Chlorine in PDB 7pjm: Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate

Enzymatic activity of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate

All present enzymatic activity of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate, PDB code: 7pjm was solved by R.Reinbold, P.Rabe, M.I.Abboud, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.01 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 96.58, 273.01, 117.42, 90, 90, 90
R / Rfree (%) 18.1 / 21

Other elements in 7pjm:

The structure of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate (pdb code 7pjm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate, PDB code: 7pjm:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7pjm

Go back to Chlorine Binding Sites List in 7pjm
Chlorine binding site 1 out of 3 in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate


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 Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:86.8
occ:1.00
 SG A:CYS297 2.9 76.8 0.2
HB3 A:CYS297 2.9 87.1 0.8
HB2 A:CYS297 3.3 86.5 0.2
HG A:CYS297 3.3 82.9 0.8
OD2 A:ASP299 3.5 90.6 1.0
HB2 A:CYS297 3.5 87.1 0.8
CB A:CYS297 3.6 72.3 0.8
CB A:CYS297 3.7 71.8 0.2
HD2 A:PRO298 3.8 87.3 1.0
HB A:THR302 3.9 75.4 1.0
SG A:CYS297 4.0 68.8 0.8
O A:LEU103 4.0 56.5 1.0
CG A:ASP299 4.0 96.9 1.0
HB3 A:CYS297 4.0 86.5 0.2
HB3 A:ASP299 4.1 114.0 1.0
H A:ASP299 4.1 114.8 1.0
HG2 A:LYS65 4.2 81.3 1.0
OD1 A:ASP299 4.6 100.8 1.0
CB A:ASP299 4.6 94.7 1.0
HA A:LEU103 4.6 61.8 1.0
CB A:THR302 4.7 62.5 1.0
HG1 A:THR302 4.7 78.2 1.0
OG1 A:THR302 4.7 64.9 1.0
CD A:PRO298 4.7 72.4 1.0
HE3 A:LYS65 4.7 102.6 1.0
HG21 A:THR302 4.8 70.5 1.0
HD22 A:LEU103 4.9 68.0 1.0
N A:ASP299 4.9 95.3 1.0
CA A:CYS297 4.9 71.7 0.8

Chlorine binding site 2 out of 3 in 7pjm

Go back to Chlorine Binding Sites List in 7pjm
Chlorine binding site 2 out of 3 in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate


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 Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:97.8
occ:1.00
 SG B:CYS297 2.7 95.5 0.2
HB3 B:CYS297 3.3 105.8 0.8
HG B:CYS297 3.4 103.3 0.8
O B:LEU103 3.7 70.8 1.0
OD2 B:ASP299 3.7 103.6 1.0
HA B:LEU103 3.9 79.7 1.0
HB2 B:CYS297 4.0 105.8 0.2
CB B:CYS297 4.1 87.9 0.8
SG B:CYS297 4.1 85.8 0.8
CB B:CYS297 4.1 87.9 0.2
HD2 B:PRO298 4.3 108.7 1.0
HD22 B:LEU103 4.3 83.0 1.0
HB2 B:CYS297 4.4 105.8 0.8
HG2 B:PRO298 4.4 111.1 1.0
HB B:THR302 4.5 97.2 1.0
HB3 B:CYS297 4.6 105.8 0.2
HB3 B:LEU103 4.6 79.1 1.0
C B:LEU103 4.6 65.8 1.0
CA B:LEU103 4.6 66.2 1.0
HD23 B:LEU103 4.7 83.0 1.0
HG21 B:THR302 4.7 93.5 1.0
CG B:ASP299 4.8 103.1 1.0
H B:ASP299 4.9 123.6 1.0

Chlorine binding site 3 out of 3 in 7pjm

Go back to Chlorine Binding Sites List in 7pjm
Chlorine binding site 3 out of 3 in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1206

b:88.5
occ:1.00
 SG C:CYS297 2.3 71.4 0.2
HB3 C:CYS297 3.0 80.1 0.8
OD2 C:ASP299 3.2 87.2 1.0
HG C:CYS297 3.6 79.2 0.8
HD2 C:PRO298 3.8 79.6 1.0
CB C:CYS297 3.8 66.5 0.8
O C:LEU103 3.9 57.6 1.0
CB C:CYS297 3.9 65.8 0.2
HB2 C:CYS297 3.9 79.4 0.2
HB2 C:CYS297 4.1 80.1 0.8
SG C:CYS297 4.1 65.7 0.8
HB C:THR302 4.3 72.4 1.0
CG C:ASP299 4.3 84.5 1.0
HB3 C:CYS297 4.3 79.4 0.2
HA C:LEU103 4.5 63.2 1.0
H C:ASP299 4.5 102.2 1.0
HG1 C:THR302 4.5 76.5 1.0
CD C:PRO298 4.7 66.0 1.0
HD22 C:LEU103 4.8 68.9 1.0
C C:LEU103 4.9 53.9 1.0
OD1 C:ASP299 4.9 83.4 1.0
HA C:CYS297 5.0 77.5 0.2
HB3 C:ASP299 5.0 103.5 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: Tue Jul 30 02:32:54 2024

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