Fluorine in PDB 7pjn: Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B

Enzymatic activity of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B

All present enzymatic activity of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B, PDB code: 7pjn was solved by R.Reinbold, P.Rabe, M.I.Abboud, C.J.Schofield, I.J.Clifton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.36 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.18, 153.05, 164.01, 90, 90, 90
R / Rfree (%) 18.6 / 22.8

Other elements in 7pjn:

The structure of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B (pdb code 7pjn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B, PDB code: 7pjn:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7pjn

Go back to Fluorine Binding Sites List in 7pjn
Fluorine binding site 1 out of 4 in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B


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 Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:85.9
occ:1.00
 F A:7SU601 0.0 85.9 1.0
C15 A:7SU601 1.4 76.6 1.0
C14 A:7SU601 2.3 70.9 1.0
C17 A:7SU601 2.4 69.6 1.0
C16 A:7SU601 2.4 66.4 1.0
H13 A:7SU601 2.6 83.5 1.0
H10 A:7SU601 2.6 79.7 1.0
H11 A:7SU601 2.7 79.7 1.0
H14 A:7SU601 2.8 83.5 1.0
O2 A:7SU601 2.8 66.9 1.0
H15 A:7SU601 3.3 83.5 1.0
H12 A:7SU601 3.3 79.7 1.0
CZ2 A:TRP267 3.4 65.7 1.0
HZ2 A:TRP267 3.5 78.8 1.0
C13 A:7SU601 3.6 64.1 1.0
CH2 A:TRP267 3.7 73.9 1.0
CE2 A:TRP267 3.8 59.3 1.0
HB2 A:CYS269 3.9 85.9 1.0
HH2 A:TRP267 3.9 88.7 1.0
N1 A:7SU601 4.1 62.0 1.0
HG23 A:ILE130 4.1 72.8 1.0
HD13 A:ILE130 4.1 89.9 1.0
CZ3 A:TRP267 4.3 72.5 1.0
HD11 A:ILE251 4.3 79.8 1.0
HG21 A:ILE130 4.3 72.8 1.0
SG A:CYS269 4.3 107.2 1.0
C12 A:7SU601 4.3 62.7 1.0
NE1 A:TRP267 4.4 57.9 1.0
CD2 A:TRP267 4.4 55.9 1.0
C18 A:7SU601 4.4 62.5 1.0
CB A:CYS269 4.4 71.6 1.0
HB3 A:CYS269 4.4 85.9 1.0
H9 A:7SU601 4.4 69.1 1.0
HE1 A:TRP267 4.5 69.5 1.0
SG A:CYS132 4.5 94.8 1.0
CE3 A:TRP267 4.6 58.8 1.0
CG2 A:ILE130 4.6 60.7 1.0
O3 A:7SU601 4.7 56.9 1.0
HZ3 A:TRP267 4.8 87.0 1.0
HB3 A:SER278 5.0 77.5 1.0
CD1 A:ILE130 5.0 74.9 1.0

Fluorine binding site 2 out of 4 in 7pjn

Go back to Fluorine Binding Sites List in 7pjn
Fluorine binding site 2 out of 4 in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B


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 Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:92.2
occ:1.00
 F B:7SU601 0.0 92.2 1.0
C15 B:7SU601 1.4 68.4 1.0
C14 B:7SU601 2.4 73.5 1.0
C17 B:7SU601 2.4 65.3 1.0
C16 B:7SU601 2.4 60.0 1.0
H10 B:7SU601 2.6 72.1 1.0
H14 B:7SU601 2.6 78.4 1.0
H15 B:7SU601 2.7 78.4 1.0
H11 B:7SU601 2.7 72.1 1.0
O2 B:7SU601 3.0 66.4 1.0
H13 B:7SU601 3.3 78.4 1.0
H12 B:7SU601 3.3 72.1 1.0
C13 B:7SU601 3.4 71.1 1.0
O B:VAL276 3.7 72.5 1.0
HD22 B:ASN271 3.9 125.8 1.0
O3 B:7SU601 4.0 59.1 1.0
C12 B:7SU601 4.0 60.7 1.0
N1 B:7SU601 4.3 70.8 1.0
HA B:GLN277 4.3 90.0 1.0
C18 B:7SU601 4.4 61.0 1.0
ND2 B:ASN271 4.6 104.8 1.0
H B:SER278 4.6 76.8 1.0
HB3 B:SER278 4.7 71.1 1.0
SG B:CYS269 4.7 92.4 1.0
HD21 B:ASN271 4.7 125.8 1.0
HG21 B:ILE130 4.8 69.1 1.0
C B:VAL276 4.8 74.0 1.0
N B:SER278 4.9 64.0 1.0
HB2 B:CYS269 4.9 75.9 1.0
SG B:CYS132 4.9 92.6 1.0

