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Fluorine in PDB 5ls6: Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor

Enzymatic activity of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor

All present enzymatic activity of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor:
2.1.1.43;

Protein crystallography data

The structure of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor, PDB code: 5ls6 was solved by Y.Zhang, N.Justin, S.Chen, J.Wilson, S.Gamblin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.84 / 3.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 131.310, 170.270, 275.540, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 29.9

Other elements in 5ls6:

The structure of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 32 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor (pdb code 5ls6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor, PDB code: 5ls6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5ls6

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Fluorine binding site 1 out of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F809

b:91.0
occ:1.00
FBI A:74D809 0.0 91.0 1.0
CBH A:74D809 1.3 81.7 1.0
FBJ A:74D809 2.1 82.0 1.0
CBG A:74D809 2.3 75.5 1.0
CBK A:74D809 2.3 82.7 1.0
NBD A:74D809 3.5 70.0 1.0
OD2 B:ASP237 3.6 79.5 1.0
CG B:ASP237 4.0 85.8 1.0
CBC A:74D809 4.1 69.6 1.0
ND2 A:ASN130 4.2 86.7 1.0
OD1 B:ASP237 4.3 83.4 1.0
CB A:PRO132 4.4 71.3 1.0
OH A:TYR661 4.5 86.8 1.0
CBE A:74D809 4.6 70.1 1.0
CG A:PRO132 4.6 70.7 1.0
CB B:ASP237 4.7 87.2 1.0
O B:ARG236 4.9 85.6 1.0
CA A:PRO132 5.0 75.9 1.0

Fluorine binding site 2 out of 8 in 5ls6

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Fluorine binding site 2 out of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F809

b:82.0
occ:1.00
FBJ A:74D809 0.0 82.0 1.0
CBH A:74D809 1.3 81.7 1.0
FBI A:74D809 2.1 91.0 1.0
CBG A:74D809 2.3 75.5 1.0
CBK A:74D809 2.3 82.7 1.0
NBD A:74D809 2.5 70.0 1.0
CBC A:74D809 2.7 69.6 1.0
CBB A:74D809 3.7 68.1 1.0
CG1 A:VAL657 3.8 71.4 1.0
CBE A:74D809 4.0 70.1 1.0
CE1 A:TYR658 4.7 63.5 1.0
CE1 A:TYR661 4.7 82.4 1.0
CBF A:74D809 4.8 68.2 1.0
CG2 A:VAL657 4.8 64.8 1.0
CBA A:74D809 4.9 63.9 1.0
OH A:TYR661 4.9 86.8 1.0
CB A:VAL657 4.9 66.7 1.0
CD1 A:TYR658 5.0 63.9 1.0

Fluorine binding site 3 out of 8 in 5ls6

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Fluorine binding site 3 out of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F809

b:68.4
occ:1.00
FBI D:74D809 0.0 68.4 1.0
CBH D:74D809 1.3 67.0 1.0
FBJ D:74D809 2.1 66.7 1.0
CBG D:74D809 2.2 65.0 1.0
CBK D:74D809 2.3 69.4 1.0
OD2 E:ASP237 2.9 82.8 1.0
CG E:ASP237 3.5 79.5 1.0
NBD D:74D809 3.5 63.8 1.0
OD1 E:ASP237 3.9 76.0 1.0
CBE D:74D809 4.1 64.7 1.0
ND2 D:ASN130 4.1 94.3 1.0
CBC D:74D809 4.2 64.2 1.0
OH D:TYR661 4.2 84.8 1.0
CB D:PRO132 4.3 67.5 1.0
CB E:ASP237 4.4 78.0 1.0
O E:ARG236 4.6 71.5 1.0
CG D:PRO132 4.7 66.8 1.0
CA D:PRO132 4.8 70.6 1.0

Fluorine binding site 4 out of 8 in 5ls6

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Fluorine binding site 4 out of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F809

b:66.7
occ:1.00
FBJ D:74D809 0.0 66.7 1.0
CBH D:74D809 1.4 67.0 1.0
FBI D:74D809 2.1 68.4 1.0
CBG D:74D809 2.4 65.0 1.0
CBK D:74D809 2.4 69.4 1.0
NBD D:74D809 2.7 63.8 1.0
CBC D:74D809 2.9 64.2 1.0
CBE D:74D809 3.0 64.7 1.0
CBB D:74D809 3.6 62.5 1.0
CE1 D:TYR661 3.8 81.9 1.0
OH D:TYR661 3.8 84.8 1.0
CG2 D:VAL657 4.1 67.1 1.0
CZ D:TYR661 4.1 80.1 1.0
CG1 D:VAL657 4.4 72.7 1.0
CBF D:74D809 4.4 64.6 1.0
CB D:PRO132 4.6 67.5 1.0
CBA D:74D809 4.6 61.5 1.0
CG D:PRO132 4.7 66.8 1.0
CD1 D:TYR661 4.7 82.9 1.0
CE1 D:TYR658 4.9 64.7 1.0
CB D:VAL657 4.9 67.9 1.0
OD2 E:ASP237 5.0 82.8 1.0

