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Chlorine in PDB 6vfz: Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor.

Enzymatic activity of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor.

All present enzymatic activity of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor.:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor., PDB code: 6vfz was solved by A.Padyana, L.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.06 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.068, 119.797, 130.973, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.9

Other elements in 6vfz:

The structure of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor. also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor. (pdb code 6vfz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor., PDB code: 6vfz:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6vfz

Go back to Chlorine Binding Sites List in 6vfz
Chlorine binding site 1 out of 2 in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:19.5
occ:0.57
 CL1 A:9UO501 0.0 19.5 0.6
C13 A:9UO501 1.1 13.4 0.4
C14 A:9UO501 1.6 13.2 0.4
C15 A:9UO501 1.8 12.5 0.6
C12 A:9UO501 2.4 12.4 0.4
N17 A:9UO501 2.6 11.7 0.6
OD1 A:ASP312 2.7 17.2 1.0
C14 A:9UO501 2.7 13.2 0.6
C15 A:9UO501 2.9 12.7 0.4
CG A:ASP312 3.3 19.0 1.0
C11 A:9UO501 3.4 12.1 0.4
CB A:ASP312 3.5 12.4 1.0
N17 A:9UO501 3.6 11.2 0.4
CA A:ASP312 3.6 8.4 1.0
OH B:TYR311 3.8 13.4 1.0
C11 A:9UO501 3.9 11.8 0.6
C13 A:9UO501 4.0 12.1 0.6
CE2 B:TYR311 4.1 17.8 1.0
NE2 A:GLN316 4.1 22.3 1.0
CD1 A:ILE290 4.2 13.5 1.0
CG1 A:ILE290 4.3 14.5 1.0
CL1 A:9UO501 4.3 15.0 0.4
OD2 A:ASP312 4.3 17.4 1.0
CZ B:TYR311 4.4 16.7 1.0
O A:ASP312 4.4 8.8 1.0
C12 A:9UO501 4.5 12.7 0.6
C A:ASP312 4.5 10.8 1.0
N A:ASP312 4.5 8.1 1.0
CG1 B:VAL315 4.7 22.6 1.0
CD2 A:TYR311 4.7 11.2 1.0
CG2 B:VAL315 4.8 18.7 1.0
CE2 A:TYR311 4.8 9.8 1.0
C10 A:9UO501 4.8 10.3 0.4
CB A:VAL315 5.0 16.2 1.0

Chlorine binding site 2 out of 2 in 6vfz

Go back to Chlorine Binding Sites List in 6vfz
Chlorine binding site 2 out of 2 in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:15.0
occ:0.43
 CL1 A:9UO501 0.0 15.0 0.4
C13 A:9UO501 0.9 12.1 0.6
C14 A:9UO501 1.6 13.2 0.6
C15 A:9UO501 1.8 12.7 0.4
C12 A:9UO501 2.2 12.7 0.6
N17 A:9UO501 2.7 11.2 0.4
C14 A:9UO501 2.8 13.2 0.4
OD1 B:ASP312 2.8 20.0 1.0
C15 A:9UO501 2.9 12.5 0.6
C11 A:9UO501 3.3 11.8 0.6
CG B:ASP312 3.5 23.9 1.0
N17 A:9UO501 3.5 11.7 0.6
CB B:ASP312 3.7 11.3 1.0
OH A:TYR311 3.8 13.6 1.0
CA B:ASP312 3.8 14.7 1.0
C11 A:9UO501 3.9 12.1 0.4
CE2 A:TYR311 4.0 9.8 1.0
CD1 B:ILE290 4.0 13.2 1.0
C13 A:9UO501 4.0 13.4 0.4
CG1 B:ILE290 4.1 16.5 1.0
CL1 A:9UO501 4.3 19.5 0.6
CZ A:TYR311 4.3 15.9 1.0
NE2 B:GLN316 4.3 22.9 1.0
OD2 B:ASP312 4.4 23.5 1.0
CG1 A:VAL315 4.4 18.8 1.0
CG2 A:VAL315 4.5 17.0 1.0
C12 A:9UO501 4.5 12.4 0.4
O B:ASP312 4.6 11.4 1.0
C10 A:9UO501 4.7 10.1 0.6
C B:ASP312 4.7 16.1 1.0
N B:ASP312 4.8 7.6 1.0
CB A:VAL315 4.9 16.2 1.0

Reference:

Z.Konteatis, E.Artin, B.Nicolay, K.Straley, A.K.Padyana, L.Jin, Y.Chen, R.Narayaraswamy, S.Tong, F.Wang, D.Zhou, D.Cui, Z.Cai, Z.Luo, C.Fang, H.Tang, X.Lv, R.Nagaraja, H.Yang, S.M.Su, Z.Sui, L.Dang, K.Yen, J.Popovici-Muller, P.Codega, C.Campos, I.K.Mellinghoff, S.Biller. Vorasidenib (Ag-881): A First-in-Class, Brain-Penetrant Dual Inhibitor of Mutant IDH1 and 2 For Treatment of Glioma Acs Med.Chem.Lett. 2020.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.9B00509
Page generated: Sat Jul 12 20:53:52 2025

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