Chlorine in PDB 7rkl: Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group)

The structure of Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group), PDB code: 7rkl was solved by R.Yadav, N.Noinaj, I.D.Iyamu, R.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.26 / 2.08
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.676, 62.031, 106.975, 82.94, 81.92, 68.52
R / Rfree (%)	19.4 / 24

The binding sites of Chlorine atom in the Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group) (pdb code 7rkl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group), PDB code: 7rkl:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:39.0 occ:1.00 CL1 A:5R4301 0.0 39.0 1.0 C02 A:5R4301 1.8 26.3 1.0 N03 A:5R4301 2.6 19.0 1.0 C07 A:5R4301 2.8 20.8 1.0 OD1 A:ASP142 3.0 25.2 1.0 C08 A:5R4301 3.4 17.3 1.0 CG2 A:THR144 3.7 25.2 1.0 N A:VAL143 3.8 17.2 1.0 CG A:ASP142 3.8 28.4 1.0 CG2 A:VAL143 3.9 15.1 1.0 C04 A:5R4301 3.9 20.0 1.0 O A:HOH423 4.0 21.8 1.0 C06 A:5R4301 4.0 19.9 1.0 CD A:LYS8 4.0 23.3 1.0 CA A:ASP142 4.1 15.5 1.0 N A:THR144 4.2 24.8 1.0 C A:ASP142 4.3 19.1 1.0 CB A:LYS8 4.3 26.4 1.0 OG1 A:THR144 4.3 25.0 1.0 CB A:ALA169 4.4 21.2 1.0 O A:ALA169 4.4 20.4 1.0 CB A:ASP142 4.5 19.5 1.0 OD2 A:ASP142 4.5 29.4 1.0 N05 A:5R4301 4.5 21.9 1.0 CD1 A:TYR86 4.5 21.6 1.0 CB A:THR144 4.6 27.3 1.0 CA A:VAL143 4.7 22.6 1.0 CG A:TYR86 4.7 22.6 1.0 C09 A:5R4301 4.7 19.1 1.0 CG A:LYS8 4.8 30.9 1.0 CB A:VAL143 4.9 23.6 1.0 CB A:TYR86 4.9 16.4 1.0 C A:VAL143 4.9 22.1 1.0 CE1 A:TYR86 5.0 24.0 1.0 CA A:ALA169 5.0 18.0 1.0 N10 A:5R4301 5.0 20.4 1.0

Chlorine binding site 2 out of 4 in the Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:43.2 occ:1.00 CL1 B:5R4301 0.0 43.2 1.0 C02 B:5R4301 1.8 21.3 1.0 N03 B:5R4301 2.6 17.8 1.0 C07 B:5R4301 2.8 21.5 1.0 OD1 B:ASP142 3.0 24.0 1.0 C08 B:5R4301 3.4 19.9 1.0 O B:HOH421 3.6 28.9 1.0 CD B:LYS8 3.7 27.8 1.0 CG2 B:THR144 3.7 26.2 1.0 CG B:ASP142 3.9 24.9 1.0 C04 B:5R4301 3.9 17.1 1.0 N B:VAL143 4.0 20.2 1.0 CB B:LYS8 4.0 23.6 1.0 C06 B:5R4301 4.0 20.7 1.0 CG2 B:VAL143 4.1 20.3 1.0 OG1 B:THR144 4.2 23.3 1.0 O B:ALA169 4.3 20.8 1.0 N B:THR144 4.3 22.3 1.0 CA B:ASP142 4.3 17.5 1.0 CB B:ALA169 4.4 20.2 1.0 CG B:LYS8 4.5 32.2 1.0 C B:ASP142 4.5 21.2 1.0 N05 B:5R4301 4.5 21.4 1.0 CB B:THR144 4.5 23.5 1.0 OD2 B:ASP142 4.6 26.0 1.0 CD1 B:TYR86 4.6 22.3 1.0 CB B:ASP142 4.7 19.7 1.0 C09 B:5R4301 4.7 15.5 1.0 CG B:TYR86 4.8 20.6 1.0 CE B:LYS8 4.9 28.1 1.0 CA B:VAL143 4.9 23.2 1.0 NZ B:LYS8 4.9 33.3 1.0 CE1 B:TYR86 5.0 24.8 1.0 CA B:ALA169 5.0 18.1 1.0

