Chlorine in PDB 7ehv: Human MTHFD2 in Complex with Compound 21 and 3

All present enzymatic activity of Human MTHFD2 in Complex with Compound 21 and 3:
1.5.1.15; 3.5.4.9;

The structure of Human MTHFD2 in Complex with Compound 21 and 3, PDB code: 7ehv 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)	27.34 / 2.61
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	112.889, 112.889, 113.883, 90, 90, 120
R / Rfree (%)	19.3 / 23.6

The binding sites of Chlorine atom in the Human MTHFD2 in Complex with Compound 21 and 3 (pdb code 7ehv). 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 3, PDB code: 7ehv:
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 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:77.4 occ:0.90 CL1 A:J4L401 0.0 77.4 0.9 CAH A:J4L401 1.7 62.0 0.9 CAI A:J4L401 2.6 60.7 0.9 CAM A:J4L401 2.6 55.8 0.9 CL2 A:J4L401 3.0 76.7 0.9 SG B:CYS166 3.6 63.5 1.0 CE A:MET211 3.7 66.6 1.0 CE B:MET211 3.7 63.0 1.0 CAL A:J4L401 3.9 55.6 0.9 CAJ A:J4L401 3.9 52.4 0.9 CB A:MET207 3.9 64.0 1.0 CB B:CYS166 4.0 53.3 1.0 SD B:MET211 4.2 86.7 1.0 SG A:CYS166 4.3 54.7 1.0 CAK A:J4L401 4.4 58.3 0.9 N A:PRO208 4.4 55.4 1.0 C A:MET207 4.5 57.4 1.0 CE A:MET207 4.6 75.7 1.0 CD A:PRO208 4.6 53.1 1.0 CG A:PRO208 4.7 54.5 1.0 CA A:PRO208 4.8 53.8 1.0 O A:MET207 4.8 53.1 1.0 CG A:MET207 4.8 67.8 1.0 CA B:CYS166 4.9 57.0 1.0 CA A:MET207 4.9 60.4 1.0 CG1 A:VAL162 5.0 50.3 1.0

Chlorine binding site 2 out of 4 in the Human MTHFD2 in Complex with Compound 21 and 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:76.7 occ:0.90 CL2 A:J4L401 0.0 76.7 0.9 CAI A:J4L401 1.7 60.7 0.9 CAH A:J4L401 2.7 62.0 0.9 CAJ A:J4L401 2.7 52.4 0.9 CL1 A:J4L401 3.0 77.4 0.9 O B:CYS166 3.3 54.3 1.0 CG A:LYS203 3.7 61.3 1.0 C B:CYS166 3.9 57.1 1.0 CAK A:J4L401 3.9 58.3 0.9 O A:LYS203 4.0 65.3 1.0 CAM A:J4L401 4.0 55.8 0.9 OD1 A:ASN204 4.0 63.7 0.6 CB B:CYS166 4.1 53.3 1.0 C A:LYS203 4.2 65.5 1.0 CD A:LYS203 4.2 61.3 1.0 CE A:LYS203 4.3 64.1 1.0 CA A:ASN204 4.3 53.7 1.0 N A:ASN204 4.4 65.0 1.0 CA B:CYS166 4.4 57.0 1.0 CAL A:J4L401 4.5 55.6 0.9 CB A:MET207 4.5 64.0 1.0 CD2 B:LEU167 4.5 51.7 1.0 CG A:ASN204 4.7 65.6 1.0 NZ A:LYS203 4.8 68.8 1.0 N B:LEU167 4.8 56.7 1.0 CB A:LYS203 4.8 57.6 1.0 CD A:PRO208 4.8 53.1 1.0 SD B:MET211 4.8 86.7 1.0 CG A:PRO208 4.9 54.5 1.0 SG B:CYS166 4.9 63.5 1.0

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


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:72.9 occ:0.90 CL1 B:J4L401 0.0 72.9 0.9 CAH B:J4L401 1.7 61.2 0.9 CAI B:J4L401 2.6 60.9 0.9 CAM B:J4L401 2.6 57.6 0.9 CL2 B:J4L401 3.0 81.9 0.9 CE B:MET211 3.6 63.0 1.0 CG B:MET207 3.7 66.1 1.0 CAJ B:J4L401 3.9 56.5 0.9 CAL B:J4L401 3.9 58.5 0.9 CB B:MET207 3.9 61.4 1.0 SG A:CYS166 4.0 54.7 1.0 CE A:MET211 4.1 66.6 1.0 N B:PRO208 4.2 55.0 1.0 CB A:CYS166 4.2 55.4 1.0 C B:MET207 4.3 57.2 1.0 CD B:PRO208 4.4 54.9 1.0 CAK B:J4L401 4.4 58.7 0.9 SG B:CYS166 4.5 63.5 1.0 CA B:PRO208 4.5 55.8 1.0 SD A:MET211 4.6 79.9 1.0 O B:MET207 4.7 52.8 1.0 CG1 B:VAL162 4.7 49.5 1.0 CG B:PRO208 4.7 55.7 1.0 CA B:MET207 4.8 58.1 1.0 CB B:PRO208 4.9 56.1 1.0

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


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:81.9 occ:0.90 CL2 B:J4L401 0.0 81.9 0.9 CAI B:J4L401 1.7 60.9 0.9 CAH B:J4L401 2.7 61.2 0.9 CAJ B:J4L401 2.7 56.5 0.9 CL1 B:J4L401 3.0 72.9 0.9 NZ B:LYS203 3.3 76.1 1.0 O A:CYS166 3.7 52.6 1.0 O B:LYS203 3.9 62.1 1.0 CG B:LYS203 4.0 69.5 1.0 CAM B:J4L401 4.0 57.6 0.9 CAK B:J4L401 4.0 58.7 0.9 C A:CYS166 4.3 53.6 1.0 CB A:CYS166 4.3 55.4 1.0 C B:LYS203 4.4 65.0 1.0 CB B:MET207 4.4 61.4 1.0 CA B:ASN204 4.4 60.4 1.0 CD B:LYS203 4.5 69.8 1.0 CAL B:J4L401 4.5 58.5 0.9 CE B:LYS203 4.5 74.4 1.0 N B:ASN204 4.5 70.1 1.0 CD2 A:LEU167 4.6 42.9 1.0 CD B:PRO208 4.6 54.9 1.0 OD1 B:ASN204 4.7 73.1 1.0 CG B:MET207 4.7 66.1 1.0 CA A:CYS166 4.8 52.3 1.0 CG1 B:VAL162 4.9 49.5 1.0 CB B:LYS203 5.0 68.7 1.0 CG B:PRO208 5.0 55.7 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