Fluorine in PDB 7kid: PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72

Enzymatic activity of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72

All present enzymatic activity of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72:
2.1.1.320;

Protein crystallography data

The structure of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72, PDB code: 7kid was solved by R.L.Palte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.79 / 2.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.678, 139.177, 178.883, 90, 90, 90
R / Rfree (%) 25.9 / 27.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72 (pdb code 7kid). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72, PDB code: 7kid:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7kid

Go back to Fluorine Binding Sites List in 7kid
Fluorine binding site 1 out of 3 in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F705

b:32.6
occ:1.00
F2 A:WFV705 0.0 32.6 1.0
C17 A:WFV705 1.4 32.5 1.0
C16 A:WFV705 2.3 32.6 1.0
C18 A:WFV705 2.4 32.7 1.0
NZ A:LYS333 2.8 77.8 1.0
C23 A:WFV705 2.8 33.3 1.0
OE1 A:GLU435 2.9 50.9 1.0
CB A:PHE327 3.3 37.5 1.0
CG A:PHE327 3.3 38.8 1.0
OH A:TYR334 3.3 52.5 1.0
CD2 A:PHE327 3.5 40.7 1.0
C15 A:WFV705 3.6 32.8 1.0
C19 A:WFV705 3.6 32.6 1.0
CD A:GLU435 3.8 55.2 1.0
CD1 A:PHE327 3.9 41.6 1.0
CE A:LYS333 4.0 70.8 1.0
C20 A:WFV705 4.1 32.6 1.0
C22 A:WFV705 4.2 33.7 1.0
CA A:PHE327 4.2 35.9 1.0
O A:HOH802 4.2 9.9 0.7
CE2 A:PHE327 4.3 43.4 1.0
O A:PHE327 4.5 40.3 1.0
CZ A:TYR334 4.5 51.4 1.0
OE2 A:GLU435 4.6 48.0 1.0
CG A:GLU435 4.6 38.3 1.0
C A:PHE327 4.6 40.6 1.0
CE1 A:PHE327 4.6 42.4 1.0
CD A:LYS333 4.7 62.6 1.0
N4 A:WFV705 4.8 33.0 1.0
CZ A:PHE327 4.8 41.3 1.0
C14 A:WFV705 4.9 32.6 1.0
C21 A:WFV705 5.0 33.6 1.0

Fluorine binding site 2 out of 3 in 7kid

Go back to Fluorine Binding Sites List in 7kid
Fluorine binding site 2 out of 3 in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F705

b:34.0
occ:1.00
F1 A:WFV705 0.0 34.0 1.0
C22 A:WFV705 1.4 33.7 1.0
C23 A:WFV705 2.3 33.3 1.0
C21 A:WFV705 2.4 33.6 1.0
O A:SER578 2.7 35.5 1.0
N5 A:WFV705 2.8 33.8 1.0
CD1 A:TRP579 3.3 32.8 1.0
C A:SER578 3.3 36.1 1.0
O A:HOH898 3.4 36.5 1.0
NE1 A:TRP579 3.4 32.3 1.0
C18 A:WFV705 3.6 32.7 1.0
O A:HOH913 3.6 34.7 1.0
N4 A:WFV705 3.6 33.0 1.0
CG A:TRP579 3.7 29.9 1.0
CB A:SER578 3.8 37.6 1.0
CE2 A:TRP579 4.0 33.7 1.0
N A:TRP579 4.0 31.1 1.0
CA A:SER578 4.1 34.2 1.0
C19 A:WFV705 4.1 32.6 1.0
CE1 A:PHE327 4.1 42.4 1.0
CD2 A:TRP579 4.2 29.8 1.0
CA A:TRP579 4.2 30.1 1.0
O A:HOH1014 4.3 53.0 1.0
CD1 A:PHE327 4.3 41.6 1.0
CB A:TRP579 4.5 28.9 1.0
O A:HOH957 4.6 21.8 1.0
OG A:SER578 4.6 46.2 1.0
C17 A:WFV705 4.8 32.5 1.0
CZ2 A:TRP579 4.9 33.1 1.0
CZ A:PHE327 4.9 41.3 1.0

Fluorine binding site 3 out of 3 in 7kid

Go back to Fluorine Binding Sites List in 7kid
Fluorine binding site 3 out of 3 in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F705

b:30.0
occ:1.00
F A:WFV705 0.0 30.0 1.0
C7 A:WFV705 1.3 29.7 1.0
C8 A:WFV705 2.4 29.9 1.0
C6 A:WFV705 2.5 29.7 1.0
SG A:CYS449 3.0 38.6 1.0
CD2 A:LEU315 3.2 40.8 1.0
N3 A:WFV705 3.2 29.4 1.0
C9 A:WFV705 3.2 29.8 1.0
O A:HOH945 3.3 38.6 1.0
CB A:LEU315 3.3 33.0 1.0
CG A:LEU315 3.5 37.8 1.0
N A:WFV705 3.5 30.4 1.0
C5 A:WFV705 3.6 30.0 1.0
CA A:LEU315 3.7 32.9 1.0
CD2 A:LEU436 4.2 33.5 1.0
N A:LEU315 4.2 33.0 1.0
CB A:CYS449 4.5 34.7 1.0
N1 A:WFV705 4.6 30.1 1.0
N2 A:WFV705 4.9 30.0 1.0
C A:PRO314 4.9 36.5 1.0
C3 A:WFV705 4.9 31.3 1.0
O A:GLU444 5.0 28.9 1.0
CD1 A:LEU315 5.0 37.8 1.0

Reference:

R.V.Quiroz, M.H.Reutershan, S.E.Schneider, D.Sloman, B.M.Lacey, B.M.Swalm, C.S.Yeung, C.Gibeau, D.S.Spellman, D.A.Rankic, D.Chen, D.Witter, D.Linn, E.Munsell, G.Feng, H.Xu, J.M.E.Hughes, J.Lim, J.Sauri, K.Geddes, M.Wan, M.S.Mansueto, N.E.Follmer, P.S.Fier, P.Siliphaivanh, P.Daublain, R.L.Palte, R.P.Hayes, S.Lee, S.Kawamura, S.Silverman, S.Sanyal, T.J.Henderson, Y.Ye, Y.Gao, B.Nicholson, M.R.Machacek. The Discovery of Two Novel Classes of 5,5-Bicyclic Nucleoside-Derived PRMT5 Inhibitors For the Treatment of Cancer. J.Med.Chem. V. 64 3911 2021.
ISSN: ISSN 0022-2623
PubMed: 33755451
DOI: 10.1021/ACS.JMEDCHEM.0C02083
Page generated: Sat Jul 10 14:10:21 2021

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