Chlorine binding site 3 out of 4 in the Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl301 b:47.6 occ:1.00 CL1 C:5R4301 0.0 47.6 1.0 C02 C:5R4301 1.8 20.1 1.0 N03 C:5R4301 2.6 22.6 1.0 C07 C:5R4301 2.8 24.6 1.0 OD1 C:ASP142 2.9 23.9 1.0 C08 C:5R4301 3.4 21.8 1.0 CD C:LYS8 3.6 26.8 1.0 CG C:ASP142 3.7 29.3 1.0 CG2 C:THR144 3.9 30.1 1.0 C04 C:5R4301 3.9 23.0 1.0 CB C:LYS8 4.0 30.8 1.0 C06 C:5R4301 4.0 22.3 1.0 N C:VAL143 4.1 20.7 1.0 OG1 C:THR144 4.1 20.4 1.0 OD2 C:ASP142 4.3 37.4 1.0 CG2 C:VAL143 4.3 26.8 1.0 CA C:ASP142 4.3 22.6 1.0 N C:THR144 4.4 21.0 1.0 CG C:LYS8 4.4 36.2 1.0 CB C:ALA169 4.4 18.9 1.0 C C:ASP142 4.5 19.8 1.0 CB C:ASP142 4.5 24.4 1.0 N05 C:5R4301 4.5 24.1 1.0 O C:ALA169 4.6 25.2 1.0 CB C:THR144 4.6 21.8 1.0 CD1 C:TYR86 4.6 27.1 1.0 C09 C:5R4301 4.7 25.3 1.0 CG C:TYR86 4.7 23.1 1.0 CE C:LYS8 4.8 30.0 1.0 NZ C:LYS8 4.9 32.6 1.0 CB C:TYR86 5.0 25.2 1.0 O C:HOH416 5.0 28.7 1.0

Chlorine binding site 4 out of 4 in the Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Nicotinamide N-Methyltransferase (Nnmt) in Complex with II399 (P1 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl301 b:44.8 occ:1.00 CL1 D:5R4301 0.0 44.8 1.0 C02 D:5R4301 1.8 18.3 1.0 N03 D:5R4301 2.6 18.8 1.0 C07 D:5R4301 2.8 19.9 1.0 OD1 D:ASP142 2.9 27.8 1.0 C08 D:5R4301 3.4 19.4 1.0 CG2 D:THR144 3.7 18.0 1.0 CG D:ASP142 3.8 29.5 1.0 CD D:LYS8 3.8 33.2 1.0 C04 D:5R4301 3.9 19.7 1.0 CG2 D:VAL143 4.0 23.5 1.0 N D:VAL143 4.0 15.3 1.0 C06 D:5R4301 4.0 16.4 1.0 OG1 D:THR144 4.1 22.5 1.0 CB D:LYS8 4.1 29.9 1.0 CB D:ALA169 4.3 25.6 1.0 N D:THR144 4.3 21.9 1.0 OD2 D:ASP142 4.4 33.2 1.0 CA D:ASP142 4.4 23.0 1.0 O D:ALA169 4.4 19.4 1.0 CB D:THR144 4.5 23.1 1.0 N05 D:5R4301 4.5 19.7 1.0 C D:ASP142 4.6 19.4 1.0 CG D:LYS8 4.6 29.9 1.0 CB D:ASP142 4.7 19.1 1.0 C09 D:5R4301 4.7 20.3 1.0 CD1 D:TYR86 4.8 22.2 1.0 CG D:TYR86 4.9 23.2 1.0 CA D:VAL143 4.9 15.9 1.0 CA D:ALA169 4.9 21.5 1.0 NZ D:LYS8 5.0 32.2 1.0 CE D:LYS8 5.0 31.9 1.0

I.D.Iyamu, J.Z.Vilseck, R.Yadav, N.Noinaj, R.Huang. Exploring Unconventional Sam Analogues to Build Cell-Potent Bisubstrate Inhibitors For Nicotinamide N-Methyltransferase. Angew.Chem.Int.Ed.Engl. V. 61 14813 2022.
ISSN: ESSN 1521-3773
PubMed: 35134268
DOI: 10.1002/ANIE.202114813