Zinc in PDB 5f3c: Crystal Structure of Human KDM4A in Complex with Compound 52D

The structure of Crystal Structure of Human KDM4A in Complex with Compound 52D, PDB code: 5f3c 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)	49.35 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.101, 101.725, 142.758, 90.00, 99.53, 90.00
R / Rfree (%)	16.1 / 19.6

The structure of Crystal Structure of Human KDM4A in Complex with Compound 52D also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Human KDM4A in Complex with Compound 52D (pdb code 5f3c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human KDM4A in Complex with Compound 52D, PDB code: 5f3c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 52D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human KDM4A in Complex with Compound 52D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:40.8 occ:0.82 O A:HOH504 2.1 52.7 1.0 OE2 A:GLU190 2.1 46.8 1.0 NE2 A:HIS188 2.1 42.1 1.0 NE2 A:HIS276 2.1 40.2 1.0 N5 A:5U8403 2.1 87.4 0.6 N5 A:5U8403 2.2 26.8 0.4 N2 A:5U8403 2.3 32.5 0.4 N2 A:5U8403 2.3 87.1 0.6 N1 A:5U8403 3.0 32.3 0.4 CE1 A:HIS276 3.0 40.8 1.0 N1 A:5U8403 3.0 87.4 0.6 C13 A:5U8403 3.0 87.3 0.6 CE1 A:HIS188 3.0 41.5 1.0 C13 A:5U8403 3.1 25.2 0.4 CD2 A:HIS188 3.1 42.4 1.0 C19 A:5U8403 3.1 86.8 0.6 CD A:GLU190 3.1 59.9 1.0 C19 A:5U8403 3.2 24.1 0.4 CD2 A:HIS276 3.2 39.4 1.0 C12 A:5U8403 3.4 35.4 0.4 C12 A:5U8403 3.5 86.8 0.6 OE1 A:GLU190 3.5 51.0 1.0 ND1 A:HIS188 4.1 42.0 1.0 ND1 A:HIS276 4.2 41.7 1.0 CG A:HIS188 4.2 40.7 1.0 C11 A:5U8403 4.2 33.8 0.4 C11 A:5U8403 4.2 86.7 0.6 O A:HOH628 4.3 65.7 1.0 CG A:HIS276 4.3 38.6 1.0 C14 A:5U8403 4.4 87.8 0.6 C18 A:5U8403 4.4 87.3 0.6 CG A:GLU190 4.4 44.2 1.0 C14 A:5U8403 4.4 25.5 0.4 C10 A:5U8403 4.4 37.8 0.4 C18 A:5U8403 4.5 24.2 0.4 C10 A:5U8403 4.5 86.2 0.6 O A:HOH561 4.5 77.8 1.0 OG A:SER196 4.5 48.2 1.0 C17 A:5U8403 4.9 88.3 0.6 C17 A:5U8403 5.0 25.4 0.4

Zinc binding site 2 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 52D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human KDM4A in Complex with Compound 52D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:50.0 occ:0.70 NE2 A:HIS240 2.0 57.1 1.0 SG A:CYS306 2.1 58.8 1.0 SG A:CYS234 2.2 60.5 1.0 SG A:CYS308 2.4 69.3 1.0 CE1 A:HIS240 2.9 56.4 1.0 CB A:CYS234 3.0 59.5 1.0 CD2 A:HIS240 3.2 55.2 1.0 CB A:CYS306 3.5 54.9 1.0 CB A:CYS308 3.5 68.3 1.0 N A:CYS308 3.7 67.9 1.0 CA A:CYS306 4.0 57.4 1.0 CA A:CYS308 4.1 68.9 1.0 ND1 A:HIS240 4.1 55.6 1.0 N A:SER307 4.1 65.9 1.0 CG A:HIS240 4.2 53.0 1.0 C A:CYS306 4.3 67.3 1.0 CA A:CYS234 4.4 62.8 1.0 C A:CYS308 4.6 73.1 1.0 CD A:ARG309 4.7 80.3 1.0 N A:ARG309 4.7 68.5 1.0 CA A:PHE237 4.7 49.3 1.0 O A:ALA236 4.7 52.8 1.0 C A:SER307 4.7 74.4 1.0 NE A:ARG309 4.8 85.5 1.0 C A:ALA236 4.9 56.2 1.0 CG A:ARG309 4.9 82.4 1.0 N A:PHE237 4.9 51.4 1.0 O A:HOH569 4.9 60.0 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 52D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human KDM4A in Complex with Compound 52D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:40.0 occ:0.84 NE2 B:HIS188 2.0 38.4 1.0 O B:HOH505 2.0 46.9 1.0 N2 B:5U8403 2.0 43.2 0.5 OE2 B:GLU190 2.1 48.9 1.0 NE2 B:HIS276 2.2 38.1 1.0 N5 B:5U8403 2.2 70.2 0.5 N2 B:5U8403 2.2 69.2 0.5 N5 B:5U8403 2.3 31.2 0.5 CE1 B:HIS188 2.9 38.1 1.0 N1 B:5U8403 2.9 42.8 0.5 N1 B:5U8403 3.0 70.1 0.5 C13 B:5U8403 3.0 36.1 0.5 CE1 B:HIS276 3.0 38.1 1.0 CD2 B:HIS188 3.0 40.0 1.0 C13 B:5U8403 3.0 71.1 0.5 CD B:GLU190 3.1 59.1 1.0 C12 B:5U8403 3.1 44.7 0.5 C19 B:5U8403 3.2 70.1 0.5 CD2 B:HIS276 3.3 36.9 1.0 C19 B:5U8403 3.3 31.2 0.5 C12 B:5U8403 3.3 68.7 0.5 OE1 B:GLU190 3.6 59.6 1.0 ND1 B:HIS188 4.0 39.8 1.0 C11 B:5U8403 4.1 45.9 0.5 CG B:HIS188 4.1 38.6 1.0 C11 B:5U8403 4.2 69.2 0.5 ND1 B:HIS276 4.2 38.5 1.0 C10 B:5U8403 4.3 48.5 0.5 CG B:HIS276 4.3 36.3 1.0 CG B:GLU190 4.4 46.5 1.0 C10 B:5U8403 4.4 68.8 0.5 C14 B:5U8403 4.4 35.5 0.5 C14 B:5U8403 4.4 72.4 0.5 C18 B:5U8403 4.5 71.0 0.5 O B:HOH611 4.6 61.2 1.0 OG B:SER196 4.6 46.8 1.0 C18 B:5U8403 4.6 32.1 0.5 O B:HOH508 4.7 75.6 1.0 C17 B:5U8403 5.0 72.6 0.5

