Fluorine in PDB 7msd: Structure of Eed Bound to Eedi-6068

Protein crystallography data

The structure of Structure of Eed Bound to Eedi-6068, PDB code: 7msd was solved by E.Petrunak, J.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.90 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.8, 85.57, 91.916, 90, 90, 90
R / Rfree (%) 17.7 / 21.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Eed Bound to Eedi-6068 (pdb code 7msd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Eed Bound to Eedi-6068, PDB code: 7msd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7msd

Go back to Fluorine Binding Sites List in 7msd
Fluorine binding site 1 out of 6 in the Structure of Eed Bound to Eedi-6068


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Eed Bound to Eedi-6068 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:25.9
occ:1.00
 F5 A:ZMY501 0.0 25.9 1.0
C22 A:ZMY501 1.3 25.4 1.0
C21 A:ZMY501 2.3 25.2 1.0
C15 A:ZMY501 2.3 25.4 1.0
H18 A:ZMY501 2.6 30.2 1.0
H12 A:ZMY501 2.8 32.0 1.0
C14 A:ZMY501 2.9 26.6 1.0
H10 A:ZMY501 2.9 33.8 1.0
N3 A:ZMY501 3.1 28.1 1.0
O A:LEU240 3.2 23.2 1.0
CB A:ASN194 3.2 20.3 1.0
CG A:ASN194 3.3 21.9 1.0
OD1 A:ASN194 3.4 23.4 1.0
NH1 A:ARG367 3.6 23.8 0.5
C20 A:ZMY501 3.6 24.8 1.0
C16 A:ZMY501 3.6 24.9 1.0
CD1 A:TYR365 3.6 36.0 1.0
CE1 A:TYR365 3.7 36.7 1.0
CD2 A:LEU240 3.9 25.1 1.0
O A:ASN194 3.9 20.4 1.0
H11 A:ZMY501 3.9 32.0 1.0
CA A:LEU240 3.9 21.5 1.0
C A:LEU240 4.0 21.9 1.0
CB A:LEU240 4.0 22.3 1.0
C19 A:ZMY501 4.0 24.5 1.0
ND2 A:ASN194 4.1 20.5 1.0
CA A:ASN194 4.1 19.5 1.0
C13 A:ZMY501 4.1 29.3 1.0
C A:ASN194 4.3 20.2 1.0
CZ A:ARG367 4.4 27.4 0.5
H19 A:ZMY501 4.4 37.9 1.0
H17 A:ZMY501 4.5 29.8 1.0
CG A:LEU240 4.6 24.8 1.0
N2 A:ZMY501 4.7 29.7 1.0
NH1 A:ARG367 4.8 17.8 0.5
N4 A:ZMY501 4.8 31.2 1.0
NH2 A:ARG367 4.8 27.4 0.5
CG A:TYR365 4.9 35.7 1.0
C17 A:ZMY501 5.0 25.1 1.0
C25 A:ZMY501 5.0 31.6 1.0

Fluorine binding site 2 out of 6 in 7msd

Go back to Fluorine Binding Sites List in 7msd
Fluorine binding site 2 out of 6 in the Structure of Eed Bound to Eedi-6068


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Eed Bound to Eedi-6068 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:45.0
occ:1.00
 F4 A:ZMY501 0.0 45.0 1.0
C8 A:ZMY501 1.3 44.0 1.0
F3 A:ZMY501 2.1 44.2 1.0
F2 A:ZMY501 2.2 45.0 1.0
C7 A:ZMY501 2.4 41.4 1.0
N1 A:ZMY501 2.7 40.3 1.0
NH2 A:ARG414 3.3 43.9 1.0
O A:HOH698 3.4 55.1 1.0
C6 A:ZMY501 3.6 39.4 1.0
C9 A:ZMY501 4.0 38.7 1.0
H7 A:ZMY501 4.0 47.3 1.0
O A:HOH812 4.3 54.2 1.0
CZ A:ARG414 4.5 40.5 1.0
H8 A:ZMY501 4.5 46.4 1.0
OD2 A:ASP430 4.6 48.6 1.0
O A:HOH673 4.7 66.2 1.0
C5 A:ZMY501 4.7 37.9 1.0
C10 A:ZMY501 4.9 36.7 1.0

Fluorine binding site 3 out of 6 in 7msd

Go back to Fluorine Binding Sites List in 7msd
Fluorine binding site 3 out of 6 in the Structure of Eed Bound to Eedi-6068


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Eed Bound to Eedi-6068 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:44.2
occ:1.00
 F3 A:ZMY501 0.0 44.2 1.0
C8 A:ZMY501 1.3 44.0 1.0
F4 A:ZMY501 2.1 45.0 1.0
F2 A:ZMY501 2.1 45.0 1.0
C7 A:ZMY501 2.4 41.4 1.0
N1 A:ZMY501 3.1 40.3 1.0
O A:HOH812 3.1 54.2 1.0
C6 A:ZMY501 3.2 39.4 1.0
H7 A:ZMY501 3.4 47.3 1.0
CG A:PRO95 3.5 34.1 1.0
NH2 A:ARG414 3.8 43.9 1.0
O A:HOH798 4.2 67.7 1.0
C9 A:ZMY501 4.2 38.7 1.0
CZ A:PHE97 4.3 27.5 1.0
O A:HOH673 4.4 66.2 1.0
C5 A:ZMY501 4.4 37.9 1.0
OD2 A:ASP430 4.4 48.6 1.0
CB A:PRO95 4.4 33.4 1.0
CE1 A:PHE97 4.5 27.7 1.0
CD A:PRO95 4.6 32.5 1.0
C10 A:ZMY501 4.8 36.7 1.0
CZ A:ARG414 4.9 40.5 1.0
CG A:ASP430 4.9 45.6 1.0
OD1 A:ASP430 5.0 47.6 1.0
H8 A:ZMY501 5.0 46.4 1.0

