Magnesium in PDB 6bl0: Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of HIS315 with CMPD11

All present enzymatic activity of Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of HIS315 with CMPD11:
1.1.1.42;

The structure of Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of HIS315 with CMPD11, PDB code: 6bl0 was solved by C.G.Jakob, W.Qiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	137.16 / 2.17
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	98.195, 274.328, 115.059, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.7

The binding sites of Magnesium atom in the Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of HIS315 with CMPD11 (pdb code 6bl0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of HIS315 with CMPD11, PDB code: 6bl0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of HIS315 with CMPD11


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of HIS315 with CMPD11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:49.9 occ:1.00 OD2 B:ASP252 1.9 52.7 1.0 O7 A:ICT502 2.0 55.2 1.0 OD1 A:ASP275 2.0 52.4 1.0 O B:HOH611 2.1 50.1 1.0 O A:HOH624 2.1 49.0 1.0 O2 A:ICT502 2.4 55.5 1.0 C2 A:ICT502 3.0 58.3 1.0 CG B:ASP252 3.1 52.9 1.0 C1 A:ICT502 3.1 55.0 1.0 CG A:ASP275 3.2 50.8 1.0 OD2 A:ASP275 3.7 51.1 1.0 CB B:ASP252 3.7 45.1 1.0 OD2 A:ASP279 3.9 71.3 1.0 O A:ASP275 3.9 40.2 1.0 OD1 B:ASP252 4.1 54.0 1.0 NZ B:LYS212 4.1 61.5 1.0 OD1 A:ASP279 4.2 59.4 1.0 CG A:ASP279 4.2 60.1 1.0 C6 A:ICT502 4.2 63.7 1.0 O6 A:ICT502 4.3 69.4 1.0 C3 A:ICT502 4.3 63.1 1.0 NH1 A:ARG109 4.3 42.9 1.0 CB A:ASP275 4.4 43.2 1.0 O1 A:ICT502 4.4 53.0 1.0 C A:ASP275 4.5 42.1 1.0 CA A:ASP275 4.5 41.0 1.0 O5 A:ICT502 4.7 57.9 1.0 C4 A:ICT502 4.9 63.5 1.0 NH1 A:ARG132 5.0 43.7 1.0

Magnesium binding site 2 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of HIS315 with CMPD11


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of HIS315 with CMPD11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:42.6 occ:1.00 OD2 A:ASP252 1.9 43.1 1.0 OD1 B:ASP275 1.9 42.1 1.0 O1 A:ICT505 2.0 45.6 1.0 O B:HOH609 2.1 34.9 1.0 O7 A:ICT505 2.2 42.9 1.0 O A:HOH631 2.2 39.5 1.0 C1 A:ICT505 2.9 44.6 1.0 CG A:ASP252 3.0 40.4 1.0 C2 A:ICT505 3.0 43.2 1.0 CG B:ASP275 3.1 43.0 1.0 CB A:ASP252 3.6 41.8 1.0 OD2 B:ASP275 3.7 45.5 1.0 O B:ASP275 3.9 45.1 1.0 OD1 A:ASP252 4.1 37.4 1.0 O2 A:ICT505 4.1 48.2 1.0 NZ A:LYS212 4.1 51.0 1.0 O A:HOH615 4.2 36.7 1.0 NH1 B:ARG109 4.2 38.1 1.0 OD1 B:ASP279 4.2 47.1 1.0 CB B:ASP275 4.3 36.2 1.0 O B:HOH642 4.3 43.7 1.0 C B:ASP275 4.3 44.4 1.0 CA B:ASP275 4.3 36.0 1.0 OD2 B:ASP279 4.4 44.5 1.0 C3 A:ICT505 4.4 49.1 1.0 CG B:ASP279 4.4 45.5 1.0 O B:ALA308 4.4 54.6 1.0 C6 A:ICT505 4.5 52.7 1.0 O6 A:ICT505 4.5 50.5 1.0 C5N B:NAP501 4.6 46.8 1.0 OG B:SER278 4.9 52.6 1.0 NH1 B:ARG132 4.9 34.9 1.0

Magnesium binding site 3 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of HIS315 with CMPD11


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of HIS315 with CMPD11 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg500 b:37.0 occ:1.00 O C:HOH606 1.9 28.9 1.0 OD1 C:ASP275 2.0 39.8 1.0 O1 C:ICT501 2.0 42.6 1.0 O C:HOH632 2.0 44.7 1.0 O7 C:ICT501 2.2 43.5 1.0 C1 C:ICT501 2.9 41.5 1.0 C2 C:ICT501 3.0 44.4 1.0 CG C:ASP275 3.1 37.6 1.0 OD2 C:ASP275 3.7 44.0 1.0 O C:ASP275 3.9 31.2 1.0 NH1 C:ARG109 4.0 34.6 1.0 O C:HOH690 4.1 47.6 1.0 OD1 C:ASP279 4.1 38.4 1.0 O2 C:ICT501 4.1 40.2 1.0 CB C:ASP275 4.3 29.1 1.0 O C:HOH664 4.3 39.3 1.0 C C:ASP275 4.3 32.0 1.0 C3 C:ICT501 4.4 47.8 1.0 C6 C:ICT501 4.4 55.5 1.0 CA C:ASP275 4.4 27.2 1.0 CG C:ASP279 4.4 38.2 1.0 OD2 C:ASP279 4.4 43.2 1.0 O6 C:ICT501 4.5 53.0 1.0 O C:ALA308 4.6 55.9 1.0 C5N C:NAP502 4.8 61.8 1.0 O5 C:ICT501 4.8 64.3 1.0 NH1 C:ARG132 4.8 34.2 1.0

C.G.Jakob, A.K.Upadhyay, P.L.Donner, E.Nicholl, S.N.Addo, W.Qiu, C.Ling, S.M.Gopalakrishnan, M.Torrent, S.P.Cepa, J.Shanley, A.R.Shoemaker, C.C.Sun, A.Vasudevan, K.R.Woller, J.B.Shotwell, B.Shaw, Z.Bian, J.E.Hutti. Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of HIS315. J. Med. Chem. V. 61 6647 2018.
ISSN: ISSN 1520-4804
PubMed: 30004704
DOI: 10.1021/ACS.JMEDCHEM.8B00305