Atomistry » Praseodymium » PDB 1k0z-6vrz » 6b41
Atomistry »
  Praseodymium »
    PDB 1k0z-6vrz »
      6b41 »

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

Go back to Praseodymium Binding Sites List in 6b41
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

Go back to Praseodymium Binding Sites List in 6b41
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

Go back to Praseodymium Binding Sites List in 6b41
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

Go back to Praseodymium Binding Sites List in 6b41
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: Wed Dec 16 02:03:12 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy