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Iron in PDB 7dyq: Crystal Structure of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 5-Hydroxy-2-Methylpyrazolo[1,5-A]Pyrido[3,2- E]Pyrimidine-3-Carbonitrile

Enzymatic activity of Crystal Structure of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 5-Hydroxy-2-Methylpyrazolo[1,5-A]Pyrido[3,2- E]Pyrimidine-3-Carbonitrile

All present enzymatic activity of Crystal Structure of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 5-Hydroxy-2-Methylpyrazolo[1,5-A]Pyrido[3,2- E]Pyrimidine-3-Carbonitrile:
1.14.11.66;

Protein crystallography data

The structure of Crystal Structure of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 5-Hydroxy-2-Methylpyrazolo[1,5-A]Pyrido[3,2- E]Pyrimidine-3-Carbonitrile, PDB code: 7dyq was solved by T.Wang, L.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.02 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.635, 71.635, 151.486, 90, 90, 90
R / Rfree (%) 16.1 / 18.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 5-Hydroxy-2-Methylpyrazolo[1,5-A]Pyrido[3,2- E]Pyrimidine-3-Carbonitrile (pdb code 7dyq). 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 Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 5-Hydroxy-2-Methylpyrazolo[1,5-A]Pyrido[3,2- E]Pyrimidine-3-Carbonitrile, PDB code: 7dyq:

Iron binding site 1 out of 1 in 7dyq

Go back to Iron Binding Sites List in 7dyq
Iron binding site 1 out of 1 in the Crystal Structure of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 5-Hydroxy-2-Methylpyrazolo[1,5-A]Pyrido[3,2- E]Pyrimidine-3-Carbonitrile


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 Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 5-Hydroxy-2-Methylpyrazolo[1,5-A]Pyrido[3,2- E]Pyrimidine-3-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:29.7
occ:1.00
 NE2 A:HIS280 2.0 20.2 1.0
OE2 A:GLU194 2.2 19.8 1.0
N6 A:HR0401 2.2 38.5 1.0
NE2 A:HIS192 2.3 27.9 1.0
H71 A:HR0401 2.5 46.0 1.0
C7 A:HR0401 2.7 38.4 1.0
CE1 A:HIS280 2.8 12.2 1.0
HE1 A:HIS280 2.9 14.7 1.0
CE1 A:HIS192 3.1 27.9 1.0
CD2 A:HIS280 3.1 14.6 1.0
HE1 A:HIS192 3.2 33.5 1.0
CD A:GLU194 3.3 24.1 1.0
C5 A:HR0401 3.4 34.2 1.0
CD2 A:HIS192 3.4 28.8 1.0
HD2 A:HIS280 3.4 17.5 1.0
N3 A:HR0401 3.4 45.7 1.0
HD2 A:HIS192 3.6 34.5 1.0
N4 A:HR0401 3.8 37.3 1.0
OE1 A:GLU194 3.8 28.4 1.0
ND1 A:HIS280 4.0 16.2 1.0
HG21 A:THR274 4.0 23.2 1.0
C8 A:HR0401 4.1 35.1 1.0
CG A:HIS280 4.2 14.4 1.0
O A:HOH547 4.2 29.8 1.0
HZ3 A:TRP212 4.2 20.3 1.0
HG1 A:THR274 4.2 22.6 1.0
ND1 A:HIS192 4.3 47.0 1.0
HG A:SER200 4.3 38.2 1.0
HG2 A:GLU194 4.4 21.4 1.0
CG A:HIS192 4.4 24.1 1.0
CG A:GLU194 4.5 17.9 1.0
C10 A:HR0401 4.5 29.6 1.0
HB3 A:SER200 4.6 23.2 1.0
H81 A:HR0401 4.7 42.1 1.0
C2 A:HR0401 4.7 28.0 1.0
HD1 A:HIS280 4.7 19.4 1.0
HB2 A:SER200 4.8 23.2 1.0
C9 A:HR0401 4.8 32.5 1.0
CG2 A:THR274 4.9 19.3 1.0
HG3 A:GLU194 4.9 21.4 1.0
CZ3 A:TRP212 5.0 16.9 1.0
CB A:SER200 5.0 19.4 1.0
HD1 A:HIS192 5.0 56.4 1.0

Reference:

T.Wang, L.Yang. Crystal Structure of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 5-Hydroxy-2-Methylpyrazolo[1,5-A]Pyrido[3, 2-E]Pyrimidine-3-Carbonitrile To Be Published.
Page generated: Wed Aug 6 21:58:12 2025

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