Fluorine 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:

Chlorine (Cl) 3 atoms
Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 3 in 8dnj

Go back to Fluorine Binding Sites List in 8dnj
Fluorine 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 Fluorine with other atoms in the F 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:F303

b:23.0
occ:1.00
 F1 A:U4U303 0.0 23.0 1.0
C6 A:U4U303 1.3 23.4 1.0
C1 A:U4U303 2.4 24.5 1.0
C5 A:U4U303 2.4 22.8 1.0
O1 A:U4U303 2.6 22.4 1.0
C14 A:U4U303 2.8 25.1 1.0
C15 A:U4U303 3.3 25.9 1.0
CL1 A:U4U303 3.5 25.4 1.0
CE A:MET72 3.6 29.6 1.0
C19 A:U4U303 3.6 26.2 1.0
C2 A:U4U303 3.6 24.2 1.0
C4 A:U4U303 3.6 22.6 1.0
NH1 A:ARG68 3.7 21.7 1.0
C9 A:U4U303 3.9 20.6 1.0
CB A:VAL9 4.0 16.0 1.0
O2 A:U4U303 4.0 26.9 1.0
CG2 A:THR58 4.0 17.8 1.0
CG1 A:VAL9 4.1 16.4 1.0
C3 A:U4U303 4.1 23.2 1.0
CD A:ARG68 4.2 21.5 1.0
CZ A:ARG68 4.2 21.2 1.0
CB A:THR58 4.3 17.7 1.0
OG1 A:THR58 4.3 17.6 1.0
C16 A:U4U303 4.3 26.7 1.0
NE A:ARG68 4.4 21.0 1.0
C18 A:U4U303 4.6 25.8 1.0
CG2 A:VAL9 4.8 16.3 1.0
SD A:MET72 4.8 29.8 1.0
C13 A:U4U303 4.8 25.5 1.0
O A:HOH404 4.9 18.1 1.0
C17 A:U4U303 4.9 26.2 1.0
CA A:VAL9 4.9 15.6 1.0
NH2 A:ARG68 5.0 21.5 1.0
C7 A:U4U303 5.0 21.4 1.0

Fluorine binding site 2 out of 3 in 8dnj

Go back to Fluorine Binding Sites List in 8dnj
Fluorine 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 Fluorine with other atoms in the F 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:F303

b:21.1
occ:1.00
 F1 B:U4U303 0.0 21.1 1.0
C6 B:U4U303 1.3 21.0 1.0
C1 B:U4U303 2.4 20.8 1.0
C5 B:U4U303 2.4 20.8 1.0
O1 B:U4U303 2.6 20.6 1.0
C14 B:U4U303 2.8 20.9 1.0
C15 B:U4U303 3.3 21.5 1.0
CE B:MET72 3.4 27.3 1.0
C19 B:U4U303 3.5 21.2 1.0
NH1 B:ARG68 3.6 19.1 1.0
CL1 B:U4U303 3.6 22.7 1.0
C2 B:U4U303 3.6 20.8 1.0
C4 B:U4U303 3.6 20.4 1.0
O2 B:U4U303 3.9 21.5 1.0
C9 B:U4U303 3.9 20.0 1.0
CG2 B:THR58 4.0 16.4 1.0
CG1 B:VAL9 4.0 18.7 1.0
C3 B:U4U303 4.1 20.8 1.0
CB B:VAL9 4.1 18.3 1.0
CB B:THR58 4.2 16.2 1.0
OG1 B:THR58 4.2 16.1 1.0
CZ B:ARG68 4.3 19.2 1.0
C16 B:U4U303 4.4 21.4 1.0
CD B:ARG68 4.5 19.2 1.0
C18 B:U4U303 4.5 21.3 1.0
NE B:ARG68 4.7 18.9 1.0
SD B:MET72 4.8 28.3 1.0
C13 B:U4U303 4.8 21.6 1.0
C17 B:U4U303 4.9 21.5 1.0
C7 B:U4U303 5.0 20.0 1.0
CA B:VAL9 5.0 17.6 1.0

Fluorine binding site 3 out of 3 in 8dnj

Go back to Fluorine Binding Sites List in 8dnj
Fluorine 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 Fluorine with other atoms in the F 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:F303

b:35.0
occ:1.00
 F1 C:U4U303 0.0 35.0 1.0
C6 C:U4U303 1.3 34.2 1.0
C5 C:U4U303 2.4 34.3 1.0
C1 C:U4U303 2.4 35.1 1.0
O1 C:U4U303 2.6 33.5 1.0
C14 C:U4U303 2.8 35.4 1.0
C15 C:U4U303 3.3 35.9 1.0
CL1 C:U4U303 3.4 37.6 1.0
C4 C:U4U303 3.6 34.1 1.0
C19 C:U4U303 3.7 36.0 1.0
C2 C:U4U303 3.7 34.8 1.0
NH1 C:ARG68 3.7 38.2 1.0
C9 C:U4U303 3.9 31.5 1.0
CG1 C:VAL9 3.9 21.9 1.0
CD C:ARG68 3.9 41.4 1.0
CE C:MET72 4.0 40.7 1.0
CG2 C:THR58 4.0 24.3 1.0
CZ C:ARG68 4.0 38.8 1.0
O2 C:U4U303 4.0 36.3 1.0
NE C:ARG68 4.1 39.7 1.0
C3 C:U4U303 4.1 34.7 1.0
CB C:VAL9 4.2 21.3 1.0
CB C:THR58 4.3 24.4 1.0
C16 C:U4U303 4.3 36.5 1.0
OG1 C:THR58 4.3 23.7 1.0
C18 C:U4U303 4.6 36.1 1.0
SD C:MET72 4.7 41.4 1.0
NH2 C:ARG68 4.8 39.2 1.0
C13 C:U4U303 4.9 35.9 1.0
CG C:ARG68 4.9 42.2 1.0
C17 C:U4U303 4.9 36.5 1.0
C7 C:U4U303 5.0 33.2 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: Fri Aug 2 17:34:27 2024

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