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Chlorine in PDB 8dnj: Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76

Enzymatic activity of Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76

All present enzymatic activity of Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76, PDB code: 8dnj was solved by C.Mohr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.594, 112.162, 57.821, 90, 96.8, 90
R / Rfree (%) 23.9 / 28.9

Other elements in 8dnj:

The structure of Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76 also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76 (pdb code 8dnj). 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 Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76, PDB code: 8dnj:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 8dnj

Go back to Chlorine Binding Sites List in 8dnj
Chlorine binding site 1 out of 3 in the Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76


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 Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:25.4
occ:1.00
 CL1 A:U4U303 0.0 25.4 1.0
C15 A:U4U303 1.7 25.9 1.0
C16 A:U4U303 2.7 26.7 1.0
C14 A:U4U303 2.7 25.1 1.0
C1 A:U4U303 3.1 24.5 1.0
F1 A:U4U303 3.5 23.0 1.0
C6 A:U4U303 3.5 23.4 1.0
O A:TYR96 3.6 25.4 1.0
CG1 A:ILE100 3.8 26.9 1.0
CB A:GLN99 3.9 30.5 1.0
CA A:TYR96 3.9 23.6 1.0
C2 A:U4U303 4.0 24.2 1.0
C17 A:U4U303 4.0 26.2 1.0
C19 A:U4U303 4.0 26.2 1.0
CB A:TYR96 4.0 22.7 1.0
CD1 A:TYR96 4.1 21.8 1.0
C A:TYR96 4.2 24.5 1.0
CD1 A:ILE100 4.3 26.4 1.0
CG2 A:VAL9 4.3 16.3 1.0
C13 A:U4U303 4.4 25.5 1.0
CG A:TYR96 4.4 22.0 1.0
N A:ILE100 4.5 28.0 1.0
C18 A:U4U303 4.5 25.8 1.0
C5 A:U4U303 4.6 22.8 1.0
CB A:VAL9 4.6 16.0 1.0
CG1 A:VAL9 4.7 16.4 1.0
C A:GLN99 4.8 28.6 1.0
CG A:GLN99 4.8 32.0 1.0
C3 A:U4U303 4.9 23.2 1.0
CA A:GLN99 5.0 29.0 1.0
CB A:ILE100 5.0 27.2 1.0

Chlorine binding site 2 out of 3 in 8dnj

Go back to Chlorine Binding Sites List in 8dnj
Chlorine binding site 2 out of 3 in the Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76


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 Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:22.7
occ:1.00
 CL1 B:U4U303 0.0 22.7 1.0
C15 B:U4U303 1.7 21.5 1.0
C16 B:U4U303 2.7 21.4 1.0
C14 B:U4U303 2.7 20.9 1.0
C1 B:U4U303 3.1 20.8 1.0
O B:TYR96 3.5 23.4 1.0
C6 B:U4U303 3.5 21.0 1.0
F1 B:U4U303 3.6 21.1 1.0
CG1 B:ILE100 3.8 25.2 1.0
C2 B:U4U303 3.8 20.8 1.0
CA B:TYR96 3.8 23.3 1.0
CB B:GLN99 3.9 30.7 1.0
C17 B:U4U303 4.0 21.5 1.0
C19 B:U4U303 4.0 21.2 1.0
CB B:TYR96 4.0 22.6 1.0
CD1 B:TYR96 4.1 21.8 1.0
C B:TYR96 4.1 23.4 1.0
C13 B:U4U303 4.2 21.6 1.0
CD1 B:ILE100 4.3 25.1 1.0
N B:ILE100 4.4 26.8 1.0
CG B:TYR96 4.4 22.1 1.0
C18 B:U4U303 4.5 21.3 1.0
C5 B:U4U303 4.5 20.8 1.0
CB B:VAL9 4.7 18.3 1.0
CG1 B:VAL9 4.7 18.7 1.0
CG2 B:VAL9 4.7 18.7 1.0
C3 B:U4U303 4.8 20.8 1.0
C B:GLN99 4.8 28.5 1.0
C23 B:U4U303 4.9 21.8 1.0
CA B:GLN99 4.9 29.5 1.0
CG B:GLN99 4.9 31.6 1.0
CB B:ILE100 4.9 25.5 1.0
CA B:ILE100 5.0 26.2 1.0

Chlorine binding site 3 out of 3 in 8dnj

Go back to Chlorine Binding Sites List in 8dnj
Chlorine binding site 3 out of 3 in the Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76


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 Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl303

b:37.6
occ:1.00
 CL1 C:U4U303 0.0 37.6 1.0
C15 C:U4U303 1.7 35.9 1.0
C14 C:U4U303 2.7 35.4 1.0
C16 C:U4U303 2.7 36.5 1.0
C1 C:U4U303 3.0 35.1 1.0
C6 C:U4U303 3.4 34.2 1.0
F1 C:U4U303 3.4 35.0 1.0
O C:TYR96 3.5 32.1 1.0
CA C:TYR96 3.8 33.4 1.0
C2 C:U4U303 3.9 34.8 1.0
CB C:TYR96 3.9 32.9 1.0
CG1 C:ILE100 4.0 33.9 1.0
C19 C:U4U303 4.0 36.0 1.0
CB C:GLN99 4.0 36.7 1.0
CD1 C:TYR96 4.0 33.1 1.0
C17 C:U4U303 4.0 36.5 1.0
C C:TYR96 4.1 33.1 1.0
C13 C:U4U303 4.3 35.9 1.0
CG1 C:VAL9 4.4 21.9 1.0
C5 C:U4U303 4.4 34.3 1.0
CG C:TYR96 4.4 32.5 1.0
CB C:VAL9 4.4 21.3 1.0
CD1 C:ILE100 4.4 33.5 1.0
C18 C:U4U303 4.5 36.1 1.0
CG2 C:VAL9 4.5 21.5 1.0
N C:ILE100 4.6 34.7 1.0
CG C:GLN99 4.7 38.2 1.0
C3 C:U4U303 4.8 34.7 1.0
SD C:MET72 4.9 41.4 1.0
C C:GLN99 4.9 34.9 1.0
C4 C:U4U303 5.0 34.1 1.0

Reference:

K.Zhu, C.Li, K.Y.Wu, C.Mohr, X.Li, B.Lanman. Modeling Receptor Flexibility in the Structure-Based Design of Kras G12C Inhibitors. J.Comput.Aided Mol.Des. V. 36 591 2022.
ISSN: ESSN 1573-4951
PubMed: 35930206
DOI: 10.1007/S10822-022-00467-0
Page generated: Sun Jul 13 10:51:27 2025

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