Fluorine binding site 4 out of 6 in 7msd

Go back to Fluorine Binding Sites List in 7msd
Fluorine binding site 4 out of 6 in the Structure of Eed Bound to Eedi-6068


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Eed Bound to Eedi-6068 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:45.0
occ:1.00
 F2 A:ZMY501 0.0 45.0 1.0
C8 A:ZMY501 1.3 44.0 1.0
F3 A:ZMY501 2.1 44.2 1.0
F4 A:ZMY501 2.2 45.0 1.0
C7 A:ZMY501 2.4 41.4 1.0
H7 A:ZMY501 2.6 47.3 1.0
C6 A:ZMY501 2.8 39.4 1.0
N1 A:ZMY501 3.5 40.3 1.0
O A:HOH812 3.9 54.2 1.0
C5 A:ZMY501 4.2 37.9 1.0
O A:HOH798 4.3 67.7 1.0
H1 A:ZMY501 4.4 47.7 1.0
C9 A:ZMY501 4.6 38.7 1.0
H5 A:ZMY501 4.9 45.3 1.0
C10 A:ZMY501 5.0 36.7 1.0

Fluorine binding site 5 out of 6 in 7msd

Go back to Fluorine Binding Sites List in 7msd
Fluorine binding site 5 out of 6 in the Structure of Eed Bound to Eedi-6068


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Eed Bound to Eedi-6068 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:42.4
occ:1.00
 F A:ZMY501 0.0 42.4 1.0
C2 A:ZMY501 1.4 41.6 1.0
F1 A:ZMY501 2.1 42.0 1.0
C3 A:ZMY501 2.4 41.9 1.0
C1 A:ZMY501 2.4 39.8 1.0
H3 A:ZMY501 2.6 50.3 1.0
H4 A:ZMY501 2.7 50.3 1.0
H A:ZMY501 2.7 47.7 1.0
N A:ZMY501 2.9 37.8 1.0
O A:ZMY501 3.2 36.1 1.0
O A:HOH744 3.2 63.6 1.0
C A:ZMY501 3.3 35.9 1.0
H1 A:ZMY501 3.3 47.7 1.0
H2 A:ZMY501 3.3 50.3 1.0
O A:HOH742 3.7 38.2 1.0
H5 A:ZMY501 3.8 45.3 1.0
C4 A:ZMY501 3.9 37.8 1.0
OH A:TYR148 4.0 31.9 1.0
H6 A:ZMY501 4.2 45.3 1.0
C24 A:ZMY501 4.5 33.7 1.0
NZ A:LYS211 4.8 38.1 1.0
N5 A:ZMY501 5.0 32.3 1.0

Fluorine binding site 6 out of 6 in 7msd

Go back to Fluorine Binding Sites List in 7msd
Fluorine binding site 6 out of 6 in the Structure of Eed Bound to Eedi-6068


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Eed Bound to Eedi-6068 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:42.0
occ:1.00
 F1 A:ZMY501 0.0 42.0 1.0
C2 A:ZMY501 1.4 41.6 1.0
F A:ZMY501 2.1 42.4 1.0
C1 A:ZMY501 2.4 39.8 1.0
C3 A:ZMY501 2.4 41.9 1.0
H5 A:ZMY501 2.4 45.3 1.0
H1 A:ZMY501 2.7 47.7 1.0
H3 A:ZMY501 2.7 50.3 1.0
H2 A:ZMY501 2.7 50.3 1.0
N A:ZMY501 2.9 37.8 1.0
C4 A:ZMY501 3.1 37.8 1.0
H A:ZMY501 3.3 47.7 1.0
H4 A:ZMY501 3.4 50.3 1.0
H6 A:ZMY501 3.5 45.3 1.0
ND2 A:ASN146 3.8 45.3 1.0
C A:ZMY501 4.0 35.9 1.0
H7 A:ZMY501 4.1 47.3 1.0
OH A:TYR148 4.1 31.9 1.0
C5 A:ZMY501 4.4 37.9 1.0
O A:ZMY501 4.4 36.1 1.0
C6 A:ZMY501 4.6 39.4 1.0

Reference:

R.K.Rej, C.Wang, J.Lu, M.Wang, E.Petrunak, K.P.Zawacki, D.Mceachern, C.Y.Yang, L.Wang, R.Li, K.Chinnaswamy, B.Wen, D.Sun, J.A.Stuckey, Y.Zhou, J.Chen, G.Tang, S.Wang. Discovery of Eedi-5273 As An Exceptionally Potent and Orally Efficacious Eed Inhibitor Capable of Achieving Complete and Persistent Tumor Regression. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34613724
DOI: 10.1021/ACS.JMEDCHEM.1C01059
Page generated: Fri Aug 2 09:47:26 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy