Calcium in PDB 6bl1: Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD13

Enzymatic activity of Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD13

All present enzymatic activity of Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD13:
1.1.1.42;

Protein crystallography data

The structure of Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD13, PDB code: 6bl1 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) 92.78 / 2.02
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 98.610, 273.806, 114.786, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.3

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 CMPD13 (pdb code 6bl1). 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 CMPD13, PDB code: 6bl1:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6bl1

Go back to Calcium Binding Sites List in 6bl1
Calcium binding site 1 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD13


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 CMPD13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:45.6
occ:1.00
O7 B:ICT501 2.1 46.2 0.9
OD1 B:ASP275 2.3 51.7 1.0
O B:HOH690 2.3 34.9 1.0
O B:HOH610 2.3 28.8 1.0
OD2 A:ASP252 2.4 42.5 1.0
O2 B:ICT501 2.6 44.7 0.9
C2 B:ICT501 3.1 46.5 0.9
OD2 B:ASP279 3.2 55.6 1.0
CG A:ASP252 3.2 40.2 1.0
C1 B:ICT501 3.3 46.4 0.9
CB A:ASP252 3.5 32.6 1.0
CG B:ASP275 3.5 50.0 1.0
CG B:ASP279 3.8 46.9 1.0
O B:ASP275 3.8 34.8 1.0
OD1 B:ASP279 3.9 47.5 1.0
O A:HOH721 3.9 48.9 1.0
OD2 B:ASP275 4.2 57.3 1.0
NZ A:LYS212 4.3 46.7 1.0
OD1 A:ASP252 4.4 42.4 1.0
O B:ALA308 4.5 51.1 1.0
C B:ASP275 4.5 34.7 1.0
C3 B:ICT501 4.5 46.3 0.9
NH1 B:ARG109 4.5 31.8 1.0
O1 B:ICT501 4.5 46.9 0.9
C6 B:ICT501 4.6 45.4 0.9
CA B:ASP275 4.6 30.1 1.0
CB B:ASP275 4.7 31.8 1.0
O B:HOH763 4.7 50.0 1.0
O6 B:ICT501 4.8 47.9 0.9
O A:HOH668 4.9 52.1 1.0
CA A:ASP252 5.0 31.0 1.0
O5 B:ICT501 5.0 41.6 0.9

Calcium binding site 2 out of 3 in 6bl1

Go back to Calcium Binding Sites List in 6bl1
Calcium binding site 2 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD13


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 CMPD13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:51.8
occ:1.00
O7 B:ICT505 2.2 47.9 0.9
OD1 A:ASP275 2.3 41.3 1.0
OD2 B:ASP252 2.3 47.2 1.0
O A:HOH627 2.4 40.4 1.0
O1 B:ICT505 2.4 46.4 0.9
O A:HOH641 2.5 47.9 1.0
OD2 A:ASP279 3.0 62.6 1.0
C2 B:ICT505 3.2 48.8 0.9
C1 B:ICT505 3.2 48.0 0.9
CG B:ASP252 3.3 45.2 1.0
CG A:ASP275 3.5 42.3 1.0
CB B:ASP252 3.7 36.3 1.0
CG A:ASP279 3.7 52.1 1.0
OD1 A:ASP279 3.8 53.5 1.0
O A:ASP275 3.9 33.1 1.0
O B:HOH631 4.1 65.7 1.0
OD2 A:ASP275 4.2 51.0 1.0
NH1 A:ARG109 4.4 34.6 1.0
C3 B:ICT505 4.5 49.3 0.9
O2 B:ICT505 4.5 49.1 0.9
NZ B:LYS212 4.5 50.1 1.0
OD1 B:ASP252 4.5 46.0 1.0
C6 B:ICT505 4.5 46.8 0.9
C A:ASP275 4.5 30.8 1.0
O5 B:ICT505 4.5 47.4 0.9
CB A:ASP275 4.6 29.9 1.0
CA A:ASP275 4.6 28.1 1.0
O A:ALA308 4.8 44.0 1.0
O A:HOH783 4.9 49.9 1.0
CB A:ASP279 4.9 31.0 1.0

Calcium binding site 3 out of 3 in 6bl1

Go back to Calcium Binding Sites List in 6bl1
Calcium binding site 3 out of 3 in the Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of HIS315 with CMPD13


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 CMPD13 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:37.8
occ:1.00
O C:HOH614 2.1 34.4 1.0
O7 C:ICT502 2.1 34.8 0.9
OD1 C:ASP275 2.2 38.5 1.0
O C:HOH669 2.4 36.9 1.0
O1 C:ICT502 2.5 37.0 0.9
C2 C:ICT502 3.2 38.4 0.9
C1 C:ICT502 3.3 38.3 0.9
OD2 C:ASP279 3.4 45.9 1.0
CG C:ASP275 3.4 38.5 1.0
O C:ASP275 3.8 22.1 1.0
OD1 C:ASP279 3.8 37.9 1.0
CG C:ASP279 3.8 36.8 1.0
OD2 C:ASP275 4.1 49.1 1.0
NH1 C:ARG109 4.3 30.4 1.0
C C:ASP275 4.4 23.3 1.0
C3 C:ICT502 4.5 40.3 0.9
C6 C:ICT502 4.5 42.1 0.9
O2 C:ICT502 4.5 41.5 0.9
CA C:ASP275 4.5 21.0 1.0
CB C:ASP275 4.6 23.9 1.0
O C:ALA308 4.6 40.3 1.0
O5 C:ICT502 4.8 45.2 0.9
O6 C:ICT502 4.9 39.4 0.9
NH1 C:ARG132 5.0 23.5 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 05:59:16 2020

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