Chlorine in PDB 7ehm: Human MTHFD2 in Complex with Compound 21 and 15

All present enzymatic activity of Human MTHFD2 in Complex with Compound 21 and 15:
1.5.1.15; 3.5.4.9;

The structure of Human MTHFD2 in Complex with Compound 21 and 15, PDB code: 7ehm was solved by L.C.Lee, Y.H.Peng, S.Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.92 / 2.13
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	114.232, 114.232, 114.164, 90, 90, 120
R / Rfree (%)	19.5 / 22.7

The binding sites of Chlorine atom in the Human MTHFD2 in Complex with Compound 21 and 15 (pdb code 7ehm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human MTHFD2 in Complex with Compound 21 and 15, PDB code: 7ehm:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Human MTHFD2 in Complex with Compound 21 and 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human MTHFD2 in Complex with Compound 21 and 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:53.7 occ:0.90 CL1 A:J4C401 0.0 53.7 0.9 CAY A:J4C401 1.7 41.3 0.9 CAZ A:J4C401 2.7 41.8 0.9 CAX A:J4C401 2.7 38.9 0.9 CL2 A:J4C401 3.0 49.4 0.9 CG A:MET207 3.6 52.3 1.0 CE A:MET211 3.8 51.9 1.0 CBA A:J4C401 4.0 39.0 0.9 CAW A:J4C401 4.0 39.4 0.9 SG B:CYS166 4.0 48.1 1.0 N A:PRO208 4.1 37.8 1.0 CE B:MET211 4.2 46.6 1.0 CB A:MET207 4.2 45.2 1.0 CB B:CYS166 4.2 40.0 1.0 CA A:PRO208 4.3 40.2 1.0 CG A:PRO208 4.3 40.5 1.0 SG A:CYS166 4.3 47.9 1.0 C A:MET207 4.3 41.0 1.0 CD A:PRO208 4.4 37.9 1.0 CAV A:J4C401 4.5 38.1 0.9 O A:MET207 4.7 42.1 1.0 CG1 A:VAL162 4.7 31.6 1.0 CB A:PRO208 4.7 37.8 1.0 CG A:MET211 4.8 50.1 1.0 SD B:MET211 4.8 61.4 1.0 CB A:MET211 4.9 48.8 1.0 CA A:MET207 4.9 41.1 1.0

Chlorine binding site 2 out of 4 in the Human MTHFD2 in Complex with Compound 21 and 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human MTHFD2 in Complex with Compound 21 and 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:49.4 occ:0.90 CL2 A:J4C401 0.0 49.4 0.9 CAZ A:J4C401 1.7 41.8 0.9 CAY A:J4C401 2.6 41.3 0.9 CBA A:J4C401 2.7 39.0 0.9 CL1 A:J4C401 3.0 53.7 0.9 O B:CYS166 3.7 43.2 1.0 OD1 A:ASN204 3.9 47.3 1.0 CAX A:J4C401 3.9 38.9 0.9 CAV A:J4C401 3.9 38.1 0.9 CG A:LYS203 4.0 45.0 1.0 O A:LYS203 4.1 44.1 1.0 CB B:CYS166 4.1 40.0 1.0 C B:CYS166 4.3 40.7 1.0 CB A:MET207 4.4 45.2 1.0 CA A:ASN204 4.4 43.3 1.0 CAW A:J4C401 4.4 39.4 0.9 CG A:PRO208 4.4 40.5 1.0 CD A:PRO208 4.5 37.9 1.0 CG A:MET207 4.5 52.3 1.0 CD2 B:LEU167 4.5 39.8 1.0 C A:LYS203 4.6 42.4 1.0 CD A:LYS203 4.6 49.7 1.0 CA B:CYS166 4.7 40.8 1.0 N A:ASN204 4.8 42.5 1.0 CE A:LYS203 4.9 50.1 1.0 CG A:ASN204 5.0 46.4 1.0 CG1 A:VAL162 5.0 31.6 1.0

Chlorine binding site 3 out of 4 in the Human MTHFD2 in Complex with Compound 21 and 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human MTHFD2 in Complex with Compound 21 and 15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:51.7 occ:0.91 CL1 B:J4C401 0.0 51.7 0.9 CAY B:J4C401 1.7 40.0 0.9 CAZ B:J4C401 2.7 39.0 0.9 CAX B:J4C401 2.7 40.4 0.9 CL2 B:J4C401 3.0 49.8 0.9 CG B:MET207 3.8 50.4 1.0 CB B:MET207 3.9 44.2 1.0 CE B:MET211 4.0 46.6 1.0 CAW B:J4C401 4.0 41.0 0.9 CBA B:J4C401 4.0 36.9 0.9 CE A:MET211 4.0 51.9 1.0 N B:PRO208 4.1 40.2 1.0 SG A:CYS166 4.3 47.9 1.0 CB A:CYS166 4.3 40.7 1.0 CG B:PRO208 4.3 42.6 1.0 C B:MET207 4.3 38.2 1.0 CA B:PRO208 4.4 39.8 1.0 CD B:PRO208 4.4 39.3 1.0 CAV B:J4C401 4.5 37.3 0.9 SG B:CYS166 4.5 48.1 1.0 CG1 B:VAL162 4.6 32.6 1.0 CB B:PRO208 4.7 37.0 1.0 O B:MET207 4.7 37.4 1.0 SD A:MET211 4.7 57.9 1.0 CA B:MET207 4.8 42.4 1.0

Chlorine binding site 4 out of 4 in the Human MTHFD2 in Complex with Compound 21 and 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human MTHFD2 in Complex with Compound 21 and 15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:49.8 occ:0.91 CL2 B:J4C401 0.0 49.8 0.9 CAZ B:J4C401 1.7 39.0 0.9 CAY B:J4C401 2.6 40.0 0.9 CBA B:J4C401 2.6 36.9 0.9 CL1 B:J4C401 3.0 51.7 0.9 O B:HOH506 3.6 59.7 1.0 OD1 B:ASN204 3.7 53.1 1.0 O A:CYS166 3.9 43.5 1.0 CAV B:J4C401 3.9 37.3 0.9 CAX B:J4C401 3.9 40.4 0.9 O B:LYS203 4.2 43.4 1.0 CB A:CYS166 4.2 40.7 1.0 CB B:MET207 4.2 44.2 1.0 CA B:ASN204 4.2 44.3 1.0 CD2 A:LEU167 4.3 36.8 1.0 CAW B:J4C401 4.4 41.0 0.9 C A:CYS166 4.5 39.1 1.0 C B:LYS203 4.6 43.3 1.0 N B:ASN204 4.6 44.4 1.0 CG B:LYS203 4.6 48.6 1.0 CG B:MET207 4.6 50.4 1.0 CG B:PRO208 4.6 42.6 1.0 CD B:PRO208 4.6 39.3 1.0 CG B:ASN204 4.7 51.8 1.0 CE B:LYS203 4.8 59.6 1.0 CA A:CYS166 4.9 39.1 1.0 CG1 B:VAL162 4.9 32.6 1.0

L.C.Lee, Y.H.Peng, H.H.Chang, T.Hsu, C.T.Lu, C.H.Huang, C.C.Hsueh, F.C.Kung, C.C.Kuo, W.T.Jiaang, S.Y.Wu. Xanthine Derivatives Reveal An Allosteric Binding Site in Methylenetetrahydrofolate Dehydrogenase 2 (MTHFD2). J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34337952
DOI: 10.1021/ACS.JMEDCHEM.1C00663