Nickel in PDB 5k4l: Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor

The structure of Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor, PDB code: 5k4l was solved by J.R.Kiefer, M.V.Vinogradova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.50 / 3.18
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	159.141, 159.141, 92.109, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 25.7

The structure of Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor (pdb code 5k4l). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor, PDB code: 5k4l:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor


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 KDM5A in Complex with A Naphthyridone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:66.8 occ:1.00 HE2 A:HIS571 1.2 0.1 1.0 HE2 A:HIS483 1.3 0.4 1.0 NE2 A:HIS571 2.0 0.1 1.0 OE1 A:GLU485 2.0 0.5 1.0 N11 A:6QN904 2.0 0.6 1.0 OE2 A:GLU485 2.1 0.2 1.0 NE2 A:HIS483 2.1 0.2 1.0 CD A:GLU485 2.2 0.3 1.0 H26 A:6QN904 2.4 0.4 1.0 C10 A:6QN904 2.7 0.5 1.0 CE1 A:HIS571 2.7 99.8 1.0 HE1 A:HIS571 2.7 0.5 1.0 CE1 A:HIS483 3.0 0.1 1.0 CD2 A:HIS483 3.1 0.8 1.0 HE1 A:HIS483 3.1 0.3 1.0 C12 A:6QN904 3.2 0.7 1.0 CD2 A:HIS571 3.2 97.7 1.0 HD2 A:HIS483 3.3 0.3 1.0 H27 A:6QN904 3.4 0.1 1.0 CG A:GLU485 3.6 0.1 1.0 HD2 A:HIS571 3.6 1.0 1.0 HG2 A:GLU485 3.7 0.5 1.0 HG A:SER491 3.7 0.1 1.0 HG3 A:GLU485 3.9 0.5 1.0 ND1 A:HIS571 3.9 96.1 1.0 C9 A:6QN904 4.0 1.0 1.0 ND1 A:HIS483 4.1 1.0 1.0 HB3 A:SER491 4.1 0.9 1.0 HB2 A:SER491 4.1 0.9 1.0 CG A:HIS483 4.1 0.4 1.0 CG A:HIS571 4.2 94.1 1.0 HG1 A:THR565 4.4 69.4 1.0 CB A:SER491 4.4 91.0 1.0 C13 A:6QN904 4.4 0.9 1.0 OG A:SER491 4.4 88.6 1.0 HA A:GLU485 4.5 0.0 1.0 HG21 A:THR565 4.6 81.3 1.0 HD1 A:HIS571 4.7 0.1 1.0 H A:GLU485 4.7 0.6 1.0 H25 A:6QN904 4.7 0.5 1.0 CB A:GLU485 4.7 0.9 1.0 C8 A:6QN904 4.7 0.4 1.0 N A:GLU485 4.8 0.2 1.0 HD1 A:HIS483 4.8 0.5 1.0 CA A:GLU485 4.9 0.6 1.0 HD21 A:ASN585 4.9 0.6 1.0 HZ3 A:TRP503 5.0 0.5 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor


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 KDM5A in Complex with A Naphthyridone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni901 b:78.8 occ:1.00 HE2 B:HIS571 1.2 51.0 1.0 N11 B:6QN904 2.0 82.5 1.0 OE2 B:GLU485 2.0 42.9 1.0 NE2 B:HIS483 2.0 56.9 1.0 NE2 B:HIS571 2.0 42.6 1.0 H27 B:6QN904 2.2 0.6 1.0 C12 B:6QN904 2.5 90.7 1.0 CE1 B:HIS483 2.9 56.4 1.0 CD2 B:HIS571 3.0 44.1 1.0 CE1 B:HIS571 3.0 39.5 1.0 CD2 B:HIS483 3.0 48.3 1.0 CD B:GLU485 3.1 43.1 1.0 HE1 B:HIS483 3.1 67.4 1.0 C10 B:6QN904 3.1 82.8 1.0 HD2 B:HIS571 3.2 52.7 1.0 HE1 B:HIS571 3.2 47.1 1.0 HD2 B:HIS483 3.2 57.8 1.0 H26 B:6QN904 3.4 99.2 1.0 OE1 B:GLU485 3.7 45.2 1.0 C13 B:6QN904 3.9 85.9 1.0 HG B:SER491 3.9 56.4 1.0 ND1 B:HIS483 4.1 51.8 1.0 HG2 B:GLU485 4.1 56.2 1.0 ND1 B:HIS571 4.1 37.8 1.0 CG B:HIS571 4.1 39.1 1.0 CG B:HIS483 4.1 48.5 1.0 CG B:GLU485 4.2 47.0 1.0 C9 B:6QN904 4.3 76.5 1.0 C8 B:6QN904 4.6 72.3 1.0 HG3 B:GLU485 4.7 56.2 1.0 H15 B:6QN904 4.7 0.7 1.0 OG B:SER491 4.7 47.2 1.0 HD2 B:PHE480 4.8 83.0 1.0 N14 B:6QN904 4.8 89.1 1.0 HD1 B:HIS483 4.8 62.0 1.0 HB2 B:SER491 4.8 53.2 1.0 HB3 B:SER491 4.9 53.2 1.0 HD1 B:HIS571 4.9 45.1 1.0 HA B:GLU485 4.9 52.2 1.0 HG21 B:THR565 4.9 0.4 1.0 HE2 B:PHE480 5.0 79.5 1.0 HD21 B:ASN493 5.0 0.5 1.0 HG1 B:THR565 5.0 0.1 1.0

S.S.Labadie, P.S.Dragovich, R.T.Cummings, G.Deshmukh, A.Gustafson, N.Han, J.C.Harmange, J.R.Kiefer, Y.Li, J.Liang, B.M.Liederer, Y.Liu, W.Manieri, W.Mao, L.Murray, D.F.Ortwine, P.Trojer, E.Vanderporten, M.Vinogradova, L.Wen. Design and Evaluation of 1,7-Naphthyridones As Novel KDM5 Inhibitors. Bioorg.Med.Chem.Lett. V. 26 4492 2016.
ISSN: ESSN 1464-3405
PubMed: 27499454
DOI: 10.1016/J.BMCL.2016.07.070