Magnesium 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:

Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor, PDB code: 6p1d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6p1d

Go back to Magnesium Binding Sites List in 6p1d
Magnesium binding site 1 out of 4 in the Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1103

b:22.0
occ:1.00
OD2 D:ASP855 1.9 31.8 1.0
O2A D:ANP1102 1.9 27.3 1.0
O D:HOH1208 1.9 21.5 1.0
O1B D:ANP1102 2.0 25.4 1.0
OD1 D:ASN842 2.0 27.6 1.0
O1G D:ANP1102 2.1 35.7 1.0
CG D:ASP855 3.1 28.9 1.0
CG D:ASN842 3.1 23.7 1.0
PB D:ANP1102 3.1 21.8 1.0
PA D:ANP1102 3.2 22.6 1.0
PG D:ANP1102 3.4 27.9 1.0
O3A D:ANP1102 3.5 27.4 1.0
ND2 D:ASN842 3.7 23.3 1.0
N3B D:ANP1102 3.8 28.0 1.0
CB D:ASP855 3.9 30.4 1.0
O5' D:ANP1102 4.0 24.7 1.0
OD1 D:ASP855 4.0 31.3 1.0
NZ D:LYS745 4.1 30.6 1.0
O2G D:ANP1102 4.3 27.1 1.0
O2B D:ANP1102 4.4 29.8 1.0
O1A D:ANP1102 4.4 32.2 1.0
CB D:ASN842 4.4 22.5 1.0
O D:ARG841 4.4 24.2 1.0
O3G D:ANP1102 4.5 31.6 1.0
O D:HOH1225 4.5 31.7 1.0
CA D:ASN842 4.6 22.5 1.0
O D:HOH1220 4.7 24.8 1.0
CG2 D:THR854 4.8 24.1 1.0
C D:ARG841 5.0 25.8 1.0
O D:HOH1249 5.0 32.9 1.0

Magnesium binding site 2 out of 4 in 6p1d

Go back to Magnesium Binding Sites List in 6p1d
Magnesium binding site 2 out of 4 in the Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
A:Mg1102

b:28.1
occ:1.00
OD2 A:ASP855 1.9 28.7 1.0
O1B A:ANP1101 1.9 30.4 1.0
O A:HOH1231 2.0 26.7 1.0
O2A A:ANP1101 2.0 28.8 1.0
OD1 A:ASN842 2.0 33.5 1.0
O1G A:ANP1101 2.2 37.6 1.0
CG A:ASP855 3.1 29.0 1.0
CG A:ASN842 3.1 29.1 1.0
PB A:ANP1101 3.2 24.9 1.0
PA A:ANP1101 3.3 30.6 1.0
PG A:ANP1101 3.5 37.3 1.0
O3A A:ANP1101 3.6 33.5 1.0
ND2 A:ASN842 3.7 24.9 1.0
N3B A:ANP1101 3.9 29.2 1.0
O5' A:ANP1101 3.9 30.0 1.0
NZ A:LYS745 4.0 31.5 1.0
CB A:ASP855 4.0 30.0 1.0
OD1 A:ASP855 4.0 31.9 1.0
O A:ARG841 4.3 26.6 1.0
O2B A:ANP1101 4.4 31.3 1.0
CB A:ASN842 4.4 26.1 1.0
O3G A:ANP1101 4.4 35.6 1.0
O1A A:ANP1101 4.5 31.5 1.0
O2G A:ANP1101 4.5 31.5 1.0
CA A:ASN842 4.6 28.8 1.0
CG2 A:THR854 4.7 21.1 1.0
O A:HOH1233 4.7 32.3 1.0
O A:HOH1211 4.7 32.5 1.0
C A:ARG841 4.9 23.1 1.0

Magnesium binding site 3 out of 4 in 6p1d

Go back to Magnesium Binding Sites List in 6p1d
Magnesium binding site 3 out of 4 in the Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg1103

b:29.1
occ:1.00
OD2 B:ASP855 1.9 31.7 1.0
O2A B:ANP1101 2.0 36.6 1.0
O1B B:ANP1101 2.0 29.4 1.0
OD1 B:ASN842 2.1 27.2 1.0
O1G B:ANP1101 2.3 33.6 1.0
O B:HOH1254 2.4 25.6 1.0
CG B:ASP855 3.1 26.8 1.0
CG B:ASN842 3.2 24.7 1.0
PB B:ANP1101 3.2 26.5 1.0
PA B:ANP1101 3.3 25.3 1.0
PG B:ANP1101 3.6 31.5 1.0
O3A B:ANP1101 3.7 31.9 1.0
ND2 B:ASN842 3.7 25.0 1.0
CB B:ASP855 3.8 26.3 1.0
N3B B:ANP1101 4.0 34.9 1.0
O5' B:ANP1101 4.0 31.4 1.0
OD1 B:ASP855 4.0 32.7 1.0
NZ B:LYS745 4.1 35.8 1.0
O B:ARG841 4.3 27.2 1.0
O2B B:ANP1101 4.4 32.8 1.0
CB B:ASN842 4.4 25.3 1.0
O1A B:ANP1101 4.4 31.3 1.0
O2G B:ANP1101 4.5 30.0 1.0
O B:HOH1222 4.6 26.1 1.0
CA B:ASN842 4.6 22.9 1.0
O3G B:ANP1101 4.6 30.8 1.0
O B:HOH1246 4.7 35.8 1.0
O B:HOH1249 4.7 37.6 1.0
CG2 B:THR854 4.8 21.4 1.0
C B:ARG841 4.9 24.5 1.0
O B:HOH1251 4.9 31.4 1.0

Magnesium binding site 4 out of 4 in 6p1d

Go back to Magnesium Binding Sites List in 6p1d
Magnesium binding site 4 out of 4 in the Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Egfr with Mutant-Selective Dihydrodibenzodiazepinone Allosteric Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:30.8
occ:1.00
O C:HOH1207 1.8 34.0 1.0
O2G C:ANP1102 1.9 36.7 1.0
OD2 C:ASP855 2.0 35.3 1.0
O2A C:ANP1102 2.0 33.5 1.0
O1B C:ANP1102 2.0 33.3 1.0
OD1 C:ASN842 2.0 29.7 1.0
CG C:ASP855 3.1 29.5 1.0
CG C:ASN842 3.2 28.9 1.0
PB C:ANP1102 3.2 28.4 1.0
PA C:ANP1102 3.3 30.4 1.0
PG C:ANP1102 3.3 37.5 1.0
O3A C:ANP1102 3.6 33.1 1.0
N3B C:ANP1102 3.8 38.7 1.0
ND2 C:ASN842 3.8 27.8 1.0
CB C:ASP855 3.9 25.2 1.0
O5' C:ANP1102 4.0 36.1 1.0
OD1 C:ASP855 4.0 33.2 1.0
O1G C:ANP1102 4.2 29.4 1.0
O C:ARG841 4.3 24.7 1.0
CB C:ASN842 4.3 25.4 1.0
O3G C:ANP1102 4.4 36.5 1.0
O2B C:ANP1102 4.4 41.9 1.0
O1A C:ANP1102 4.4 34.0 1.0
CA C:ASN842 4.5 25.5 1.0
NZ C:LYS745 4.6 34.2 1.0
C C:ARG841 4.7 24.2 1.0
O C:HOH1211 4.8 27.3 1.0
CG C:ARG841 4.8 29.9 1.0
N C:ASN842 4.9 26.4 1.0
CG2 C:THR854 5.0 23.1 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: Mon Dec 14 23:45:29 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy