Nickel in PDB 6cg1: Crystal Structure of KDM4A with Compound 14

The structure of Crystal Structure of KDM4A with Compound 14, PDB code: 6cg1 was solved by D.J.Hosfield, Z.Nie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	140.38 / 2.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.582, 101.651, 142.430, 90.00, 99.73, 90.00
R / Rfree (%)	17.5 / 24

The structure of Crystal Structure of KDM4A with Compound 14 also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Zinc	(Zn)	4 atoms

The binding sites of Nickel atom in the Crystal Structure of KDM4A with Compound 14 (pdb code 6cg1). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of KDM4A with Compound 14, PDB code: 6cg1:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of KDM4A with Compound 14


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of KDM4A with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:24.8 occ:1.00 O A:HOH621 1.9 23.4 1.0 NE2 A:HIS188 2.0 19.2 1.0 OE2 A:GLU190 2.0 31.8 1.0 O A:HOH673 2.1 22.5 1.0 N4 A:QC1503 2.1 29.8 1.0 NE2 A:HIS276 2.1 19.2 1.0 CE1 A:HIS188 3.0 23.7 1.0 C3 A:QC1503 3.0 32.8 1.0 C5 A:QC1503 3.0 28.8 1.0 CD2 A:HIS188 3.0 21.4 1.0 CE1 A:HIS276 3.1 21.4 1.0 CD A:GLU190 3.1 32.8 1.0 CD2 A:HIS276 3.2 21.0 1.0 OE1 A:GLU190 3.5 31.9 1.0 ND1 A:HIS188 4.1 20.4 1.0 CG A:HIS188 4.1 21.5 1.0 ND1 A:HIS276 4.2 21.4 1.0 CG A:HIS276 4.3 20.8 1.0 C6 A:QC1503 4.3 32.1 1.0 C2 A:QC1503 4.4 30.4 1.0 O A:HOH743 4.5 65.2 1.0 OG A:SER196 4.5 31.5 1.0 CG A:GLU190 4.5 29.2 1.0 O A:HOH678 4.9 55.3 1.0 C1 A:QC1503 4.9 33.5 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of KDM4A with Compound 14


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of KDM4A with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:26.0 occ:1.00 O B:HOH650 2.0 31.2 1.0 O B:HOH649 2.0 23.8 1.0 OE2 B:GLU190 2.1 28.0 1.0 N4 B:QC1503 2.2 25.4 1.0 NE2 B:HIS188 2.2 24.1 1.0 NE2 B:HIS276 2.2 21.7 1.0 C3 B:QC1503 3.0 25.1 1.0 CE1 B:HIS188 3.0 27.3 1.0 C5 B:QC1503 3.1 25.0 1.0 CE1 B:HIS276 3.1 27.9 1.0 CD B:GLU190 3.1 27.4 1.0 CD2 B:HIS188 3.2 27.2 1.0 CD2 B:HIS276 3.2 25.4 1.0 OE1 B:GLU190 3.5 24.2 1.0 ND1 B:HIS188 4.1 25.8 1.0 ND1 B:HIS276 4.2 24.0 1.0 CG B:HIS188 4.2 25.8 1.0 CG B:HIS276 4.3 22.1 1.0 C2 B:QC1503 4.4 27.7 1.0 C6 B:QC1503 4.4 27.3 1.0 CG B:GLU190 4.5 26.8 1.0 OG B:SER196 4.5 34.1 1.0 C1 B:QC1503 4.9 30.3 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of KDM4A with Compound 14


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of KDM4A with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni501 b:25.3 occ:1.00 N4 C:QC1503 2.1 26.8 1.0 NE2 C:HIS188 2.1 19.6 1.0 O C:HOH612 2.2 25.9 1.0 NE2 C:HIS276 2.2 16.8 1.0 OE2 C:GLU190 2.2 25.6 1.0 C5 C:QC1503 2.9 29.0 1.0 C3 C:QC1503 3.0 29.7 1.0 CE1 C:HIS188 3.0 20.8 1.0 CD C:GLU190 3.1 24.3 1.0 CE1 C:HIS276 3.1 18.7 1.0 CD2 C:HIS188 3.1 20.8 1.0 CD2 C:HIS276 3.2 18.2 1.0 OE1 C:GLU190 3.3 23.6 1.0 ND1 C:HIS188 4.2 19.9 1.0 CG C:HIS188 4.2 20.3 1.0 ND1 C:HIS276 4.2 18.4 1.0 C6 C:QC1503 4.3 30.2 1.0 CG C:HIS276 4.3 20.4 1.0 C2 C:QC1503 4.3 30.4 1.0 CG C:GLU190 4.4 26.4 1.0 OG C:SER196 4.5 27.1 1.0 O C:HOH718 4.8 44.7 1.0 C1 C:QC1503 4.8 29.5 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of KDM4A with Compound 14


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of KDM4A with Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni501 b:21.5 occ:1.00 O D:HOH639 1.9 26.7 1.0 O D:HOH635 2.0 24.1 1.0 NE2 D:HIS276 2.1 20.6 1.0 N4 D:QC1503 2.1 19.6 1.0 NE2 D:HIS188 2.2 22.4 1.0 OE2 D:GLU190 2.3 23.4 1.0 CE1 D:HIS188 2.9 23.7 1.0 CE1 D:HIS276 3.0 22.6 1.0 C3 D:QC1503 3.0 21.0 1.0 C5 D:QC1503 3.1 24.8 1.0 CD2 D:HIS276 3.1 21.5 1.0 CD2 D:HIS188 3.3 23.5 1.0 CD D:GLU190 3.3 23.8 1.0 OE1 D:GLU190 3.8 25.1 1.0 ND1 D:HIS188 4.0 21.6 1.0 ND1 D:HIS276 4.1 19.7 1.0 CG D:HIS276 4.2 19.7 1.0 CG D:HIS188 4.3 20.5 1.0 C2 D:QC1503 4.4 24.1 1.0 C6 D:QC1503 4.4 23.8 1.0 OG D:SER196 4.4 27.1 1.0 CG D:GLU190 4.6 22.1 1.0 O D:HOH770 4.8 37.4 1.0 CG2 D:THR270 4.9 24.8 1.0 C1 D:QC1503 4.9 23.7 1.0

Z.Nie, L.Shi, C.Lai, S.M.O'connell, J.Xu, R.K.Stansfield, D.J.Hosfield, J.M.Veal, J.A.Stafford. Structure-Based Design and Discovery of Potent and Selective KDM5 Inhibitors. Bioorg. Med. Chem. Lett. V. 28 1490 2018.
ISSN: ESSN 1464-3405
PubMed: 29627262
DOI: 10.1016/J.BMCL.2018.03.083