Calcium in PDB 6bl2: Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD15

Enzymatic activity of Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD15

All present enzymatic activity of Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD15:
1.1.1.42;

Protein crystallography data

The structure of Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD15, PDB code: 6bl2 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) 28.14 / 1.92
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 95.508, 274.889, 116.143, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD15 (pdb code 6bl2). 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 CMPD15, PDB code: 6bl2:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6bl2

Go back to Calcium Binding Sites List in 6bl2
Calcium binding site 1 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD15


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 CMPD15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:39.0
occ:1.00
O7 A:ICT502 2.1 27.2 1.0
OD2 C:ASP252 2.1 30.9 1.0
OD1 A:ASP275 2.1 30.5 1.0
O2 A:ICT502 2.1 28.8 1.0
O A:HOH603 2.2 22.8 1.0
O A:HOH744 2.2 32.1 1.0
C1 A:ICT502 3.0 29.9 1.0
C2 A:ICT502 3.0 28.5 1.0
CG C:ASP252 3.2 28.8 1.0
CG A:ASP275 3.3 30.7 1.0
CB C:ASP252 3.7 23.3 1.0
OD2 A:ASP275 3.8 36.9 1.0
OD2 A:ASP279 4.0 47.2 1.0
O A:ASP275 4.0 27.8 1.0
NZ C:LYS212 4.0 27.9 1.0
OD1 A:ASP279 4.1 38.8 1.0
O1 A:ICT502 4.2 29.3 1.0
NH1 A:ARG109 4.2 25.0 1.0
CG A:ASP279 4.2 38.5 1.0
C6 A:ICT502 4.2 29.9 1.0
C3 A:ICT502 4.3 28.4 1.0
OD1 C:ASP252 4.3 29.8 1.0
O5 A:ICT502 4.4 29.2 1.0
CB A:ASP275 4.4 20.8 1.0
C A:ASP275 4.5 26.6 1.0
CA A:ASP275 4.5 19.2 1.0
O6 A:ICT502 4.5 30.8 1.0
O A:ALA308 4.6 39.0 1.0
O C:HOH693 4.7 49.8 1.0
NH1 A:ARG132 4.7 23.5 1.0
C4 A:ICT502 4.9 29.2 1.0

Calcium binding site 2 out of 3 in 6bl2

Go back to Calcium Binding Sites List in 6bl2
Calcium binding site 2 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD15


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 CMPD15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:40.2
occ:1.00
OD2 A:ASP252 2.1 31.3 1.0
O C:HOH615 2.1 24.4 1.0
OD1 C:ASP275 2.1 33.5 1.0
O1 A:ICT505 2.1 28.1 1.0
O7 A:ICT505 2.2 27.7 1.0
O C:HOH762 2.2 29.4 1.0
C1 A:ICT505 3.0 28.2 1.0
C2 A:ICT505 3.1 28.9 1.0
CG A:ASP252 3.2 27.1 1.0
CG C:ASP275 3.3 32.6 1.0
CB A:ASP252 3.7 24.7 1.0
OD2 C:ASP275 3.9 34.5 1.0
OD2 C:ASP279 3.9 49.6 1.0
O C:ASP275 3.9 26.1 1.0
OD1 C:ASP279 4.0 40.4 1.0
NZ A:LYS212 4.1 29.2 1.0
NH1 C:ARG109 4.1 23.8 1.0
CG C:ASP279 4.2 40.6 1.0
O2 A:ICT505 4.2 29.4 1.0
C6 A:ICT505 4.2 30.4 1.0
O A:HOH694 4.2 56.8 1.0
OD1 A:ASP252 4.2 28.5 1.0
C3 A:ICT505 4.3 30.9 1.0
O C:ALA308 4.4 36.6 1.0
O6 A:ICT505 4.5 28.8 1.0
CB C:ASP275 4.5 21.3 1.0
C C:ASP275 4.5 24.8 1.0
CA C:ASP275 4.5 19.7 1.0
O5 A:ICT505 4.5 30.5 1.0
NH1 C:ARG132 4.7 21.3 1.0
O C:HOH646 4.7 63.9 1.0
C4 A:ICT505 5.0 33.9 1.0
O C:HOH689 5.0 50.1 1.0

Calcium binding site 3 out of 3 in 6bl2

Go back to Calcium Binding Sites List in 6bl2
Calcium binding site 3 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD15


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 CMPD15 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:35.4
occ:1.00
O B:HOH610 2.1 22.4 1.0
O B:HOH767 2.1 31.3 1.0
O1 B:ICT502 2.1 24.8 1.0
OD1 B:ASP275 2.1 27.9 1.0
O7 B:ICT502 2.2 21.7 1.0
C1 B:ICT502 3.0 25.3 1.0
C2 B:ICT502 3.1 24.8 1.0
CG B:ASP275 3.3 27.8 1.0
OD2 B:ASP279 3.8 53.3 1.0
OD2 B:ASP275 3.9 35.9 1.0
O B:ASP275 4.0 21.6 1.0
OD1 B:ASP279 4.1 39.3 1.0
CG B:ASP279 4.2 41.7 1.0
C6 B:ICT502 4.2 27.5 1.0
O2 B:ICT502 4.2 28.6 1.0
NH1 B:ARG109 4.2 23.3 1.0
C3 B:ICT502 4.3 24.4 1.0
O5 B:ICT502 4.4 29.4 1.0
CB B:ASP275 4.4 16.7 1.0
O6 B:ICT502 4.5 26.6 1.0
C B:ASP275 4.5 21.1 1.0
CA B:ASP275 4.5 16.2 1.0
O B:ALA308 4.5 37.0 1.0
O B:HOH889 4.6 50.3 1.0
NH1 B:ARG132 4.8 17.9 1.0
C4 B:ICT502 5.0 26.5 1.0

Reference:

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
Page generated: Sat Dec 12 05:59:17 2020

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