Zinc binding site 4 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 52D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human KDM4A in Complex with Compound 52D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:52.3 occ:0.75 NE2 B:HIS240 2.1 57.9 1.0 SG B:CYS306 2.1 60.3 1.0 SG B:CYS234 2.2 63.4 1.0 SG B:CYS308 2.4 79.2 1.0 CE1 B:HIS240 3.0 57.5 1.0 CB B:CYS234 3.1 61.7 1.0 CD2 B:HIS240 3.2 55.6 1.0 CB B:CYS306 3.5 55.4 1.0 CB B:CYS308 3.6 80.4 1.0 N B:CYS308 3.6 79.5 1.0 N B:SER307 4.0 72.7 1.0 CA B:CYS306 4.0 58.2 1.0 CA B:CYS308 4.1 81.9 1.0 ND1 B:HIS240 4.2 56.1 1.0 CG B:HIS240 4.3 52.7 1.0 C B:CYS306 4.4 70.8 1.0 CA B:CYS234 4.5 64.6 1.0 C B:CYS308 4.6 89.2 1.0 N B:ARG309 4.7 88.0 1.0 CD B:ARG309 4.7 88.0 1.0 C B:SER307 4.7 85.3 1.0 O B:ALA236 4.7 49.6 1.0 O B:HOH703 4.8 61.5 1.0 CA B:PHE237 4.8 48.2 1.0 O B:HOH687 4.9 56.5 1.0 CA B:SER307 4.9 77.1 1.0 C B:ALA236 5.0 53.4 1.0 NE B:ARG309 5.0 92.7 1.0 O B:HOH589 5.0 68.4 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 52D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human KDM4A in Complex with Compound 52D within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:46.0 occ:0.94 N2 C:5U8403 2.0 37.2 0.4 NE2 C:HIS188 2.1 43.3 1.0 O C:HOH502 2.1 76.3 1.0 N5 C:5U8403 2.1 84.9 0.6 N2 C:5U8403 2.1 80.6 0.6 OE2 C:GLU190 2.2 54.5 1.0 N5 C:5U8403 2.2 32.5 0.4 NE2 C:HIS276 2.2 43.2 1.0 N1 C:5U8403 2.9 37.3 0.4 N1 C:5U8403 2.9 81.9 0.6 C13 C:5U8403 3.0 83.7 0.6 C13 C:5U8403 3.0 32.7 0.4 CD2 C:HIS188 3.0 44.9 1.0 CE1 C:HIS188 3.1 42.8 1.0 C12 C:5U8403 3.1 36.7 0.4 C19 C:5U8403 3.1 84.4 0.6 CE1 C:HIS276 3.1 43.4 1.0 CD C:GLU190 3.2 58.8 1.0 C19 C:5U8403 3.2 29.0 0.4 CD2 C:HIS276 3.3 41.9 1.0 C12 C:5U8403 3.3 79.4 0.6 OE1 C:GLU190 3.5 50.3 1.0 C11 C:5U8403 4.1 37.3 0.4 C11 C:5U8403 4.1 80.0 0.6 CG C:HIS188 4.2 43.7 1.0 ND1 C:HIS188 4.2 44.1 1.0 C10 C:5U8403 4.3 37.4 0.4 ND1 C:HIS276 4.3 43.4 1.0 C14 C:5U8403 4.3 84.7 0.6 CG C:HIS276 4.3 40.7 1.0 C14 C:5U8403 4.4 28.5 0.4 C10 C:5U8403 4.4 78.7 0.6 C18 C:5U8403 4.4 84.7 0.6 O C:HOH615 4.4 59.9 1.0 CG C:GLU190 4.5 53.3 1.0 C18 C:5U8403 4.5 28.0 0.4 O C:HOH517 4.6 69.9 1.0 OG C:SER196 4.6 53.7 1.0 C17 C:5U8403 4.9 85.3 0.6 C17 C:5U8403 4.9 28.7 0.4

