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Praseodymium in PDB 7m4t: Menin Bound to M-1121

Protein crystallography data

The structure of Menin Bound to M-1121, PDB code: 7m4t was solved by J.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.55 / 2.74
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 153.52, 153.52, 81.93, 90, 90, 90
R / Rfree (%) 20.2 / 21.5

Other elements in 7m4t:

The structure of Menin Bound to M-1121 also contains other interesting chemical elements:

Fluorine (F) 1 atom

Praseodymium Binding Sites:

The binding sites of Praseodymium atom in the Menin Bound to M-1121 (pdb code 7m4t). 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 M-1121, PDB code: 7m4t:
Jump to Praseodymium binding site number: 1; 2; 3; 4; 5;

Praseodymium binding site 1 out of 5 in 7m4t

Go back to Praseodymium Binding Sites List in 7m4t
Praseodymium binding site 1 out of 5 in the Menin Bound to M-1121


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 M-1121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr702

b:53.4
occ:0.50
PR A:7PR702 0.0 53.4 0.5
O A:7PR702 2.4 66.0 0.5
O1 A:7PR702 2.4 59.5 0.5
O3 A:7PR702 2.5 64.8 0.5
C2 A:7PR702 3.5 65.3 0.5
C1 A:7PR702 3.5 78.8 0.5
C4 A:7PR702 3.6 76.3 0.5
C A:7PR702 3.7 92.2 0.5
O2 A:7PR702 3.8 65.3 0.5
O4 A:7PR702 4.0 75.9 0.5
O5 A:7PR702 4.6 78.7 0.5
OE1 A:GLU366 4.7 42.3 1.0
C3 A:7PR702 4.7 70.9 0.5
OE2 A:GLU366 4.7 54.7 1.0
C5 A:7PR702 4.8 88.9 0.5

Praseodymium binding site 2 out of 5 in 7m4t

Go back to Praseodymium Binding Sites List in 7m4t
Praseodymium binding site 2 out of 5 in the Menin Bound to M-1121


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 M-1121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr703

b:83.4
occ:1.00
PR A:7PR703 0.0 83.4 1.0
O A:7PR703 2.4 86.9 1.0
O3 A:7PR703 2.5 86.1 1.0
O1 A:7PR703 2.5 79.5 1.0
C1 A:7PR703 3.5 90.0 1.0
C2 A:7PR703 3.6 74.7 1.0
C4 A:7PR703 3.7 87.9 1.0
C A:7PR703 3.8 92.2 1.0
O2 A:7PR703 3.9 73.9 1.0
C5 A:7PR703 4.1 88.9 1.0
O A:ARG131 4.3 45.7 1.0
O5 A:7PR703 4.6 90.8 1.0
O4 A:7PR703 4.7 88.5 1.0
C3 A:7PR703 4.8 70.9 1.0

Praseodymium binding site 3 out of 5 in 7m4t

Go back to Praseodymium Binding Sites List in 7m4t
Praseodymium binding site 3 out of 5 in the Menin Bound to M-1121


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 M-1121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr704

b:95.0
occ:1.00
PR A:7PR704 0.0 95.0 1.0
O3 A:7PR704 2.5 92.9 1.0
O A:7PR704 2.5 94.5 1.0
O1 A:7PR704 2.5 87.8 1.0
C2 A:7PR704 3.6 79.5 1.0
C1 A:7PR704 3.6 93.3 1.0
C4 A:7PR704 3.7 90.8 1.0
C A:7PR704 3.8 92.2 1.0
C3 A:7PR704 4.2 70.9 1.0
C5 A:7PR704 4.3 88.9 1.0
O2 A:7PR704 4.4 79.5 1.0
O4 A:7PR704 4.5 90.5 1.0
O5 A:7PR704 4.6 93.0 1.0
OE1 A:GLU363 4.9 49.2 1.0

Praseodymium binding site 4 out of 5 in 7m4t

Go back to Praseodymium Binding Sites List in 7m4t
Praseodymium binding site 4 out of 5 in the Menin Bound to M-1121


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 M-1121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr705

b:105.0
occ:0.50
PR A:7PR705 0.0 105.0 0.5
O1 A:7PR705 2.5 93.7 0.5
O3 A:7PR705 2.5 99.6 0.5
O A:7PR705 2.5 101.0 0.5
C2 A:7PR705 3.6 82.0 0.5
C1 A:7PR705 3.6 96.8 0.5
C4 A:7PR705 3.7 94.3 0.5
C A:7PR705 3.8 92.2 0.5
C3 A:7PR705 3.9 70.9 0.5
O4 A:7PR705 4.1 93.9 0.5
O2 A:7PR705 4.5 81.3 0.5
O5 A:7PR705 4.6 96.7 0.5
C5 A:7PR705 4.9 89.0 0.5

Praseodymium binding site 5 out of 5 in 7m4t

Go back to Praseodymium Binding Sites List in 7m4t
Praseodymium binding site 5 out of 5 in the Menin Bound to M-1121


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 M-1121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr706

b:102.4
occ:1.00
PR A:7PR706 0.0 102.4 1.0
O A:7PR706 2.5 98.9 1.0
O3 A:7PR706 2.5 98.2 1.0
O1 A:7PR706 2.5 92.6 1.0
C1 A:7PR706 3.6 95.6 1.0
C2 A:7PR706 3.6 82.2 1.0
C4 A:7PR706 3.7 93.7 1.0
C A:7PR706 3.8 92.2 1.0
O2 A:7PR706 4.0 82.3 1.0
O4 A:7PR706 4.1 93.9 1.0
O5 A:7PR706 4.6 96.1 1.0
C3 A:7PR706 4.7 70.9 1.0
OD1 A:ASP252 4.8 53.9 1.0
C5 A:7PR706 4.8 89.0 1.0
OD2 A:ASP252 4.8 63.7 1.0

Reference:

M.Zhang, A.Aguilar, S.Xu, L.Huang, K.Chinnaswamy, T.Sleger, B.Wang, S.Gross, B.N.Nicolay, S.Ronseaux, K.Harvey, Y.Wang, D.Mceachern, P.D.Kirchhoff, Z.Liu, J.Stuckey, A.E.Tron, T.Liu, S.Wang. Discovery of M-1121 As An Orally Active Covalent Inhibitor of Menin-Mll Interaction Capable of Achieving Complete and Long-Lasting Tumor Regression. J.Med.Chem. V. 64 10333 2021.
ISSN: ISSN 0022-2623
PubMed: 34196551
DOI: 10.1021/ACS.JMEDCHEM.1C00789
Page generated: Sat Aug 21 17:31:42 2021

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