Praseodymium in PDB 6wnh: Menin Bound to Inhibitor M-808
Protein crystallography data
The structure of Menin Bound to Inhibitor M-808, PDB code: 6wnh
was solved by
J.A.Stuckey,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.56 /
2.10
|
Space group
|
I 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
153.549,
153.549,
81.283,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
22.8
|
Other elements in 6wnh:
The structure of Menin Bound to Inhibitor M-808 also contains other interesting chemical elements:
Praseodymium Binding Sites:
The binding sites of Praseodymium atom in the Menin Bound to Inhibitor M-808
(pdb code 6wnh). This binding sites where shown within
5.0 Angstroms radius around Praseodymium atom.
In total 5 binding sites of Praseodymium where determined in the
Menin Bound to Inhibitor M-808, PDB code: 6wnh:
Jump to Praseodymium binding site number:
1;
2;
3;
4;
5;
Praseodymium binding site 1 out
of 5 in 6wnh
Go back to
Praseodymium Binding Sites List in 6wnh
Praseodymium binding site 1 out
of 5 in the Menin Bound to Inhibitor M-808
![](/pictures/PR/pdb/wn/6wnh-PR-sphere_01.jpg) Mono view
![](/pictures/PR/pdb/wn/6wnh-PR-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Praseodymium with other atoms in the Pr binding
site number 1 of Menin Bound to Inhibitor M-808 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pr702
b:30.2
occ:0.50
|
PR
|
A:7PR702
|
0.0
|
30.2
|
0.5
|
O3
|
A:7PR702
|
2.5
|
51.6
|
0.5
|
O1
|
A:7PR702
|
2.5
|
49.0
|
0.5
|
O
|
A:7PR702
|
2.5
|
54.3
|
0.5
|
H2
|
A:7PR702
|
3.2
|
91.6
|
0.5
|
H4
|
A:7PR702
|
3.3
|
0.1
|
0.5
|
C1
|
A:7PR702
|
3.5
|
79.2
|
0.5
|
C2
|
A:7PR702
|
3.5
|
67.3
|
0.5
|
H7
|
A:7PR702
|
3.6
|
0.9
|
0.5
|
C4
|
A:7PR702
|
3.7
|
75.1
|
0.5
|
C
|
A:7PR702
|
3.7
|
0.6
|
0.5
|
H6
|
A:7PR702
|
3.7
|
0.1
|
0.5
|
C3
|
A:7PR702
|
3.8
|
85.6
|
0.5
|
C5
|
A:7PR702
|
4.1
|
1.0
|
0.5
|
H1
|
A:7PR702
|
4.2
|
92.2
|
0.5
|
H8
|
A:7PR702
|
4.4
|
0.6
|
0.5
|
OD2
|
A:ASP370
|
4.5
|
62.1
|
1.0
|
O2
|
A:7PR702
|
4.5
|
68.0
|
0.5
|
OE1
|
A:GLU366
|
4.6
|
30.4
|
1.0
|
OE2
|
A:GLU366
|
4.6
|
33.8
|
1.0
|
O5
|
A:7PR702
|
4.6
|
79.6
|
0.5
|
O4
|
A:7PR702
|
4.6
|
74.0
|
0.5
|
H3
|
A:7PR702
|
4.7
|
91.4
|
0.5
|
H5
|
A:7PR702
|
4.8
|
0.1
|
0.5
|
|
Praseodymium binding site 2 out
of 5 in 6wnh
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Praseodymium Binding Sites List in 6wnh
Praseodymium binding site 2 out
of 5 in the Menin Bound to Inhibitor M-808
![](/pictures/PR/pdb/wn/6wnh-PR-sphere_02.jpg) Mono view
![](/pictures/PR/pdb/wn/6wnh-PR-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Praseodymium with other atoms in the Pr binding
