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Fluorine in PDB 6p1d: Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor

Enzymatic activity of Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor

All present enzymatic activity of Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor, PDB code: 6p1d was solved by D.E.Heppner, M.J.Eck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.17 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.946, 101.812, 86.510, 90.00, 101.04, 90.00
R / Rfree (%) 19.5 / 21.3

Other elements in 6p1d:

The structure of Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor (pdb code 6p1d). 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 Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor, PDB code: 6p1d:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6p1d

Go back to Fluorine Binding Sites List in 6p1d
Fluorine binding site 1 out of 3 in the Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor


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 Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1101

b:31.7
occ:1.00
F03 D:NQ11101 0.0 31.7 1.0
C02 D:NQ11101 1.4 29.4 1.0
C01 D:NQ11101 2.4 29.9 1.0
C04 D:NQ11101 2.4 31.7 1.0
C D:ARG776 3.2 25.7 1.0
CB D:CYS775 3.2 21.5 1.0
O D:ARG776 3.2 22.4 1.0
C D:CYS775 3.2 27.0 1.0
O D:CYS775 3.3 26.9 1.0
N D:LEU777 3.4 26.7 1.0
N D:ARG776 3.5 27.4 1.0
CE D:MET790 3.6 21.2 1.0
SD D:MET790 3.7 32.3 1.0
C05 D:NQ11101 3.7 29.2 1.0
C07 D:NQ11101 3.7 31.6 1.0
CA D:ARG776 3.8 29.6 1.0
CA D:CYS775 3.8 26.7 1.0
CA D:LEU777 3.9 25.8 1.0
CB D:MET790 4.0 21.3 1.0
C06 D:NQ11101 4.1 33.6 1.0
OG1 D:THR854 4.3 22.4 1.0
O D:HOH1209 4.3 27.3 1.0
CG D:MET790 4.5 24.4 1.0
CB D:LEU777 4.6 25.4 1.0
SG D:CYS775 4.7 21.2 1.0
N17 D:NQ11101 4.9 33.5 1.0
N D:CYS775 5.0 26.6 1.0

Fluorine binding site 2 out of 3 in 6p1d

Go back to Fluorine Binding Sites List in 6p1d
Fluorine binding site 2 out of 3 in the Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor


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 Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1102

b:35.1
occ:1.00
F03 B:NQ11102 0.0 35.1 1.0
C02 B:NQ11102 1.4 33.6 1.0
C01 B:NQ11102 2.4 34.6 1.0
C04 B:NQ11102 2.4 31.1 1.0
CB B:CYS775 3.1 25.4 1.0
C B:CYS775 3.2 23.5 1.0
O B:CYS775 3.2 23.6 1.0
C B:ARG776 3.2 25.1 1.0
O B:ARG776 3.2 24.1 1.0
N B:ARG776 3.4 26.7 1.0
N B:LEU777 3.5 27.8 1.0
CE B:MET790 3.5 28.7 1.0
C07 B:NQ11102 3.7 34.2 1.0
C05 B:NQ11102 3.7 30.4 1.0
SD B:MET790 3.7 33.1 1.0
CA B:CYS775 3.7 22.1 1.0
CA B:ARG776 3.8 29.6 1.0
CA B:LEU777 4.0 26.3 1.0
C06 B:NQ11102 4.2 36.5 1.0
CB B:MET790 4.2 26.9 1.0
OG1 B:THR854 4.2 23.4 1.0
O B:HOH1224 4.5 24.0 1.0
CG B:MET790 4.6 26.3 1.0
SG B:CYS775 4.7 24.0 1.0
CB B:LEU777 4.7 26.1 1.0
N B:CYS775 4.8 23.2 1.0
N17 B:NQ11102 4.9 32.3 1.0

Fluorine binding site 3 out of 3 in 6p1d

Go back to Fluorine Binding Sites List in 6p1d
Fluorine binding site 3 out of 3 in the Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor


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 Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:26.0
occ:1.00
F03 C:NQ11101 0.0 26.0 1.0
C02 C:NQ11101 1.4 26.5 1.0
C01 C:NQ11101 2.4 25.0 1.0
C04 C:NQ11101 2.4 23.5 1.0
O C:ARG776 3.2 22.6 1.0
C C:ARG776 3.2 21.9 1.0
CB C:CYS775 3.2 22.9 1.0
C C:CYS775 3.4 24.1 1.0
CE C:MET790 3.4 24.3 1.0
N C:ARG776 3.5 22.5 1.0
O C:CYS775 3.6 20.3 1.0
N C:LEU777 3.6 21.4 1.0
SD C:MET790 3.7 26.8 1.0
C05 C:NQ11101 3.7 23.8 1.0
C07 C:NQ11101 3.7 26.8 1.0
CA C:ARG776 3.7 27.7 1.0
CA C:CYS775 3.9 26.7 1.0
OG1 C:THR854 4.1 26.6 1.0
CA C:LEU777 4.1 24.6 1.0
C06 C:NQ11101 4.1 32.4 1.0
CB C:MET790 4.2 19.3 1.0
CG C:MET790 4.6 25.4 1.0
CB C:LEU777 4.8 23.5 1.0
SG C:CYS775 4.8 23.7 1.0
O C:HOH1233 4.8 23.4 1.0
N17 C:NQ11101 4.9 30.3 1.0

Reference:

D.J.H.De Clercq, D.E.Heppner, C.To, J.Jang, E.Park, C.H.Yun, M.Mushajiang, B.H.Shin, T.W.Gero, D.A.Scott, P.A.Janne, M.J.Eck, N.S.Gray. Discovery and Optimization of Dibenzodiazepinones As Allosteric Mutant-Selective Egfr Inhibitors. Acs Med.Chem.Lett. V. 10 1549 2019.
ISSN: ISSN 1948-5875
PubMed: 31749909
DOI: 10.1021/ACSMEDCHEMLETT.9B00381
Page generated: Fri Aug 2 00:03:24 2024

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