Fluorine in PDB 6vei: Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor

Enzymatic activity of Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor

All present enzymatic activity of Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor, PDB code: 6vei 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) 35.51 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 117.213, 85.099, 96.663, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.5

Other elements in 6vei:

The structure of Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor (pdb code 6vei). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor, PDB code: 6vei:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6vei

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Fluorine binding site 1 out of 6 in the Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:37.1
occ:1.00
 F04 B:9UO502 0.0 37.1 1.0
C03 B:9UO502 1.4 34.0 1.0
F06 B:9UO502 2.2 41.7 1.0
F05 B:9UO502 2.2 30.7 1.0
C02 B:9UO502 2.4 29.9 1.0
C01 B:9UO502 2.9 19.6 1.0
CG B:MET259 3.1 54.7 1.0
CZ2 B:TRP124 3.4 19.1 1.0
N B:MET259 3.5 20.3 1.0
N07 B:9UO502 3.6 20.3 1.0
CA B:MET259 3.7 31.9 1.0
CB B:ALA258 3.8 18.4 1.0
O B:VAL255 3.8 20.9 1.0
CB B:MET259 3.8 35.0 1.0
CH2 B:TRP124 3.9 17.6 1.0
C B:ALA258 3.9 17.9 1.0
O B:ALA258 4.4 23.7 1.0
SD B:MET259 4.4 62.3 1.0
CA B:ALA258 4.5 18.9 1.0
CE2 B:TRP124 4.6 21.5 1.0
C08 B:9UO502 4.8 17.0 1.0
C B:VAL255 4.8 23.0 1.0
CZ3 B:TRP267 4.9 19.2 1.0
CG1 B:VAL255 4.9 17.6 1.0

Fluorine binding site 2 out of 6 in 6vei

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Fluorine binding site 2 out of 6 in the Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:30.7
occ:1.00
 F05 B:9UO502 0.0 30.7 1.0
C03 B:9UO502 1.4 34.0 1.0
F04 B:9UO502 2.2 37.1 1.0
F06 B:9UO502 2.2 41.7 1.0
C02 B:9UO502 2.4 29.9 1.0
N07 B:9UO502 2.8 20.3 1.0
O B:VAL255 3.2 20.9 1.0
CG1 B:VAL255 3.4 17.6 1.0
CH2 B:TRP267 3.4 19.8 1.0
CA B:VAL255 3.4 19.5 1.0
CZ3 B:TRP267 3.5 19.2 1.0
OE1 B:GLN277 3.6 22.9 1.0
CB B:ALA258 3.6 18.4 1.0
C01 B:9UO502 3.7 19.6 1.0
C B:VAL255 3.7 23.0 1.0
C08 B:9UO502 3.8 17.0 1.0
CB B:VAL255 3.9 21.9 1.0
CG2 B:VAL255 4.2 18.8 1.0
N B:MET259 4.5 20.3 1.0
CD B:GLN277 4.5 25.5 1.0
N27 B:9UO502 4.5 14.8 1.0
CG B:MET259 4.6 54.7 1.0
N09 B:9UO502 4.6 20.4 1.0
O B:MET254 4.6 19.9 1.0
N B:VAL255 4.6 21.3 1.0
CZ2 B:TRP267 4.7 21.8 1.0
CA B:ALA258 4.7 18.9 1.0
C B:ALA258 4.8 17.9 1.0
CE3 B:TRP267 4.9 18.7 1.0
NE2 B:GLN277 5.0 17.5 1.0

Fluorine binding site 3 out of 6 in 6vei

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Fluorine binding site 3 out of 6 in the Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:41.7
occ:1.00
 F06 B:9UO502 0.0 41.7 1.0
C03 B:9UO502 1.4 34.0 1.0
F04 B:9UO502 2.2 37.1 1.0
F05 B:9UO502 2.2 30.7 1.0
C02 B:9UO502 2.4 29.9 1.0
C01 B:9UO502 2.8 19.6 1.0
N07 B:9UO502 2.8 20.3 1.0
OE1 B:GLN277 3.2 22.9 1.0
OG B:SER280 3.5 24.9 0.6
CG2 B:VAL281 3.5 15.5 1.0
CZ3 B:TRP267 3.6 19.2 1.0
CH2 B:TRP124 4.0 17.6 1.0
CZ2 B:TRP124 4.1 19.1 1.0
CH2 B:TRP267 4.2 19.8 1.0
C08 B:9UO502 4.3 17.0 1.0
CB B:ALA258 4.4 18.4 1.0
CD B:GLN277 4.4 25.5 1.0
CB B:SER280 4.5 25.1 0.4
CB B:SER280 4.5 24.3 0.6
N B:VAL281 4.6 20.9 1.0
CE3 B:TRP267 4.7 18.7 1.0
CA B:VAL281 4.8 20.9 1.0
CB B:VAL281 4.8 18.1 1.0
C B:SER280 4.9 22.4 1.0

