Nickel in PDB 5d3p: First Bromodomain of BRD4 Bound to Inhibitor XD41

The structure of First Bromodomain of BRD4 Bound to Inhibitor XD41, PDB code: 5d3p was solved by D.Wohlwend, M.Huegle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.70 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.700, 44.550, 78.620, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.7

The binding sites of Nickel atom in the First Bromodomain of BRD4 Bound to Inhibitor XD41 (pdb code 5d3p). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the First Bromodomain of BRD4 Bound to Inhibitor XD41, PDB code: 5d3p:

Nickel binding site 1 out of 1 in the First Bromodomain of BRD4 Bound to Inhibitor XD41


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of First Bromodomain of BRD4 Bound to Inhibitor XD41 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:35.7 occ:1.00 O A:HOH396 2.8 26.9 1.0 O A:HOH305 3.8 20.5 1.0 OE1 A:GLN123 3.9 17.8 0.7 NH2 A:ARG58 3.9 20.2 1.0 ND2 A:ASN121 4.0 14.6 1.0 O A:HOH403 4.2 22.0 1.0 O A:HOH322 4.4 24.0 1.0 OE1 A:GLU167 4.5 31.1 1.0 NE2 A:GLN123 4.6 15.4 0.7 CB A:ASN121 4.6 13.3 1.0 CD A:GLN123 4.6 16.4 0.7 CG A:ASN121 4.8 13.5 1.0

M.Hugle, X.Lucas, G.Weitzel, D.Ostrovskyi, B.Breit, S.Gerhardt, O.Einsle, S.Gunther, D.Wohlwend. 4-Acyl Pyrrole Derivatives Yield Novel Vectors For Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1). J.Med.Chem. V. 59 1518 2016.
ISSN: ISSN 0022-2623
PubMed: 26731611
DOI: 10.1021/ACS.JMEDCHEM.5B01267