Fluorine binding site 3 out of 4 in 7pjn

Go back to Fluorine Binding Sites List in 7pjn
Fluorine binding site 3 out of 4 in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B


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 Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F601

b:82.4
occ:1.00
 F C:7SU601 0.0 82.4 1.0
C15 C:7SU601 1.4 62.8 1.0
C16 C:7SU601 2.4 67.7 1.0
C17 C:7SU601 2.4 72.8 1.0
C14 C:7SU601 2.4 68.4 1.0
H15 C:7SU601 2.6 87.3 1.0
H12 C:7SU601 2.6 81.2 1.0
H11 C:7SU601 2.7 81.2 1.0
H13 C:7SU601 2.7 87.3 1.0
O2 C:7SU601 2.8 61.6 1.0
H14 C:7SU601 3.3 87.3 1.0
H10 C:7SU601 3.3 81.2 1.0
C13 C:7SU601 3.6 67.2 1.0
HG23 B:VAL276 3.7 93.4 1.0
HG21 B:VAL276 3.8 93.4 1.0
N1 C:7SU601 4.1 60.8 1.0
CG2 B:VAL276 4.1 77.8 1.0
HD11 C:ILE251 4.2 75.7 1.0
HB2 C:CYS269 4.3 89.0 1.0
HG22 B:VAL276 4.3 93.4 1.0
SG C:CYS269 4.3 107.5 1.0
C12 C:7SU601 4.4 65.7 1.0
C18 C:7SU601 4.4 62.5 1.0
O3 C:7SU601 4.5 65.3 1.0
HZ2 C:TRP267 4.8 79.3 1.0
CB C:CYS269 4.8 74.2 1.0
CZ2 C:TRP267 4.9 66.1 1.0
HB3 C:SER278 4.9 106.8 1.0
HG21 C:ILE130 5.0 86.2 1.0
SG C:CYS132 5.0 107.2 1.0

Fluorine binding site 4 out of 4 in 7pjn

Go back to Fluorine Binding Sites List in 7pjn
Fluorine binding site 4 out of 4 in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B


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 Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and Inhibitor Ds-1001B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F601

b:91.4
occ:1.00
 F D:7SU601 0.0 91.4 1.0
C15 D:7SU601 1.4 78.3 1.0
C14 D:7SU601 2.4 73.1 1.0
C17 D:7SU601 2.4 84.7 1.0
C16 D:7SU601 2.4 76.6 1.0
H15 D:7SU601 2.6 101.6 1.0
H11 D:7SU601 2.6 92.0 1.0
H12 D:7SU601 2.7 92.0 1.0
H14 D:7SU601 2.7 101.6 1.0
O2 D:7SU601 2.8 70.2 1.0
H13 D:7SU601 3.3 101.6 1.0
H10 D:7SU601 3.3 92.0 1.0
C13 D:7SU601 3.5 73.0 1.0
N1 D:7SU601 4.1 63.0 1.0
HB3 D:SER278 4.2 126.4 1.0
C12 D:7SU601 4.3 68.7 1.0
C18 D:7SU601 4.4 64.3 1.0
O3 D:7SU601 4.4 69.7 1.0
HD11 D:ILE251 4.5 82.0 1.0
SG D:CYS269 4.6 95.1 1.0
HB2 D:CYS269 4.6 87.3 1.0
OG D:SER278 4.6 103.0 1.0
HG21 D:ILE130 4.8 88.3 1.0
CB D:SER278 4.9 105.3 1.0
HZ2 D:TRP267 5.0 86.4 1.0

Reference:

R.Reinbold, I.C.Hvinden, P.Rabe, R.A.Herold, A.Finch, J.Wood, M.Morgan, M.Staudt, I.J.Clifton, F.A.Armstrong, J.S.O.Mccullagh, J.Redmond, C.Bardella, M.I.Abboud, C.J.Schofield. Resistance to the Isocitrate Dehydrogenase 1 Mutant Inhibitor Ivosidenib Can Be Overcome By Alternative Dimer-Interface Binding Inhibitors. Nat Commun V. 13 4785 2022.
ISSN: ESSN 2041-1723
PubMed: 35970853
DOI: 10.1038/S41467-022-32436-4
Page generated: Fri Aug 2 11:00:55 2024

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