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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

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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: Tue Oct 1 13:47:34 2024

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