Calcium in PDB 6bkx: Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD1

All present enzymatic activity of Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD1:
1.1.1.42;

The structure of Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD1, PDB code: 6bkx 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)	137.46 / 1.65
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	95.301, 274.911, 116.897, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.7

The binding sites of Calcium atom in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD1 (pdb code 6bkx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD1, PDB code: 6bkx:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:20.0 occ:1.00 O7 C:ICT502 2.3 20.8 0.9 OD1 C:ASP275 2.3 20.5 1.0 O2 C:ICT502 2.3 16.7 0.9 O C:HOH726 2.3 26.0 1.0 O C:HOH651 2.3 19.3 1.0 OD2 C:ASP279 2.7 29.0 1.0 C1 C:ICT502 3.1 17.5 0.9 C2 C:ICT502 3.2 19.8 0.9 CG C:ASP275 3.5 23.9 1.0 CG C:ASP279 3.6 28.6 1.0 OD1 C:ASP279 3.9 28.4 1.0 O C:ASP275 4.0 16.0 1.0 OD2 C:ASP275 4.2 24.2 1.0 NH1 C:ARG109 4.3 19.5 1.0 O1 C:ICT502 4.4 20.8 0.9 C3 C:ICT502 4.5 18.7 0.9 C6 C:ICT502 4.5 21.5 0.9 C C:ASP275 4.6 16.8 1.0 CB C:ASP275 4.6 14.8 1.0 CA C:ASP275 4.6 13.5 1.0 O C:HOH954 4.6 62.0 1.0 O C:ALA308 4.7 27.2 1.0 O6 C:ICT502 4.7 21.5 0.9 O5 C:ICT502 4.8 18.2 0.9 CB C:ASP279 4.9 17.7 1.0 NH1 C:ARG132 5.0 16.8 1.0

Calcium binding site 2 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:21.2 occ:1.00 O B:HOH619 2.2 22.3 1.0 O7 B:ICT501 2.3 20.0 0.9 OD1 B:ASP275 2.3 21.2 1.0 O1 B:ICT501 2.3 19.8 0.9 O B:HOH727 2.3 22.8 1.0 OD2 A:ASP252 2.3 21.9 1.0 OD2 B:ASP279 2.7 33.1 1.0 C1 B:ICT501 3.2 18.2 0.9 C2 B:ICT501 3.2 19.2 0.9 CG A:ASP252 3.3 21.2 1.0 CG B:ASP275 3.5 23.3 1.0 CG B:ASP279 3.6 30.9 1.0 CB A:ASP252 3.7 18.8 1.0 O A:HOH836 3.8 37.2 1.0 OD1 B:ASP279 3.9 30.2 1.0 O B:ASP275 4.0 18.2 1.0 OD2 B:ASP275 4.2 25.2 1.0 NH1 B:ARG109 4.3 19.3 1.0 NZ A:LYS212 4.4 22.5 1.0 O2 B:ICT501 4.4 21.6 0.9 OD1 A:ASP252 4.4 20.4 1.0 C B:ASP275 4.5 17.9 1.0 O B:HOH614 4.5 32.8 1.0 C3 B:ICT501 4.5 19.9 0.9 C6 B:ICT501 4.5 20.7 0.9 O B:ALA308 4.5 28.2 1.0 O B:HOH901 4.5 37.4 1.0 CB B:ASP275 4.6 16.9 1.0 CA B:ASP275 4.6 15.3 1.0 O5 B:ICT501 4.8 20.9 0.9 O6 B:ICT501 4.8 19.4 0.9 CB B:ASP279 4.8 17.8 1.0

Calcium binding site 3 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:23.6 occ:1.00 O A:HOH608 2.2 25.5 1.0 O7 B:ICT505 2.2 24.0 0.9 O2 B:ICT505 2.3 23.2 0.9 OD1 A:ASP275 2.3 23.5 1.0 O A:HOH753 2.3 28.7 1.0 OD2 B:ASP252 2.4 22.9 1.0 OD2 A:ASP279 2.7 30.7 1.0 C1 B:ICT505 3.1 23.9 0.9 C2 B:ICT505 3.2 24.2 0.9 CG B:ASP252 3.4 23.1 1.0 CG A:ASP275 3.5 26.4 1.0 CG A:ASP279 3.5 27.4 1.0 O B:HOH801 3.6 52.9 1.0 CB B:ASP252 3.8 17.7 1.0 OD1 A:ASP279 3.8 28.2 1.0 O A:ASP275 3.9 20.8 1.0 OD2 A:ASP275 4.2 29.7 1.0 NH1 A:ARG109 4.3 22.8 1.0 O1 B:ICT505 4.3 24.8 0.9 NZ B:LYS212 4.5 23.1 1.0 C3 B:ICT505 4.5 25.0 0.9 C A:ASP275 4.5 21.1 1.0 OD1 B:ASP252 4.5 24.6 1.0 C6 B:ICT505 4.5 26.8 0.9 CA A:ASP275 4.6 16.6 1.0 CB A:ASP275 4.6 19.2 1.0 O A:HOH632 4.6 37.7 1.0 O A:ALA308 4.7 31.1 1.0 CB A:ASP279 4.8 20.0 1.0 O6 B:ICT505 4.8 25.8 0.9 O A:HOH894 4.8 63.9 1.0 O5 B:ICT505 4.8 23.4 0.9

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