site number 2 of Menin Bound to Inhibitor M-808 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pr703
b:64.8
occ:0.50
|
PR
|
A:7PR703
|
0.0
|
64.8
|
0.5
|
O3
|
A:7PR703
|
2.5
|
56.0
|
0.5
|
O
|
A:7PR703
|
2.5
|
56.0
|
0.5
|
O1
|
A:7PR703
|
2.5
|
55.5
|
0.5
|
H1
|
A:7PR703
|
3.2
|
45.5
|
0.5
|
C1
|
A:7PR703
|
3.6
|
50.0
|
0.5
|
C2
|
A:7PR703
|
3.6
|
48.7
|
0.5
|
C4
|
A:7PR703
|
3.7
|
50.1
|
0.5
|
CG
|
A:GLN64
|
3.7
|
26.3
|
1.0
|
O5
|
A:7PR703
|
3.8
|
49.2
|
0.5
|
C3
|
A:7PR703
|
3.9
|
45.7
|
0.5
|
CB
|
A:SER66
|
3.9
|
29.8
|
1.0
|
H7
|
A:7PR703
|
3.9
|
45.5
|
0.5
|
O
|
A:PRO65
|
4.1
|
29.2
|
1.0
|
NE2
|
A:GLN64
|
4.2
|
13.3
|
1.0
|
CD
|
A:GLN64
|
4.3
|
27.8
|
1.0
|
C5
|
A:7PR703
|
4.3
|
46.8
|
0.5
|
O
|
A:ARG14
|
4.4
|
30.9
|
1.0
|
O4
|
A:7PR703
|
4.4
|
48.2
|
0.5
|
O
|
A:HOH859
|
4.5
|
28.4
|
1.0
|
H3
|
A:7PR703
|
4.5
|
45.5
|
0.5
|
CB
|
A:SER15
|
4.6
|
22.4
|
1.0
|
O2
|
A:7PR703
|
4.6
|
44.8
|
0.5
|
H2
|
A:7PR703
|
4.6
|
45.5
|
0.5
|
OG
|
A:SER66
|
4.7
|
31.8
|
1.0
|
H9
|
A:7PR703
|
4.8
|
45.5
|
0.5
|
C
|
A:7PR703
|
4.8
|
46.7
|
0.5
|
H4
|
A:7PR703
|
4.9
|
45.5
|
0.5
|
CA
|
A:SER66
|
5.0
|
29.8
|
1.0
|
|
Praseodymium binding site 3 out
of 5 in 6wnh
Go back to
Praseodymium Binding Sites List in 6wnh
Praseodymium binding site 3 out
of 5 in the Menin Bound to Inhibitor M-808
![](/pictures/PR/pdb/wn/6wnh-PR-sphere_03.jpg) Mono view
![](/pictures/PR/pdb/wn/6wnh-PR-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Praseodymium with other atoms in the Pr binding
site number 3 of Menin Bound to Inhibitor M-808 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pr704
b:72.5
occ:1.00
|
PR
|
A:7PR704
|
0.0
|
72.5
|
1.0
|
O
|
A:7PR704
|
2.5
|
66.4
|
1.0
|
O1
|
A:7PR704
|
2.5
|
67.2
|
1.0
|
O3
|
A:7PR704
|
2.5
|
67.0
|
1.0
|
H4
|
A:7PR704
|
3.4
|
45.5
|
1.0
|
C1
|
A:7PR704
|
3.5
|
59.2
|
1.0
|
H6
|
A:7PR704
|
3.6
|
45.5
|
1.0
|
C2
|
A:7PR704
|
3.6
|
58.9
|
1.0
|
H7
|
A:7PR704
|
3.6
|
45.5
|
1.0
|
C4
|
A:7PR704
|
3.7
|
60.3
|
1.0
|
C
|
A:7PR704
|
3.7
|
48.7
|
1.0
|
O2
|
A:7PR704
|
3.8
|
59.0
|
1.0
|
C5
|
A:7PR704
|
4.0
|
49.0
|
1.0
|
H9
|
A:7PR704
|
4.2
|
45.5
|
1.0
|
O
|
A:ARG131
|
4.4
|
48.5
|
1.0
|
O5
|
A:7PR704
|
4.6
|
61.1
|
1.0
|
O4
|
A:7PR704
|
4.7
|
62.1
|
1.0
|
H5
|
A:7PR704
|
4.8
|
45.5
|
1.0
|
C3
|
A:7PR704
|
4.8
|
48.7
|
1.0
|
H1
|
A:7PR704
|
4.8
|
45.5
|
1.0
|
|
Praseodymium binding site 4 out
of 5 in 6wnh
Go back to
Praseodymium Binding Sites List in 6wnh
Praseodymium binding site 4 out
of 5 in the Menin Bound to Inhibitor M-808
![](/pictures/PR/pdb/wn/6wnh-PR-sphere_04.jpg) Mono view
