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:
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: Tue Oct 1 13:47:34 2024
|