Fluorine binding site 4 out of 6 in 6vei

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Fluorine binding site 4 out of 6 in the Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:38.1
occ:1.00
 F24 B:9UO502 0.0 38.1 1.0
C23 B:9UO502 1.4 36.0 1.0
F25 B:9UO502 2.2 31.8 1.0
F26 B:9UO502 2.2 33.3 1.0
C21 B:9UO502 2.3 28.2 1.0
N20 B:9UO502 2.8 24.6 1.0
CG A:MET259 3.0 23.6 1.0
N27 B:9UO502 3.1 14.8 1.0
C19 B:9UO502 3.2 19.0 1.0
CG1 A:VAL255 3.3 18.7 1.0
SD A:MET259 3.6 31.6 1.0
C22 B:9UO502 3.7 20.9 1.0
O A:VAL255 3.8 14.5 1.0
C08 B:9UO502 4.2 17.0 1.0
N18 B:9UO502 4.2 19.6 1.0
C01 B:9UO502 4.2 19.6 1.0
CB A:MET259 4.4 17.1 1.0
CE A:MET259 4.6 29.9 1.0
C A:VAL255 4.6 18.4 1.0
N A:MET259 4.6 19.3 1.0
CB A:VAL255 4.7 16.4 1.0
C02 B:9UO502 4.7 29.9 1.0
CA A:MET259 4.8 20.5 1.0
N07 B:9UO502 4.8 20.3 1.0
CA A:VAL255 4.8 18.6 1.0

Fluorine binding site 5 out of 6 in 6vei

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Fluorine binding site 5 out of 6 in the Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:31.8
occ:1.00
 F25 B:9UO502 0.0 31.8 1.0
C23 B:9UO502 1.4 36.0 1.0
F24 B:9UO502 2.2 38.1 1.0
F26 B:9UO502 2.2 33.3 1.0
C21 B:9UO502 2.4 28.2 1.0
N20 B:9UO502 2.7 24.6 1.0
C22 B:9UO502 2.9 20.9 1.0
CZ2 A:TRP124 3.9 32.6 1.0
C19 B:9UO502 3.9 19.0 1.0
OE1 A:GLN277 4.0 22.5 1.0
CB A:ALA258 4.1 14.6 1.0
CH2 A:TRP124 4.1 33.5 1.0
CZ3 A:TRP267 4.3 18.9 1.0
CG A:MET259 4.3 23.6 1.0
N27 B:9UO502 4.5 14.8 1.0
O A:VAL255 4.6 14.5 1.0
CG1 A:VAL255 4.6 18.7 1.0
N A:MET259 4.7 19.3 1.0
CH2 A:TRP267 4.8 19.2 1.0
N18 B:9UO502 4.8 19.6 1.0
C A:ALA258 4.8 18.2 1.0
CG1 A:VAL281 4.9 22.0 0.3
CG2 A:VAL281 4.9 21.0 0.7

Fluorine binding site 6 out of 6 in 6vei

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Fluorine binding site 6 out of 6 in the Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:33.3
occ:1.00
 F26 B:9UO502 0.0 33.3 1.0
C23 B:9UO502 1.4 36.0 1.0
F25 B:9UO502 2.2 31.8 1.0
F24 B:9UO502 2.2 38.1 1.0
C21 B:9UO502 2.4 28.2 1.0
C22 B:9UO502 2.8 20.9 1.0
CZ2 A:TRP124 3.2 32.6 1.0
CH2 A:TRP124 3.2 33.5 1.0
N20 B:9UO502 3.6 24.6 1.0
CG A:MET259 3.6 23.6 1.0
CG2 A:VAL121 4.1 29.9 1.0
SD B:MET259 4.2 62.3 1.0
CE2 A:TRP124 4.5 30.5 1.0
N27 B:9UO502 4.5 14.8 1.0
CZ3 A:TRP124 4.5 33.1 1.0
CB A:MET259 4.5 17.1 1.0
C19 B:9UO502 4.5 19.0 1.0
SD A:MET259 4.6 31.6 1.0
CA A:MET259 4.6 20.5 1.0
CE A:MET259 4.8 29.9 1.0
N A:MET259 4.8 19.3 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: Sun Dec 13 13:23:35 2020

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