Chlorine in PDB 5f3i: Crystal Structure of Human KDM4A in Complex with Compound 54J

The structure of Crystal Structure of Human KDM4A in Complex with Compound 54J, PDB code: 5f3i was solved by Y.-V.Le Bihan, S.Dempster, 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)	48.29 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.794, 101.566, 142.328, 90.00, 99.42, 90.00
R / Rfree (%)	16.9 / 21.3

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

Zinc

(Zn)

8 atoms

The binding sites of Chlorine atom in the Crystal Structure of Human KDM4A in Complex with Compound 54J (pdb code 5f3i). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Human KDM4A in Complex with Compound 54J, PDB code: 5f3i:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of Human KDM4A in Complex with Compound 54J


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 54J within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:92.1 occ:0.80 CL1 B:5UJ403 0.0 92.1 0.8 C4 B:5UJ403 1.7 90.1 0.8 C5 B:5UJ403 2.7 91.3 0.8 C3 B:5UJ403 2.7 86.8 0.8 CG2 B:VAL313 3.6 77.5 1.0 C B:5UJ403 4.0 93.3 0.8 C2 B:5UJ403 4.0 84.3 0.8 O B:HOH671 4.2 75.7 1.0 C1 B:5UJ403 4.5 89.7 0.8 CB B:VAL313 4.6 77.0 1.0 CA B:VAL313 4.8 74.8 1.0 N B:VAL313 4.9 77.9 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of Human KDM4A in Complex with Compound 54J


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human KDM4A in Complex with Compound 54J within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:97.6 occ:0.80 CL B:5UJ403 0.0 97.6 0.8 C B:5UJ403 1.7 93.3 0.8 C5 B:5UJ403 2.7 91.3 0.8 C1 B:5UJ403 2.7 89.7 0.8 C4 B:5UJ403 4.0 90.1 0.8 C2 B:5UJ403 4.0 84.3 0.8 C3 B:5UJ403 4.5 86.8 0.8 OH B:TYR175 4.5 76.9 1.0 OD1 B:ASN137 4.6 78.5 1.0 ND2 B:ASN137 4.6 81.6 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of Human KDM4A in Complex with Compound 54J


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human KDM4A in Complex with Compound 54J within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl403 b:0.2 occ:0.82 CL1 C:5UJ403 0.0 0.2 0.8 C4 C:5UJ403 1.7 0.1 0.8 C5 C:5UJ403 2.7 0.7 0.8 C3 C:5UJ403 2.7 0.4 0.8 C C:MET312 3.8 91.6 1.0 O C:MET312 3.8 92.5 1.0 N C:MET312 3.9 92.4 1.0 C C:5UJ403 4.0 0.0 0.8 C2 C:5UJ403 4.0 0.1 0.8 CG2 C:VAL313 4.0 84.6 1.0 CA C:MET312 4.2 89.5 1.0 N C:VAL313 4.2 85.2 1.0 O C:HOH573 4.5 75.0 1.0 C1 C:5UJ403 4.5 0.1 0.8 CA C:VAL313 4.7 83.8 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of Human KDM4A in Complex with Compound 54J


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human KDM4A in Complex with Compound 54J within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl403 b:1.0 occ:0.82 CL C:5UJ403 0.0 1.0 0.8 C C:5UJ403 1.7 0.0 0.8 C5 C:5UJ403 2.7 0.7 0.8 C1 C:5UJ403 2.7 0.1 0.8 C4 C:5UJ403 4.0 0.1 0.8 C2 C:5UJ403 4.0 0.1 0.8 C3 C:5UJ403 4.5 0.4 0.8 OH C:TYR175 4.7 80.8 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of Human KDM4A in Complex with Compound 54J


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human KDM4A in Complex with Compound 54J within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl404 b:0.2 occ:1.00 NH1 C:ARG294 3.8 0.4 1.0 NE C:ARG294 3.9 0.3 1.0 CG C:PRO348 4.0 85.5 1.0 CZ C:ARG294 4.3 0.9 1.0 CB C:ARG294 4.3 64.1 1.0 O C:ARG294 4.7 67.2 1.0 CB C:PRO348 4.7 82.4 1.0 O C:PHE324 4.8 0.5 1.0 CG C:ARG294 4.8 77.6 1.0 CD C:ARG294 5.0 94.8 1.0 CD C:PRO348 5.0 78.8 1.0

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