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

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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

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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

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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

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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

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