Zinc binding site 6 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 52D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human KDM4A in Complex with Compound 52D within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:55.5 occ:0.83 NE2 C:HIS240 2.1 59.8 1.0 SG C:CYS306 2.1 63.2 1.0 SG C:CYS234 2.2 71.1 1.0 SG C:CYS308 2.5 84.2 1.0 CE1 C:HIS240 3.0 59.2 1.0 CD2 C:HIS240 3.1 58.2 1.0 CB C:CYS234 3.1 68.0 1.0 CB C:CYS306 3.3 57.4 1.0 CB C:CYS308 3.5 85.3 1.0 N C:CYS308 3.6 82.4 1.0 CA C:CYS306 3.9 60.9 1.0 N C:SER307 3.9 75.6 1.0 CA C:CYS308 4.0 85.8 1.0 ND1 C:HIS240 4.2 58.3 1.0 CG C:HIS240 4.2 56.0 1.0 C C:CYS306 4.2 73.1 1.0 N C:ARG309 4.4 91.3 1.0 C C:CYS308 4.4 94.2 1.0 CA C:CYS234 4.4 70.5 1.0 CD C:ARG309 4.6 85.7 1.0 C C:SER307 4.7 86.4 1.0 CG C:ARG309 4.8 90.9 1.0 NE C:ARG309 4.8 87.0 1.0 O C:ALA236 4.8 59.4 1.0 CA C:SER307 4.9 80.0 1.0 CA C:PHE237 4.9 52.5 1.0 O C:HOH690 5.0 68.8 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 52D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human KDM4A in Complex with Compound 52D within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:36.6 occ:0.86 OE2 D:GLU190 2.0 36.3 1.0 NE2 D:HIS188 2.1 36.0 1.0 N5 D:5U8403 2.1 32.4 0.8 N2 D:5U8403 2.2 38.2 0.8 NE2 D:HIS276 2.2 33.0 1.0 N1 D:5U8403 2.9 36.0 0.8 C13 D:5U8403 2.9 32.8 0.8 CE1 D:HIS188 2.9 35.9 1.0 CE1 D:HIS276 3.0 32.7 1.0 CD D:GLU190 3.1 41.1 1.0 C19 D:5U8403 3.1 32.3 0.8 CD2 D:HIS188 3.2 36.0 1.0 CD2 D:HIS276 3.3 33.1 1.0 C12 D:5U8403 3.3 40.1 0.8 OE1 D:GLU190 3.4 45.1 1.0 ND1 D:HIS188 4.1 36.7 1.0 C11 D:5U8403 4.2 39.6 0.8 ND1 D:HIS276 4.2 33.7 1.0 CG D:HIS188 4.2 35.0 1.0 C14 D:5U8403 4.3 32.0 0.8 CG D:HIS276 4.3 31.9 1.0 CG D:GLU190 4.4 35.5 1.0 C10 D:5U8403 4.4 44.1 0.8 C18 D:5U8403 4.4 32.0 0.8 O D:HOH590 4.5 46.4 1.0 OG D:SER196 4.6 44.2 1.0 C17 D:5U8403 4.9 32.9 0.8

Zinc binding site 8 out of 8 in the Crystal Structure of Human KDM4A in Complex with Compound 52D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human KDM4A in Complex with Compound 52D within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:43.8 occ:0.93 NE2 D:HIS240 2.1 42.7 1.0 SG D:CYS306 2.2 46.9 1.0 SG D:CYS234 2.3 44.4 1.0 SG D:CYS308 2.4 55.2 1.0 CE1 D:HIS240 3.1 43.1 1.0 CD2 D:HIS240 3.1 42.6 1.0 CB D:CYS234 3.2 42.4 1.0 CB D:CYS306 3.4 42.2 1.0 N D:CYS308 3.6 56.9 1.0 CB D:CYS308 3.6 54.6 1.0 CA D:CYS306 3.9 43.0 1.0 N D:SER307 3.9 50.4 1.0 CA D:CYS308 4.1 56.8 1.0 C D:CYS306 4.2 49.9 1.0 CG D:HIS240 4.2 41.7 1.0 ND1 D:HIS240 4.2 44.2 1.0 N D:ARG309 4.4 66.5 1.0 CA D:CYS234 4.5 45.3 1.0 C D:CYS308 4.6 67.3 1.0 CG D:ARG309 4.6 64.2 1.0 CD D:ARG309 4.6 66.5 1.0 O D:HOH779 4.6 65.0 1.0 C D:SER307 4.7 62.4 1.0 O D:ALA236 4.7 40.4 1.0 CA D:PHE237 4.9 36.9 1.0 CA D:SER307 4.9 53.6 1.0 C D:ALA236 5.0 42.9 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