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Chlorine in PDB 7kib: PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4

Enzymatic activity of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4

All present enzymatic activity of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4:
2.1.1.320;

Protein crystallography data

The structure of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4, PDB code: 7kib was solved by R.L.Palte, R.P.Hayes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.55 / 2.52
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.8, 138.95, 179.06, 90, 90, 90
R / Rfree (%) 19.3 / 24.5

Other elements in 7kib:

The structure of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4 also contains other interesting chemical elements:

Bromine (Br) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4 (pdb code 7kib). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4, PDB code: 7kib:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7kib

Go back to Chlorine Binding Sites List in 7kib
Chlorine binding site 1 out of 3 in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl710

b:81.3
occ:1.00
O A:HOH1061 3.0 67.1 1.0
OG1 A:THR132 3.2 49.7 1.0
O A:GLU129 3.7 55.3 1.0
N A:ASN131 3.7 45.4 1.0
O A:HOH846 3.9 57.2 1.0
OD1 A:ASP130 4.0 47.4 1.0
CA A:ASP130 4.0 44.3 1.0
CD1 A:LEU195 4.1 44.8 1.0
CB A:ASN191 4.1 39.0 1.0
N A:THR132 4.2 47.0 1.0
C A:ASP130 4.4 48.5 1.0
ND2 A:ASN191 4.5 41.9 1.0
CB A:THR132 4.5 49.4 1.0
C A:GLU129 4.6 52.4 1.0
CA A:THR132 4.6 46.0 1.0
C A:ASN131 4.7 49.3 1.0
CA A:ASN131 4.7 43.6 1.0
CG A:ASN191 4.8 46.8 1.0
CG A:ASP130 4.8 48.2 1.0
N A:ASP130 4.8 46.1 1.0
CB A:ASP130 4.8 44.5 1.0

Chlorine binding site 2 out of 3 in 7kib

Go back to Chlorine Binding Sites List in 7kib
Chlorine binding site 2 out of 3 in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl711

b:92.7
occ:1.00
N A:GLN511 3.0 49.5 1.0
CA A:HIS510 3.6 45.1 1.0
C A:HIS510 3.7 50.9 1.0
CB A:GLN511 3.8 50.1 1.0
O A:PHE509 3.9 51.0 1.0
CA A:GLN511 3.9 49.1 1.0
CD2 A:HIS510 4.1 48.5 1.0
N A:HIS510 4.4 45.8 1.0
O A:HOH1081 4.5 67.2 1.0
C A:PHE509 4.5 51.0 1.0
CZ A:PHE509 4.6 47.0 1.0
CE2 A:PHE509 4.6 49.9 1.0
O A:GLN511 4.7 50.1 1.0
CB A:HIS510 4.8 45.2 1.0
C A:GLN511 4.8 51.2 1.0
CG A:HIS510 4.8 48.0 1.0
CE1 A:PHE509 4.9 47.4 1.0
CD2 A:PHE509 4.9 47.4 1.0
O A:HIS510 4.9 49.2 1.0

Chlorine binding site 3 out of 3 in 7kib

Go back to Chlorine Binding Sites List in 7kib
Chlorine binding site 3 out of 3 in the PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl712

b:83.0
occ:1.00
O A:LEU308 3.9 55.5 1.0
OG A:SER310 4.1 68.5 1.0
CE2 A:TYR502 4.2 41.0 1.0
N A:SER310 4.2 49.1 1.0
CD2 A:TYR502 4.4 41.1 1.0
C A:LEU308 4.4 54.9 1.0
CA A:GLN309 4.5 48.4 1.0
C A:GLN309 4.5 52.0 1.0
SG A:CYS487 4.7 54.1 1.0
N A:GLN309 4.7 49.3 1.0
CB A:LEU308 4.8 50.0 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: Sun Jul 13 03:20:17 2025

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