Nickel in PDB 6cg2: Crystal Structure of KDM4A with Compound 8

The structure of Crystal Structure of KDM4A with Compound 8, PDB code: 6cg2 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)	140.30 / 2.34
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.457, 101.739, 142.287, 90.00, 99.51, 90.00
R / Rfree (%)	17.4 / 23.4

The structure of Crystal Structure of KDM4A with Compound 8 also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of KDM4A with Compound 8 (pdb code 6cg2). 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 8, PDB code: 6cg2:
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 8


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 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:26.9 occ:1.00 OE2 A:GLU190 2.0 27.2 1.0 NE2 A:HIS188 2.1 23.6 1.0 N14 A:QC2503 2.1 33.3 1.0 N4 A:QC2503 2.1 32.2 1.0 O A:HOH624 2.2 27.1 1.0 NE2 A:HIS276 2.2 24.0 1.0 N10 A:QC2503 2.8 33.8 1.0 C3 A:QC2503 2.9 34.5 1.0 CE1 A:HIS188 3.1 27.3 1.0 CE1 A:HIS276 3.1 23.9 1.0 CD2 A:HIS188 3.1 27.0 1.0 CD A:GLU190 3.1 30.4 1.0 C5 A:QC2503 3.1 31.5 1.0 C13 A:QC2503 3.2 34.8 1.0 CD2 A:HIS276 3.3 23.7 1.0 OE1 A:GLU190 3.5 30.6 1.0 C11 A:QC2503 3.9 36.5 1.0 C12 A:QC2503 4.1 33.6 1.0 ND1 A:HIS188 4.2 26.6 1.0 CG A:HIS188 4.2 27.9 1.0 ND1 A:HIS276 4.2 26.1 1.0 C2 A:QC2503 4.2 31.8 1.0 CG A:HIS276 4.4 23.7 1.0 C6 A:QC2503 4.4 33.7 1.0 O A:HOH680 4.4 38.7 1.0 CG A:GLU190 4.4 29.5 1.0 OG A:SER196 4.5 34.6 1.0 O A:HOH690 4.5 38.9 1.0 C1 A:QC2503 4.9 33.0 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of KDM4A with Compound 8


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 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:28.8 occ:1.00 O B:HOH633 1.8 30.7 1.0 N14 B:QC2503 2.0 34.6 1.0 NE2 B:HIS188 2.0 27.8 1.0 NE2 B:HIS276 2.1 27.4 1.0 OE2 B:GLU190 2.2 32.4 1.0 N4 B:QC2503 2.2 32.1 1.0 N10 B:QC2503 2.7 34.4 1.0 C3 B:QC2503 2.9 33.2 1.0 CE1 B:HIS188 2.9 29.3 1.0 C13 B:QC2503 3.1 31.9 1.0 CD2 B:HIS188 3.1 27.3 1.0 CD2 B:HIS276 3.1 29.4 1.0 CD B:GLU190 3.1 28.4 1.0 CE1 B:HIS276 3.1 30.0 1.0 C5 B:QC2503 3.3 32.5 1.0 OE1 B:GLU190 3.4 29.8 1.0 C11 B:QC2503 3.9 35.3 1.0 C12 B:QC2503 4.0 33.0 1.0 ND1 B:HIS188 4.1 26.9 1.0 CG B:HIS188 4.2 27.3 1.0 ND1 B:HIS276 4.2 29.5 1.0 CG B:HIS276 4.2 26.8 1.0 C2 B:QC2503 4.3 31.4 1.0 OG B:SER196 4.4 34.9 1.0 CG B:GLU190 4.5 30.8 1.0 C6 B:QC2503 4.5 33.2 1.0 C1 B:QC2503 4.9 36.2 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of KDM4A with Compound 8


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 8 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni501 b:30.4 occ:1.00 O C:HOH625 1.9 19.9 1.0 NE2 C:HIS188 2.1 23.0 1.0 OE2 C:GLU190 2.1 29.9 1.0 N4 C:QC2503 2.1 38.8 1.0 NE2 C:HIS276 2.2 26.0 1.0 N14 C:QC2503 2.3 38.6 1.0 N10 C:QC2503 2.9 43.3 1.0 C3 C:QC2503 3.0 39.9 1.0 CE1 C:HIS188 3.0 24.6 1.0 C5 C:QC2503 3.1 34.7 1.0 CD2 C:HIS188 3.1 23.1 1.0 CD C:GLU190 3.2 29.6 1.0 CD2 C:HIS276 3.2 25.1 1.0 CE1 C:HIS276 3.2 26.5 1.0 C13 C:QC2503 3.4 39.4 1.0 OE1 C:GLU190 3.6 29.8 1.0 C11 C:QC2503 4.1 45.1 1.0 ND1 C:HIS188 4.2 24.3 1.0 CG C:HIS188 4.2 23.8 1.0 C12 C:QC2503 4.3 39.5 1.0 C2 C:QC2503 4.3 38.2 1.0 ND1 C:HIS276 4.3 25.2 1.0 CG C:HIS276 4.4 24.5 1.0 C6 C:QC2503 4.4 37.4 1.0 CG C:GLU190 4.5 30.9 1.0 OG C:SER196 4.5 35.4 1.0 O C:HOH694 4.8 51.0 1.0 C1 C:QC2503 4.9 38.3 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of KDM4A with Compound 8


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 8 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni501 b:25.7 occ:1.00 N14 D:QC2503 2.0 25.5 1.0 OE2 D:GLU190 2.1 26.0 1.0 NE2 D:HIS188 2.1 25.0 1.0 O D:HOH639 2.1 23.5 1.0 NE2 D:HIS276 2.2 19.9 1.0 N4 D:QC2503 2.3 25.7 1.0 N10 D:QC2503 2.8 25.5 1.0 CE1 D:HIS188 2.9 28.8 1.0 C3 D:QC2503 3.0 27.3 1.0 C13 D:QC2503 3.0 25.3 1.0 CE1 D:HIS276 3.1 21.0 1.0 CD D:GLU190 3.1 26.8 1.0 CD2 D:HIS188 3.2 25.3 1.0 CD2 D:HIS276 3.2 20.6 1.0 C5 D:QC2503 3.3 29.8 1.0 OE1 D:GLU190 3.6 31.2 1.0 C11 D:QC2503 3.9 28.5 1.0 C12 D:QC2503 4.0 26.6 1.0 ND1 D:HIS188 4.1 21.9 1.0 CG D:HIS188 4.2 23.8 1.0 ND1 D:HIS276 4.2 20.1 1.0 CG D:HIS276 4.3 20.3 1.0 C2 D:QC2503 4.3 26.9 1.0 OG D:SER196 4.4 30.8 1.0 CG D:GLU190 4.4 25.9 1.0 C6 D:QC2503 4.6 28.5 1.0 O D:HOH673 4.6 33.6 1.0 C1 D:QC2503 5.0 30.4 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