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Chlorine in PDB 5kr7: KDM4C Bound to Pyrazolo-Pyrimidine Scaffold

Protein crystallography data

The structure of KDM4C Bound to Pyrazolo-Pyrimidine Scaffold, PDB code: 5kr7 was solved by S.F.Bellon, F.Poy, J.W.Setser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.82 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.817, 89.876, 100.011, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.4

Other elements in 5kr7:

The structure of KDM4C Bound to Pyrazolo-Pyrimidine Scaffold also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the KDM4C Bound to Pyrazolo-Pyrimidine Scaffold (pdb code 5kr7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the KDM4C Bound to Pyrazolo-Pyrimidine Scaffold, PDB code: 5kr7:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5kr7

Go back to Chlorine Binding Sites List in 5kr7
Chlorine binding site 1 out of 2 in the KDM4C Bound to Pyrazolo-Pyrimidine Scaffold


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of KDM4C Bound to Pyrazolo-Pyrimidine Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:18.7
occ:1.00
O A:HOH687 3.1 24.9 1.0
NE1 A:TRP183 3.2 13.8 1.0
O A:HOH611 3.2 17.9 1.0
CG A:ASN126 3.6 17.9 1.0
CB A:ASN126 3.7 15.8 1.0
CE2 A:TRP183 3.9 14.7 1.0
CZ2 A:TRP183 3.9 15.2 1.0
ND2 A:ASN126 3.9 16.8 1.0
CG A:PRO111 4.0 15.5 1.0
OD1 A:ASN126 4.1 17.0 1.0
CD A:PRO111 4.2 14.9 1.0
CB A:PRO111 4.3 15.6 1.0
CD1 A:TRP183 4.3 13.4 1.0
CD A:LYS184 4.7 15.4 1.0
O A:HOH640 4.7 17.9 1.0
O A:LYS122 4.8 15.9 1.0
O A:HOH668 4.9 19.5 1.0

Chlorine binding site 2 out of 2 in 5kr7

Go back to Chlorine Binding Sites List in 5kr7
Chlorine binding site 2 out of 2 in the KDM4C Bound to Pyrazolo-Pyrimidine Scaffold


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of KDM4C Bound to Pyrazolo-Pyrimidine Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:18.6
occ:1.00
O B:HOH609 3.1 19.0 1.0
O B:HOH685 3.2 22.9 1.0
NE1 B:TRP183 3.3 13.1 1.0
CG B:ASN126 3.6 19.1 1.0
CB B:ASN126 3.6 17.0 1.0
ND2 B:ASN126 3.8 18.5 1.0
CZ2 B:TRP183 3.8 14.3 1.0
CE2 B:TRP183 3.9 13.6 1.0
CG B:PRO111 4.0 15.9 1.0
OD1 B:ASN126 4.1 20.8 1.0
CD B:PRO111 4.2 15.0 1.0
CB B:PRO111 4.3 16.4 1.0
CD1 B:TRP183 4.4 13.1 1.0
O B:HOH548 4.5 25.3 1.0
CD B:LYS184 4.7 15.5 1.0
O B:HOH643 4.7 20.8 1.0
O B:LYS122 4.8 17.0 1.0

Reference:

V.S.Gehling, S.F.Bellon, J.C.Harmange, Y.Leblanc, F.Poy, S.Odate, S.Buker, F.Lan, S.Arora, K.E.Williamson, P.Sandy, R.T.Cummings, C.M.Bailey, L.Bergeron, W.Mao, A.Gustafson, Y.Liu, E.Vanderporten, J.E.Audia, P.Trojer, B.K.Albrecht. Identification of Potent, Selective KDM5 Inhibitors. Bioorg.Med.Chem.Lett. V. 26 4350 2016.
ISSN: ESSN 1464-3405
PubMed: 27476424
DOI: 10.1016/J.BMCL.2016.07.026
Page generated: Sat Dec 12 11:57:18 2020

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