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Praseodymium in PDB 6b41: Menin Bound to M-525

Protein crystallography data

The structure of Menin Bound to M-525, PDB code: 6b41 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) 48.67 / 2.61
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 153.920, 153.920, 81.618, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.2

Other elements in 6b41:

The structure of Menin Bound to M-525 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-525 (pdb code 6b41). 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-525, PDB code: 6b41:
Jump to Praseodymium binding site number: 1; 2; 3; 4; 5;

Praseodymium binding site 1 out of 5 in 6b41

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Praseodymium binding site 1 out of 5 in the Menin Bound to M-525


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-525 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr702

b:35.7
occ:0.50
PR A:7PR702 0.0 35.7 0.5
PR A:7PR702 0.9 0.3 0.5
O A:7PR702 2.1 0.7 0.5
O1 A:7PR702 2.4 0.7 0.5
O3 A:7PR702 2.4 0.7 0.5
O3 A:7PR702 2.4 36.4 0.5
O1 A:7PR702 2.5 37.2 0.5
O A:7PR702 2.5 37.0 0.5
C1 A:7PR702 3.2 0.2 0.5
C1 A:7PR702 3.5 34.6 0.5
C2 A:7PR702 3.5 37.9 0.5
C A:7PR702 3.5 0.9 0.5
C4 A:7PR702 3.6 39.4 0.5
C2 A:7PR702 3.6 0.1 0.5
C A:7PR702 3.7 32.6 0.5
C4 A:7PR702 3.7 0.6 0.5
C3 A:7PR702 3.9 36.7 0.5
O2 A:7PR702 3.9 0.9 0.5
C5 A:7PR702 4.1 38.4 0.5
O4 A:7PR702 4.2 0.1 0.5
OD2 A:ASP370 4.2 53.3 1.0
O5 A:7PR702 4.2 0.1 0.5
O2 A:7PR702 4.4 39.8 0.5
O4 A:7PR702 4.5 41.8 0.5
O5 A:7PR702 4.6 36.6 0.5
OE1 A:GLU366 4.7 23.3 1.0
C3 A:7PR702 4.8 0.0 0.5
C5 A:7PR702 4.8 0.3 0.5
OE2 A:GLU366 4.9 51.2 1.0

Praseodymium binding site 2 out of 5 in 6b41

Go back to Praseodymium Binding Sites List in 6b41
Praseodymium binding site 2 out of 5 in the Menin Bound to M-525


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-525 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr702

b:0.3
occ:0.50
PR A:7PR702 0.0 0.3 0.5
PR A:7PR702 0.9 35.7 0.5
O3 A:7PR702 2.5 0.7 0.5
O A:7PR702 2.5 0.7 0.5
O1 A:7PR702 2.5 0.7 0.5
O3 A:7PR702 2.5 36.4 0.5
O1 A:7PR702 2.5 37.2 0.5
O A:7PR702 3.3 37.0 0.5
C2 A:7PR702 3.4 37.9 0.5
C1 A:7PR702 3.6 0.2 0.5
C2 A:7PR702 3.6 0.1 0.5
C4 A:7PR702 3.7 0.6 0.5
C4 A:7PR702 3.7 39.4 0.5
C3 A:7PR702 3.7 36.7 0.5
C A:7PR702 3.8 0.9 0.5
O2 A:7PR702 3.9 0.9 0.5
O4 A:7PR702 4.1 0.1 0.5
O2 A:7PR702 4.2 39.8 0.5
C1 A:7PR702 4.3 34.6 0.5
C5 A:7PR702 4.3 38.4 0.5
C A:7PR702 4.3 32.6 0.5
O5 A:7PR702 4.6 0.1 0.5
O4 A:7PR702 4.6 41.8 0.5
C3 A:7PR702 4.7 0.0 0.5
C5 A:7PR702 4.8 0.3 0.5
OD2 A:ASP370 4.9 53.3 1.0

Praseodymium binding site 3 out of 5 in 6b41

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Praseodymium binding site 3 out of 5 in the Menin Bound to M-525


