Zinc in PDB 5vgi: Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352

The structure of Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352, PDB code: 5vgi was solved by D.J.Hosfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.318, 101.594, 141.893, 90.00, 99.64, 90.00
R / Rfree (%)	18.9 / 24.9

The structure of Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 also contains other interesting chemical elements:

Nickel

(Ni)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 (pdb code 5vgi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352, PDB code: 5vgi:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352


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 KDM4 with the Small Molecule Inhibitor QC6352 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:38.7 occ:1.00 SG A:CYS306 2.2 38.5 1.0 SG A:CYS234 2.2 35.3 1.0 NE2 A:HIS240 2.2 33.3 1.0 SG A:CYS308 2.5 39.2 1.0 CE1 A:HIS240 3.1 33.7 1.0 CB A:CYS234 3.2 41.3 1.0 CB A:CYS308 3.2 50.6 1.0 CD2 A:HIS240 3.3 29.1 1.0 CB A:CYS306 3.4 40.9 1.0 N A:CYS308 3.5 56.0 1.0 CA A:CYS308 3.8 54.7 1.0 CA A:CYS306 3.8 39.9 1.0 N A:SER307 4.0 48.3 1.0 C A:CYS306 4.1 42.2 1.0 CD A:ARG309 4.1 57.3 1.0 N A:ARG309 4.2 55.9 1.0 ND1 A:HIS240 4.3 31.9 1.0 C A:CYS308 4.4 57.1 1.0 CG A:HIS240 4.4 29.0 1.0 CA A:CYS234 4.5 44.5 1.0 C A:SER307 4.5 59.6 1.0 NE A:ARG309 4.6 59.0 1.0 O A:ALA236 4.8 28.2 1.0 CA A:PHE237 4.9 31.0 1.0 CA A:SER307 4.9 53.1 1.0 O A:CYS306 4.9 47.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352


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 KDM4 with the Small Molecule Inhibitor QC6352 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:42.5 occ:1.00 NE2 B:HIS240 2.1 34.9 1.0 SG B:CYS234 2.2 37.7 1.0 SG B:CYS306 2.2 41.4 1.0 SG B:CYS308 2.5 43.4 1.0 CE1 B:HIS240 3.0 34.6 1.0 CD2 B:HIS240 3.2 32.4 1.0 CB B:CYS306 3.2 42.4 1.0 CB B:CYS234 3.3 42.9 1.0 N B:CYS308 3.4 55.0 1.0 CB B:CYS308 3.6 52.8 1.0 CA B:CYS306 3.7 43.3 1.0 N B:SER307 3.9 46.4 1.0 CA B:CYS308 4.0 55.3 1.0 C B:CYS306 4.0 45.0 1.0 ND1 B:HIS240 4.1 32.4 1.0 CG B:HIS240 4.2 32.2 1.0 C B:CYS308 4.5 57.8 1.0 C B:SER307 4.5 54.2 1.0 N B:ARG309 4.5 60.6 1.0 CA B:CYS234 4.6 47.3 1.0 CG B:ARG309 4.7 58.5 1.0 O B:ALA236 4.7 34.3 1.0 CA B:SER307 4.8 51.7 1.0 NE B:ARG309 4.8 59.2 1.0 CD B:ARG309 4.8 58.2 1.0 O B:CYS306 4.9 39.6 1.0 CA B:PHE237 4.9 33.0 1.0 C B:ALA236 5.0 35.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352


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 KDM4 with the Small Molecule Inhibitor QC6352 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:29.7 occ:1.00 NE2 C:HIS240 2.0 26.5 1.0 SG C:CYS306 2.2 28.4 1.0 SG C:CYS234 2.3 27.5 1.0 SG C:CYS308 2.5 30.9 1.0 CE1 C:HIS240 3.0 26.3 1.0 CD2 C:HIS240 3.1 25.9 1.0 CB C:CYS306 3.2 30.5 1.0 CB C:CYS234 3.3 33.1 1.0 CB C:CYS308 3.6 36.6 1.0 N C:CYS308 3.7 44.4 1.0 CA C:CYS306 3.9 31.1 1.0 N C:SER307 4.0 39.4 1.0 ND1 C:HIS240 4.1 25.1 1.0 CA C:CYS308 4.2 42.9 1.0 C C:CYS306 4.2 35.1 1.0 CG C:HIS240 4.2 27.2 1.0 N C:ARG309 4.6 48.5 1.0 CA C:CYS234 4.6 39.9 1.0 C C:SER307 4.7 49.1 1.0 C C:CYS308 4.7 47.5 1.0 O C:ALA236 4.8 28.9 1.0 CD C:ARG309 4.8 51.6 1.0 CA C:PHE237 4.9 26.5 1.0 CA C:SER307 4.9 47.4 1.0 NE C:ARG309 4.9 55.1 1.0 CG C:ARG309 4.9 50.9 1.0 O C:CYS306 5.0 31.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352


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 KDM4 with the Small Molecule Inhibitor QC6352 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:42.4 occ:1.00 NE2 D:HIS240 2.1 40.6 1.0 SG D:CYS306 2.1 39.5 1.0 SG D:CYS234 2.3 40.7 1.0 SG D:CYS308 2.4 41.2 1.0 CE1 D:HIS240 2.9 40.1 1.0 CB D:CYS234 3.2 46.0 1.0 CD2 D:HIS240 3.2 37.7 1.0 CB D:CYS308 3.3 45.5 1.0 CB D:CYS306 3.4 41.5 1.0 N D:CYS308 3.6 53.3 1.0 CA D:CYS306 3.9 44.2 1.0 CA D:CYS308 3.9 51.8 1.0 N D:SER307 4.0 50.5 1.0 ND1 D:HIS240 4.1 39.9 1.0 C D:CYS306 4.2 46.8 1.0 CG D:HIS240 4.3 37.8 1.0 N D:ARG309 4.3 57.6 1.0 C D:CYS308 4.4 54.9 1.0 CA D:CYS234 4.6 48.8 1.0 C D:SER307 4.7 54.8 1.0 NE D:ARG309 4.9 59.1 1.0 O D:ALA236 4.9 33.0 1.0 CA D:PHE237 4.9 35.1 1.0 CA D:SER307 5.0 55.3 1.0

Y.K.Chen, T.Bonaldi, A.Cuomo, J.R.Del Rosario, D.J.Hosfield, T.Kanouni, S.C.Kao, C.Lai, N.A.Lobo, J.Matuszkiewicz, A.Mcgeehan, S.M.O'connell, L.Shi, J.A.Stafford, R.K.Stansfield, J.M.Veal, M.S.Weiss, N.Y.Yuen, M.B.Wallace. Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models. Acs Med Chem Lett V. 8 869 2017.
ISSN: ISSN 1948-5875
PubMed: 28835804
DOI: 10.1021/ACSMEDCHEMLETT.7B00220