Chlorine in PDB 7ump: Crystal Structure of PHD2 Catalytic Domain (Cid 7465) in Complex with Akb-6548 at 1.8 A Resolution

All present enzymatic activity of Crystal Structure of PHD2 Catalytic Domain (Cid 7465) in Complex with Akb-6548 at 1.8 A Resolution:
1.14.11.29;

The structure of Crystal Structure of PHD2 Catalytic Domain (Cid 7465) in Complex with Akb-6548 at 1.8 A Resolution, PDB code: 7ump was solved by D.R.Davie, J.Abendroth, J.Boyd, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.71 / 1.80
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	111.4, 111.4, 40.42, 90, 90, 120
R / Rfree (%)	16.9 / 20.2

The structure of Crystal Structure of PHD2 Catalytic Domain (Cid 7465) in Complex with Akb-6548 at 1.8 A Resolution also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of PHD2 Catalytic Domain (Cid 7465) in Complex with Akb-6548 at 1.8 A Resolution (pdb code 7ump). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of PHD2 Catalytic Domain (Cid 7465) in Complex with Akb-6548 at 1.8 A Resolution, PDB code: 7ump:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of PHD2 Catalytic Domain (Cid 7465) in Complex with Akb-6548 at 1.8 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of PHD2 Catalytic Domain (Cid 7465) in Complex with Akb-6548 at 1.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1002 b:32.2 occ:0.66 CL A:A1Z1002 0.0 32.2 0.7 C19 A:A1Z1002 1.7 31.6 0.3 C16 A:A1Z1002 1.8 32.3 0.7 C20 A:A1Z1002 2.6 28.9 0.3 C18 A:A1Z1002 2.7 32.2 0.3 C15 A:A1Z1002 2.7 30.1 0.7 C18 A:A1Z1002 2.8 31.7 0.7 CZ2 A:TRP258 3.7 28.1 1.0 CD1 A:ILE256 3.8 26.5 1.0 C14 A:A1Z1002 3.9 24.5 0.3 C16 A:A1Z1002 4.0 32.7 0.3 SD A:MET299 4.0 30.5 1.0 C14 A:A1Z1002 4.0 22.5 0.7 C19 A:A1Z1002 4.0 33.0 0.7 CH2 A:TRP258 4.4 29.6 1.0 C15 A:A1Z1002 4.4 28.1 0.3 CE2 A:TRP258 4.5 29.6 1.0 C20 A:A1Z1002 4.5 26.3 0.7 NE1 A:TRP258 4.7 30.7 1.0 CG A:MET299 4.9 27.6 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of PHD2 Catalytic Domain (Cid 7465) in Complex with Akb-6548 at 1.8 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of PHD2 Catalytic Domain (Cid 7465) in Complex with Akb-6548 at 1.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1002 b:42.1 occ:0.34 CL A:A1Z1002 0.0 42.1 0.3 C19 A:A1Z1002 1.8 33.0 0.7 C16 A:A1Z1002 1.8 32.7 0.3 C18 A:A1Z1002 2.7 31.7 0.7 C18 A:A1Z1002 2.7 32.2 0.3 C15 A:A1Z1002 2.8 28.1 0.3 C20 A:A1Z1002 2.8 26.3 0.7 O A:HOH1225 3.1 52.1 1.0 O A:HOH1207 3.5 41.9 1.0 O A:HOH1141 3.6 34.4 1.0 C16 A:A1Z1002 4.0 32.3 0.7 C19 A:A1Z1002 4.0 31.6 0.3 C14 A:A1Z1002 4.1 24.5 0.3 C14 A:A1Z1002 4.1 22.5 0.7 O A:HOH1182 4.2 28.2 1.0 O A:HOH1118 4.3 34.8 1.0 OH A:TYR310 4.5 29.9 1.0 C15 A:A1Z1002 4.5 30.1 0.7 C20 A:A1Z1002 4.6 28.9 0.3

A.Zuk, Z.Si, S.Loi, S.Bommegowda, D.Hoivik, S.Danthi, G.Molnar, V.Csizmadia, M.Rabinowitz. Preclinical Characterization of Vadadustat (Akb-6548), An Oral Small Molecule Hypoxia-Inducible Factor Prolyl-4-Hydroxylase Inhibitor, For the Potential Treatment of Renal Anemia. J.Pharmacol.Exp.Ther. V. 383 11 2022.
ISSN: ESSN 1521-0103
PubMed: 35926869
DOI: 10.1124/JPET.122.001126