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-525 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr703

b:89.0
occ:1.00
PR A:7PR703 0.0 89.0 1.0
O A:7PR703 2.4 89.5 1.0
O1 A:7PR703 2.5 87.8 1.0
O3 A:7PR703 2.5 93.1 1.0
C1 A:7PR703 3.5 89.8 1.0
C2 A:7PR703 3.5 86.8 1.0
C4 A:7PR703 3.7 95.3 1.0
O5 A:7PR703 3.7 89.1 1.0
H8 A:7PR703 3.7 96.0 1.0
O2 A:7PR703 3.7 87.4 1.0
H9 A:7PR703 4.0 96.0 1.0
C5 A:7PR703 4.0 96.0 1.0
O A:ARG131 4.4 36.5 1.0
O4 A:7PR703 4.7 95.8 1.0
C A:7PR703 4.8 91.1 1.0
C3 A:7PR703 4.8 85.8 1.0
H6 A:7PR703 4.8 91.2 1.0
H3 A:7PR703 5.0 85.8 1.0

Praseodymium binding site 4 out of 5 in 6b41

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Praseodymium binding site 4 out of 5 in the Menin Bound to M-525


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-525 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr704

b:0.0
occ:1.00
PR A:7PR704 0.0 0.0 1.0
O3 A:7PR704 2.5 0.7 1.0
O1 A:7PR704 2.5 0.2 1.0
O A:7PR704 2.5 0.2 1.0
H4 A:7PR704 3.0 0.6 1.0
C1 A:7PR704 3.5 0.2 1.0
C2 A:7PR704 3.6 0.1 1.0
C4 A:7PR704 3.6 0.2 1.0
C A:7PR704 3.7 0.7 1.0
O2 A:7PR704 4.1 0.8 1.0
O4 A:7PR704 4.3 0.8 1.0
H3 A:7PR704 4.3 0.5 1.0
H5 A:7PR704 4.3 0.6 1.0
OD2 A:ASP252 4.3 51.5 1.0
C3 A:7PR704 4.5 0.5 1.0
C5 A:7PR704 4.5 0.0 1.0
H7 A:7PR704 4.5 1.0 1.0
H6 A:7PR704 4.5 0.6 1.0
OD1 A:ASP252 4.6 45.1 1.0
H8 A:7PR704 4.6 0.0 1.0
O5 A:7PR704 4.6 1.0 1.0
CG A:ASP252 4.9 46.3 1.0

Praseodymium binding site 5 out of 5 in 6b41

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Praseodymium binding site 5 out of 5 in the Menin Bound to M-525


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-525 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr705

b:0.8
occ:1.00
PR A:7PR705 0.0 0.8 1.0
O A:7PR705 2.5 0.2 1.0
O1 A:7PR705 2.5 0.6 1.0
O3 A:7PR705 2.5 0.5 1.0
H6 A:7PR705 3.5 0.3 1.0
C1 A:7PR705 3.6 0.9 1.0
C2 A:7PR705 3.6 0.4 1.0
C4 A:7PR705 3.7 0.2 1.0
H9 A:7PR705 3.8 0.9 1.0
H4 A:7PR705 3.8 0.2 1.0
C A:7PR705 3.8 0.3 1.0
H3 A:7PR705 3.9 0.2 1.0
C5 A:7PR705 4.3 0.9 1.0
C3 A:7PR705 4.3 0.2 1.0
O2 A:7PR705 4.4 0.3 1.0
O4 A:7PR705 4.6 0.0 1.0
O5 A:7PR705 4.6 0.6 1.0
H5 A:7PR705 4.9 0.2 1.0
H7 A:7PR705 4.9 0.9 1.0
H1 A:7PR705 5.0 0.2 1.0

Reference:

S.Xu, A.Aguilar, T.Xu, K.Zheng, L.Huang, J.Stuckey, K.Chinnaswamy, D.Bernard, E.Fernandez-Salas, L.Liu, M.Wang, D.Mceachern, S.Przybranowski, C.Foster, S.Wang. Design of the First-in-Class, Highly Potent Irreversible Inhibitor Targeting the Menin-Mll Protein-Protein Interaction. Angew. Chem. Int. Ed. Engl. V. 57 1601 2018.
ISSN: ESSN 1521-3773
PubMed: 29284071
DOI: 10.1002/ANIE.201711828
Page generated: Thu Oct 29 06:39:32 2020

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