Fluorine binding site 5 out of 8 in 5ls6

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Fluorine binding site 5 out of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F809

b:61.1
occ:1.00
FBI G:74D809 0.0 61.1 1.0
CBH G:74D809 1.3 67.5 1.0
CBG G:74D809 2.3 70.7 1.0
FBJ G:74D809 2.3 63.8 1.0
CBK G:74D809 2.3 69.4 1.0
NBD G:74D809 3.5 76.4 1.0
CB G:PRO132 3.7 82.2 1.0
CG G:PRO132 4.0 79.8 1.0
CBE G:74D809 4.0 77.1 1.0
OD2 H:ASP237 4.2 65.3 1.0
OH G:TYR661 4.3 0.8 1.0
CA G:PRO132 4.3 80.9 1.0
CG2 G:VAL657 4.3 62.9 1.0
CBC G:74D809 4.4 76.4 1.0
CG H:ASP237 4.4 71.2 1.0
OD1 H:ASP237 4.5 79.0 1.0
ND2 G:ASN130 4.7 97.1 1.0
CE1 G:TYR661 4.8 87.6 1.0
CBF G:74D809 4.8 72.9 1.0
CZ G:TYR661 4.9 89.1 1.0

Fluorine binding site 6 out of 8 in 5ls6

Go back to Fluorine Binding Sites List in 5ls6
Fluorine binding site 6 out of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F809

b:63.8
occ:1.00
FBJ G:74D809 0.0 63.8 1.0
CBH G:74D809 1.4 67.5 1.0
FBI G:74D809 2.3 61.1 1.0
CBG G:74D809 2.4 70.7 1.0
CBK G:74D809 2.4 69.4 1.0
NBD G:74D809 2.7 76.4 1.0
CBE G:74D809 3.0 77.1 1.0
CBC G:74D809 3.1 76.4 1.0
CBB G:74D809 3.2 74.2 1.0
CBF G:74D809 3.2 72.9 1.0
CG2 G:VAL657 3.6 62.9 1.0
CBA G:74D809 3.9 69.5 1.0
CE1 G:TYR661 3.9 87.6 1.0
CG1 G:VAL657 4.2 66.4 1.0
CZ G:TYR661 4.5 89.1 1.0
CD1 G:TYR661 4.5 87.7 1.0
OH G:TYR661 4.5 0.8 1.0
CB G:VAL657 4.6 63.7 1.0
CE1 G:TYR658 4.8 57.6 1.0
CD1 G:TYR658 4.9 55.3 1.0

Fluorine binding site 7 out of 8 in 5ls6

Go back to Fluorine Binding Sites List in 5ls6
Fluorine binding site 7 out of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F809

b:89.7
occ:1.00
FBI J:74D809 0.0 89.7 1.0
CBH J:74D809 1.4 84.6 1.0
FBJ J:74D809 2.2 90.0 1.0
CBG J:74D809 2.4 81.4 1.0
CBK J:74D809 2.4 83.0 1.0
NBD J:74D809 3.3 79.4 1.0
CBC J:74D809 3.7 76.8 1.0
O K:ARG236 3.9 66.7 1.0
CBE J:74D809 4.6 79.5 1.0
CBB J:74D809 4.9 74.3 1.0

Fluorine binding site 8 out of 8 in 5ls6

Go back to Fluorine Binding Sites List in 5ls6
Fluorine binding site 8 out of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F809

b:90.0
occ:1.00
FBJ J:74D809 0.0 90.0 1.0
CBH J:74D809 1.4 84.6 1.0
FBI J:74D809 2.2 89.7 1.0
CBG J:74D809 2.3 81.4 1.0
CBK J:74D809 2.4 83.0 1.0
NBD J:74D809 2.4 79.4 1.0
CBC J:74D809 3.2 76.8 1.0
CBE J:74D809 3.6 79.5 1.0
OD1 K:ASP237 3.7 67.1 1.0
CE1 K:HIS213 3.8 58.4 1.0
CBB J:74D809 3.9 74.3 1.0
O K:ARG236 4.0 66.7 1.0
CG K:ASP237 4.0 66.0 1.0
NE2 K:HIS213 4.1 58.0 1.0
CBF J:74D809 4.3 78.4 1.0
OD2 K:ASP237 4.4 61.7 1.0
CB K:ASP237 4.7 67.2 1.0
CBA J:74D809 4.7 74.1 1.0
CA K:ASP237 4.8 69.4 1.0
ND1 K:HIS213 5.0 58.9 1.0
OH J:TYR661 5.0 78.3 1.0

Reference:

R.G.Vaswani, V.S.Gehling, L.A.Dakin, A.S.Cook, C.G.Nasveschuk, M.Duplessis, P.Iyer, S.Balasubramanian, F.Zhao, A.C.Good, R.Campbell, C.Lee, N.Cantone, R.T.Cummings, E.Normant, S.F.Bellon, B.K.Albrecht, J.C.Harmange, P.Trojer, J.E.Audia, Y.Zhang, N.Justin, S.Chen, J.R.Wilson, S.J.Gamblin. Identification of (R)-N-((4-Methoxy-6-Methyl-2-Oxo-1,2-Dihydropyridin-3-Yl) Methyl)-2-Methyl-1-(1-(1-(2,2,2-Trifluoroethyl) Piperidin-4-Yl)Ethyl)-1H-Indole-3-Carboxamide (Cpi-1205), A Potent and Selective Inhibitor of Histone Methyltransferase EZH2, Suitable For Phase I Clinical Trials For B-Cell Lymphomas. J. Med. Chem. V. 59 9928 2016.
ISSN: ISSN 1520-4804
PubMed: 27739677
DOI: 10.1021/ACS.JMEDCHEM.6B01315
Page generated: Sun Dec 13 12:27:23 2020

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