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Chlorine in PDB 5f3e: Crystal Structure of Human KDM4A in Complex with Compound 54A

Protein crystallography data

The structure of Crystal Structure of Human KDM4A in Complex with Compound 54A, PDB code: 5f3e was solved by Y.-V.Le Bihan, I.M.Westwood, R.L.M.Van Montfort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.62 / 2.16
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.912, 101.626, 142.412, 90.00, 99.41, 90.00
R / Rfree (%) 16.2 / 21

Other elements in 5f3e:

The structure of Crystal Structure of Human KDM4A in Complex with Compound 54A also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human KDM4A in Complex with Compound 54A (pdb code 5f3e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Crystal Structure of Human KDM4A in Complex with Compound 54A, PDB code: 5f3e:

Chlorine binding site 1 out of 1 in 5f3e

Go back to Chlorine Binding Sites List in 5f3e
Chlorine binding site 1 out of 1 in the Crystal Structure of Human KDM4A in Complex with Compound 54A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human KDM4A in Complex with Compound 54A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:78.2
occ:0.77
CL B:5UO403 0.0 78.2 0.8
C14 B:5UO403 1.7 72.7 0.8
C15 B:5UO403 2.7 70.9 0.8
C13 B:5UO403 2.7 67.9 0.8
C16 B:5UO403 4.0 67.4 0.8
C12 B:5UO403 4.0 65.7 0.8
C11 B:5UO403 4.5 63.3 0.8

Reference:

V.Bavetsias, R.M.Lanigan, G.F.Ruda, B.Atrash, M.G.Mclaughlin, A.Tumber, N.Y.Mok, Y.V.Le Bihan, S.Dempster, K.J.Boxall, F.Jeganathan, S.B.Hatch, P.Savitsky, S.Velupillai, T.Krojer, K.S.England, J.Sejberg, C.Thai, A.Donovan, A.Pal, G.Scozzafava, J.M.Bennett, A.Kawamura, C.Johansson, A.Szykowska, C.Gileadi, N.A.Burgess-Brown, F.Von Delft, U.Oppermann, Z.Walters, J.Shipley, F.I.Raynaud, S.M.Westaway, R.K.Prinjha, O.Fedorov, R.Burke, C.J.Schofield, I.M.Westwood, C.Bountra, S.Muller, R.L.Van Montfort, P.E.Brennan, J.Blagg. 8-Substituted Pyrido[3,4-D]Pyrimidin-4(3H)-One Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J.Med.Chem. V. 59 1388 2016.
ISSN: ISSN 0022-2623
PubMed: 26741168
DOI: 10.1021/ACS.JMEDCHEM.5B01635
Page generated: Sat Dec 12 11:42:46 2020

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