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Praseodymium in PDB 6e1a: Menin Bound to M-89

Protein crystallography data

The structure of Menin Bound to M-89, PDB code: 6e1a 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) 48.77 / 3.10
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 154.210, 154.210, 82.620, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23.5

Praseodymium Binding Sites:

The binding sites of Praseodymium atom in the Menin Bound to M-89 (pdb code 6e1a). 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-89, PDB code: 6e1a:
Jump to Praseodymium binding site number: 1; 2; 3; 4; 5;

Praseodymium binding site 1 out of 5 in 6e1a

Go back to Praseodymium Binding Sites List in 6e1a
Praseodymium binding site 1 out of 5 in the Menin Bound to M-89


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-89 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr702

b:57.9
occ:0.50
PR A:7PR702 0.0 57.9 0.5
O3 A:7PR702 2.4 58.2 0.5
O A:7PR702 2.4 57.8 0.5
O1 A:7PR702 2.5 54.6 0.5
C1 A:7PR702 3.5 57.8 0.5
C2 A:7PR702 3.6 51.5 0.5
C4 A:7PR702 3.6 59.0 0.5
O5 A:7PR702 3.7 59.2 0.5
O4 A:7PR702 3.9 59.4 0.5
C3 A:7PR702 4.0 51.2 0.5
O2 A:7PR702 4.5 51.2 0.5
C A:7PR702 4.8 57.5 0.5
C5 A:7PR702 4.8 60.2 0.5
OD2 A:ASP370 5.0 69.4 1.0

Praseodymium binding site 2 out of 5 in 6e1a

Go back to Praseodymium Binding Sites List in 6e1a
Praseodymium binding site 2 out of 5 in the Menin Bound to M-89


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-89 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr703

b:0.3
occ:1.00
PR A:7PR703 0.0 0.3 1.0
O1 A:7PR703 2.5 0.6 1.0
O A:7PR703 2.5 0.5 1.0
O3 A:7PR703 2.5 0.5 1.0
C1 A:7PR703 3.6 0.2 1.0
C2 A:7PR703 3.6 0.5 1.0
C4 A:7PR703 3.7 0.7 1.0
C A:7PR703 3.8 0.8 1.0
C3 A:7PR703 4.1 0.6 1.0
O A:ARG131 4.3 64.6 1.0
O4 A:7PR703 4.4 0.5 1.0
C5 A:7PR703 4.5 0.7 1.0
O2 A:7PR703 4.5 0.7 1.0
O5 A:7PR703 4.6 0.5 1.0

Praseodymium binding site 3 out of 5 in 6e1a

Go back to Praseodymium Binding Sites List in 6e1a
Praseodymium binding site 3 out of 5 in the Menin Bound to M-89


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-89 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
O1 A:7PR704 2.5 0.9 1.0
O3 A:7PR704 2.5 0.3 1.0
O A:7PR704 2.5 0.8 1.0
C2 A:7PR704 3.6 0.3 1.0
C1 A:7PR704 3.6 0.7 1.0
C4 A:7PR704 3.7 0.8 1.0
O2 A:7PR704 3.8 0.4 1.0
O5 A:7PR704 3.9 0.8 1.0
O4 A:7PR704 4.1 0.8 1.0
OD2 A:ASP252 4.5 77.2 1.0
C5 A:7PR704 4.7 0.1 1.0
C3 A:7PR704 4.9 0.3 1.0
C A:7PR704 4.9 0.1 1.0
OD1 A:ASP252 4.9 70.2 1.0

Praseodymium binding site 4 out of 5 in 6e1a

Go back to Praseodymium Binding Sites List in 6e1a
Praseodymium binding site 4 out of 5 in the Menin Bound to M-89


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-89 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr705

b:0.4
occ:0.50
PR A:7PR705 0.0 0.4 0.5
O1 A:7PR705 2.5 0.5 0.5
O A:7PR705 2.5 0.9 0.5
O3 A:7PR705 2.5 0.3 0.5
C1 A:7PR705 3.6 0.5 0.5
C2 A:7PR705 3.6 0.7 0.5
C4 A:7PR705 3.7 0.0 0.5
O5 A:7PR705 3.8 0.5 0.5
C5 A:7PR705 4.2 0.9 0.5
C3 A:7PR705 4.3 0.4 0.5
O2 A:7PR705 4.3 0.4 0.5
O4 A:7PR705 4.6 0.9 0.5
C A:7PR705 4.8 0.3 0.5

Praseodymium binding site 5 out of 5 in 6e1a

Go back to Praseodymium Binding Sites List in 6e1a
Praseodymium binding site 5 out of 5 in the Menin Bound to M-89


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-89 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr706

b:0.8
occ:1.00
PR A:7PR706 0.0 0.8 1.0
O1 A:7PR706 2.5 0.3 1.0
O3 A:7PR706 2.5 0.0 1.0
O A:7PR706 2.5 0.2 1.0
C2 A:7PR706 3.5 0.7 1.0
C1 A:7PR706 3.6 0.9 1.0
C4 A:7PR706 3.7 0.9 1.0
C A:7PR706 3.8 0.5 1.0
C3 A:7PR706 3.9 0.9 1.0
C5 A:7PR706 4.3 0.3 1.0
OE2 A:GLU363 4.3 70.7 1.0
O4 A:7PR706 4.5 0.8 1.0
O2 A:7PR706 4.5 0.4 1.0
O5 A:7PR706 4.6 0.9 1.0

Reference:

A.Aguilar, K.Zheng, T.Xu, S.Xu, L.Huang, E.Fernandez-Salas, L.Liu, D.Bernard, K.P.Harvey, C.Foster, D.Mceachern, J.Stuckey, K.Chinnaswamy, J.Delproposto, J.W.Kampf, S.Wang. Structure-Based Discovery of M-89 As A Highly Potent Inhibitor of the Menin-Mixed Lineage Leukemia (Menin-Mll) Protein-Protein Interaction. J.Med.Chem. V. 62 6015 2019.
ISSN: ISSN 0022-2623
PubMed: 31244110
DOI: 10.1021/ACS.JMEDCHEM.9B00021
Page generated: Thu Oct 29 06:39:32 2020

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