	17.8 / 19.8

The binding sites of Chlorine atom in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A3 (pdb code 8tm7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A3, PDB code: 8tm7:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl705 b:42.1 occ:1.00 N A:LYS77 3.1 22.6 1.0 CA A:THR76 3.5 22.4 1.0 NZ A:LYS73 3.7 29.0 1.0 CB A:THR76 3.7 21.7 1.0 C A:THR76 3.8 23.3 1.0 CB A:LYS77 4.0 29.5 1.0 CD1 A:LEU105 4.1 19.5 1.0 OE1 A:GLU78 4.1 31.4 1.0 CA A:LYS77 4.2 24.8 1.0 CD2 A:LEU105 4.2 21.4 1.0 CE A:LYS73 4.2 26.6 1.0 CG2 A:THR76 4.3 22.4 1.0 CG A:LEU105 4.7 19.3 1.0 OG1 A:THR76 4.9 21.6 1.0 N A:THR76 4.9 22.1 1.0 O A:VAL75 5.0 22.1 1.0

Chlorine binding site 2 out of 3 in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl706 b:25.8 occ:1.00 O A:HOH933 2.9 22.0 1.0 NH2 A:ARG311 2.9 18.3 1.0 OH B:TYR18 3.0 13.7 1.0 CB A:GLU246 3.6 14.6 1.0 CA A:GLU246 3.7 14.6 1.0 NH1 A:ARG311 3.8 20.1 1.0 CZ A:ARG311 3.8 19.5 1.0 O A:HOH895 3.8 18.9 1.0 CE2 B:TYR18 3.9 14.7 1.0 CZ B:TYR18 3.9 14.0 1.0 ND1 A:HIS247 4.2 15.7 1.0 C2 A:NCA703 4.2 15.3 1.0 N A:HIS247 4.2 15.6 1.0 N1 A:NCA703 4.2 15.8 1.0 CE1 A:HIS247 4.5 16.8 1.0 C A:GLU246 4.5 14.7 1.0 O A:ALA245 4.6 16.0 1.0 NH1 A:ARG196 4.7 18.6 1.0 O B:HOH609 4.9 32.7 1.0 N A:GLU246 4.9 15.4 1.0

Chlorine binding site 3 out of 3 in the Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Nampt in Complex with Substrate Nam and Small Molecule Activator Np-A3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl707 b:22.2 occ:1.00 O B:HOH677 2.9 21.1 1.0 OH A:TYR18 2.9 13.3 1.0 NH2 B:ARG311 3.1 17.1 1.0 CB B:GLU246 3.6 13.4 1.0 CA B:GLU246 3.7 12.8 1.0 O A:HOH946 3.8 16.3 1.0 CE2 A:TYR18 3.9 14.2 1.0 CZ A:TYR18 3.9 13.5 1.0 NH1 B:ARG311 3.9 17.1 1.0 CZ B:ARG311 3.9 18.0 1.0 C2 B:NCA501 4.2 16.3 1.0 N1 B:NCA501 4.2 15.9 1.0 N B:HIS247 4.2 13.7 1.0 ND1 B:HIS247 4.2 14.9 1.0 C B:GLU246 4.5 13.6 1.0 O B:ALA245 4.5 12.7 1.0 CE1 B:HIS247 4.6 15.5 1.0 NH1 B:ARG196 4.8 18.7 1.0 N B:GLU246 4.9 13.6 1.0 O A:HOH802 4.9 27.8 1.0 CG B:GLU246 5.0 13.6 1.0

J.Gordon-Blake, K.Ratia, V.Weidig, G.R.Velma, M.Ackerman-Berrier, C.Penton, S.R.Musku, E.T.M.Alves, T.Driver, L.Tai, G.R.J.Thatcher. Nicotinamide Phosphoribosyltransferase Positive Allosteric Modulators Attenuate Neuronal Oxidative Stress. Acs Med.Chem.Lett. V. 15 205 2024.
ISSN: ISSN 1948-5875
PubMed: 38352833
DOI: 10.1021/ACSMEDCHEMLETT.3C00391