Fluorine in PDB 7u1m: Crystal Structure of NTMT1 in Complex with Compound YD206

All present enzymatic activity of Crystal Structure of NTMT1 in Complex with Compound YD206:
2.1.1.244;

The structure of Crystal Structure of NTMT1 in Complex with Compound YD206, PDB code: 7u1m was solved by R.Yadav, N.Noinaj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.80 / 3.17
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	89.609, 89.609, 141.502, 90, 90, 120
R / Rfree (%)	25.1 / 28.3

The binding sites of Fluorine atom in the Crystal Structure of NTMT1 in Complex with Compound YD206 (pdb code 7u1m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of NTMT1 in Complex with Compound YD206, PDB code: 7u1m:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of NTMT1 in Complex with Compound YD206


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of NTMT1 in Complex with Compound YD206 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:140.6 occ:1.00 F25 A:KYF302 0.0 140.6 1.0 C24 A:KYF302 1.4 134.7 1.0 C26 A:KYF302 2.4 143.5 1.0 C23 A:KYF302 2.4 137.1 1.0 CA A:GLY139 3.4 139.6 1.0 N A:GLY139 3.5 135.3 1.0 CD2 A:HIS140 3.6 142.2 1.0 C27 A:KYF302 3.7 144.7 1.0 C22 A:KYF302 3.7 137.7 1.0 CB A:SER182 3.8 150.3 1.0 NE2 A:HIS140 3.8 142.7 1.0 C A:GLY139 3.8 147.2 1.0 N A:HIS140 3.9 148.4 1.0 C A:VAL137 4.1 139.2 1.0 CG A:HIS140 4.1 145.5 1.0 CA A:VAL137 4.1 131.2 1.0 O A:VAL137 4.1 143.8 1.0 O A:TRP136 4.2 134.8 1.0 C21 A:KYF302 4.2 137.1 1.0 OG A:SER182 4.2 150.0 1.0 N A:VAL137 4.3 128.0 1.0 C A:TRP136 4.3 128.7 1.0 CE1 A:HIS140 4.4 144.2 1.0 ND1 A:HIS140 4.5 147.8 1.0 N A:ILE138 4.6 132.6 1.0 O A:GLY139 4.6 153.3 1.0 C A:ILE138 4.7 133.4 1.0 OD2 A:ASP167 4.8 141.8 1.0 CB A:HIS140 4.8 142.9 1.0 OD1 A:ASP180 4.8 151.1 1.0 OD1 A:ASP167 4.8 140.6 1.0 CA A:HIS140 4.9 148.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of NTMT1 in Complex with Compound YD206


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of NTMT1 in Complex with Compound YD206 within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:171.7 occ:1.00 F25 B:KYF302 0.0 171.7 1.0 C24 B:KYF302 1.4 172.4 1.0 C26 B:KYF302 2.4 180.6 1.0 C23 B:KYF302 2.4 174.9 1.0 CD2 B:HIS140 3.4 174.4 1.0 CB B:SER182 3.5 173.2 1.0 NE2 B:HIS140 3.5 180.4 1.0 CA B:GLY139 3.6 167.9 1.0 C27 B:KYF302 3.7 182.9 1.0 C22 B:KYF302 3.7 181.7 1.0 N B:GLY139 3.8 162.4 1.0 C B:GLY139 3.9 167.9 1.0 CG B:HIS140 3.9 173.2 1.0 N B:HIS140 4.0 163.0 1.0 OG B:SER182 4.0 173.8 1.0 CE1 B:HIS140 4.1 182.4 1.0 C21 B:KYF302 4.2 185.0 1.0 ND1 B:HIS140 4.3 177.4 1.0 O B:VAL137 4.3 168.7 1.0 C B:VAL137 4.3 165.0 1.0 CA B:VAL137 4.4 161.7 1.0 O B:TRP136 4.4 172.7 1.0 O B:GLY139 4.6 171.6 1.0 C B:TRP136 4.7 169.8 1.0 N B:VAL137 4.7 164.3 1.0 CB B:HIS140 4.7 170.4 1.0 CA B:SER182 4.8 173.2 1.0 CA B:HIS140 4.8 167.7 1.0 OD2 B:ASP180 4.8 179.4 1.0 N B:ILE138 4.9 160.9 1.0

G.Dong, Y.Deng, A.Yasgar, R.Yadav, D.Talley, A.V.Zakharov, S.Jain, G.Rai, N.Noinaj, A.Simeonov, R.Huang. Venglustat Inhibits Protein N-Terminal Methyltransferase 1 in A Substrate-Competitive Manner. J.Med.Chem. V. 65 12334 2022.
ISSN: ISSN 0022-2623
PubMed: 36074125
DOI: 10.1021/ACS.JMEDCHEM.2C01050