![](/pictures/PR/pdb/wn/6wnh-PR-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Praseodymium with other atoms in the Pr binding
site number 4 of Menin Bound to Inhibitor M-808 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pr705
b:60.9
occ:0.50
|
PR
|
A:7PR705
|
0.0
|
60.9
|
0.5
|
O1
|
A:7PR705
|
2.4
|
40.6
|
0.5
|
O
|
A:7PR705
|
2.4
|
56.8
|
0.5
|
O3
|
A:7PR705
|
2.5
|
56.3
|
0.5
|
H4
|
A:7PR705
|
3.3
|
45.5
|
0.5
|
O2
|
A:7PR705
|
3.4
|
3.0
|
0.5
|
C2
|
A:7PR705
|
3.4
|
25.4
|
0.5
|
O
|
A:HOH1010
|
3.5
|
37.5
|
1.0
|
C1
|
A:7PR705
|
3.5
|
52.3
|
0.5
|
C
|
A:7PR705
|
3.7
|
47.2
|
0.5
|
C4
|
A:7PR705
|
3.7
|
51.1
|
0.5
|
H6
|
A:7PR705
|
3.7
|
45.5
|
0.5
|
H9
|
A:7PR705
|
3.9
|
45.5
|
0.5
|
C5
|
A:7PR705
|
4.1
|
47.3
|
0.5
|
H8
|
A:7PR705
|
4.1
|
45.5
|
0.5
|
OD2
|
A:ASP285
|
4.3
|
42.9
|
1.0
|
O
|
A:HOH812
|
4.3
|
44.8
|
1.0
|
O5
|
A:7PR705
|
4.6
|
52.5
|
0.5
|
O4
|
A:7PR705
|
4.6
|
49.2
|
0.5
|
O
|
A:HOH973
|
4.7
|
27.4
|
1.0
|
H5
|
A:7PR705
|
4.7
|
45.5
|
0.5
|
C3
|
A:7PR705
|
4.8
|
40.9
|
0.5
|
|
Praseodymium binding site 5 out
of 5 in 6wnh
Go back to
Praseodymium Binding Sites List in 6wnh
Praseodymium binding site 5 out
of 5 in the Menin Bound to Inhibitor M-808
![](/pictures/PR/pdb/wn/6wnh-PR-sphere_05.jpg) Mono view
![](/pictures/PR/pdb/wn/6wnh-PR-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Praseodymium with other atoms in the Pr binding
site number 5 of Menin Bound to Inhibitor M-808 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pr706
b:0.0
occ:0.50
|
PR
|
A:7PR706
|
0.0
|
0.0
|
0.5
|
O1
|
A:7PR706
|
2.5
|
0.8
|
0.5
|
O
|
A:7PR706
|
2.5
|
0.4
|
0.5
|
O3
|
A:7PR706
|
2.5
|
0.0
|
0.5
|
H2
|
A:7PR706
|
3.3
|
91.6
|
0.5
|
H4
|
A:7PR706
|
3.5
|
0.1
|
0.5
|
C2
|
A:7PR706
|
3.6
|
99.3
|
0.5
|
C1
|
A:7PR706
|
3.6
|
0.3
|
0.5
|
C4
|
A:7PR706
|
3.7
|
0.7
|
0.5
|
H5
|
A:7PR706
|
3.8
|
0.1
|
0.5
|
C
|
A:7PR706
|
3.8
|
0.6
|
0.5
|
C3
|
A:7PR706
|
3.9
|
93.6
|
0.5
|
H8
|
A:7PR706
|
4.1
|
0.6
|
0.5
|
H3
|
A:7PR706
|
4.2
|
91.4
|
0.5
|
O
|
A:HOH913
|
4.4
|
33.8
|
1.0
|
O4
|
A:7PR706
|
4.4
|
0.4
|
0.5
|
C5
|
A:7PR706
|
4.5
|
0.7
|
0.5
|
O2
|
A:7PR706
|
4.6
|
99.2
|
0.5
|
O5
|
A:7PR706
|
4.6
|
1.0
|
0.5
|
H1
|
A:7PR706
|
4.8
|
92.2
|
0.5
|
H6
|
A:7PR706
|
4.9
|
0.1
|
0.5
|
|
Reference:
S.Xu,
A.Aguilar,
L.Huang,
T.Xu,
K.Zheng,
D.Mceachern,
S.Przybranowski,
C.Foster,
K.Zawacki,
Z.Liu,
K.Chinnaswamy,
J.Stuckey,
S.Wang.
Discovery of M-808 As A Highly Potent, Covalent, Small-Molecule Inhibitor of the Menin-Mll Interaction with Strongin Vivoantitumor Activity. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32338903
DOI: 10.1021/ACS.JMEDCHEM.0C00547
Page generated: Wed Dec 16 02:03:22 2020
|