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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy