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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:

Fluorine (F) 1 atom

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


Mono view


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

Go back to Praseodymium Binding Sites List in 6wnh
Praseodymium binding site 2 out of 5 in the Menin Bound to Inhibitor M-808


Mono view


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


Mono view


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


Mono view


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


Mono view


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: Thu Oct 29 06:39:41 2020

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