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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 7ump:

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:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total only one binding site of Iron was determined in the Crystal Structure of PHD2 Catalytic Domain (Cid 7465) in Complex with Akb-6548 at 1.8 A Resolution, PDB code: 7ump:

Iron binding site 1 out of 1 in 7ump

Go back to Iron Binding Sites List in 7ump
Iron binding site 1 out of 1 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 Iron with other atoms in the Fe 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:Fe1001

b:16.1
occ:1.00
 O10 A:A1Z1002 2.1 14.3 0.7
OD2 A:ASP315 2.2 17.3 1.0
NE2 A:HIS374 2.2 19.3 1.0
NE2 A:HIS313 2.2 16.8 1.0
N11 A:A1Z1002 2.2 19.1 0.7
O A:HOH1108 2.2 16.7 1.0
O10 A:A1Z1002 2.3 20.6 0.3
N11 A:A1Z1002 2.3 20.9 0.3
C04 A:A1Z1002 2.8 17.1 0.7
C04 A:A1Z1002 2.9 13.5 0.3
C03 A:A1Z1002 2.9 14.1 0.7
C03 A:A1Z1002 3.0 18.1 0.3
CE1 A:HIS313 3.1 17.9 1.0
CG A:ASP315 3.1 18.6 1.0
CE1 A:HIS374 3.1 18.4 1.0
CD2 A:HIS374 3.1 17.8 1.0
C12 A:A1Z1002 3.2 20.8 0.7
C12 A:A1Z1002 3.3 22.1 0.3
CD2 A:HIS313 3.3 19.4 1.0
OD1 A:ASP315 3.4 17.6 1.0
N05 A:A1Z1002 4.1 16.0 0.7
N05 A:A1Z1002 4.2 22.2 0.3
ND1 A:HIS313 4.2 20.6 1.0
O A:HOH1156 4.2 20.2 1.0
ND1 A:HIS374 4.2 18.2 1.0
C02 A:A1Z1002 4.3 22.6 0.7
CG A:HIS374 4.3 18.5 1.0
C02 A:A1Z1002 4.3 20.6 0.3
CG A:HIS313 4.4 19.2 1.0
C13 A:A1Z1002 4.4 25.1 0.7
CB A:ASP315 4.5 17.8 1.0
C13 A:A1Z1002 4.5 23.9 0.3
C06 A:A1Z1002 4.7 18.4 0.7
C06 A:A1Z1002 4.7 18.1 0.3
CZ A:PHE366 4.8 16.1 1.0
CA A:ASP315 4.8 20.1 1.0
C21 A:A1Z1002 4.9 21.2 0.7
C21 A:A1Z1002 5.0 22.4 0.3
N A:ASP315 5.0 17.3 1.0

Reference:

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
Page generated: Thu Aug 7 06:22:38 2025

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