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Arsenic in PDB 3d3p: Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor

Enzymatic activity of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor

All present enzymatic activity of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor, PDB code: 3d3p was solved by D.O.Somers, M.Neu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.75
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.448, 94.725, 105.671, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.1

Other elements in 3d3p:

The structure of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor (pdb code 3d3p). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor, PDB code: 3d3p:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 3d3p

Go back to Arsenic Binding Sites List in 3d3p
Arsenic binding site 1 out of 4 in the Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As506

b:25.9
occ:0.50
 AS A:ARS506 0.0 25.9 0.5
AS A:ARS506 1.5 28.0 0.5
SG A:CYS194 2.3 20.3 0.5
CB A:CYS194 3.1 21.1 0.5
CB A:CYS194 3.1 20.2 0.5
SG A:CYS194 3.2 24.4 0.5
CA A:CYS194 3.4 20.1 0.5
CA A:CYS194 3.4 19.5 0.5
O A:CYS194 3.7 21.2 1.0
C A:CYS194 3.9 19.5 1.0
CD2 A:TYR197 4.4 31.7 1.0
O A:ILE153 4.5 45.0 1.0
CD2 A:LEU166 4.5 25.3 1.0
CB A:TYR197 4.6 21.8 1.0
CD1 A:LEU170 4.6 25.6 1.0
N A:CYS194 4.6 19.6 1.0
O A:HOH689 5.0 47.4 1.0
CG A:TYR197 5.0 24.0 1.0

Arsenic binding site 2 out of 4 in 3d3p

Go back to Arsenic Binding Sites List in 3d3p
Arsenic binding site 2 out of 4 in the Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As506

b:28.0
occ:0.50
 AS A:ARS506 0.0 28.0 0.5
AS A:ARS506 1.5 25.9 0.5
SG A:CYS194 2.2 24.4 0.5
SG A:CYS194 2.8 20.3 0.5
CB A:CYS194 3.0 20.2 0.5
CB A:CYS194 3.0 21.1 0.5
CA A:CYS194 3.5 19.5 0.5
CA A:CYS194 3.5 20.1 0.5
CE2 A:PHE156 3.9 32.6 1.0
CD2 A:LEU166 4.2 25.3 1.0
CD2 A:PHE156 4.2 36.7 1.0
O A:ILE153 4.5 45.0 1.0
N A:CYS194 4.5 19.6 1.0
C A:CYS194 4.6 19.5 1.0
O A:CYS194 4.7 21.2 1.0

Arsenic binding site 3 out of 4 in 3d3p

Go back to Arsenic Binding Sites List in 3d3p
Arsenic binding site 3 out of 4 in the Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As2

b:47.6
occ:1.00
 SG A:CYS320 2.1 33.4 1.0
CB A:CYS320 2.9 31.2 1.0
CG A:GLU317 3.6 47.3 1.0
CB A:GLU317 3.7 42.6 1.0
N A:CYS320 4.0 32.2 1.0
CA A:CYS320 4.0 28.9 1.0
C A:HIS319 4.4 38.9 1.0
O A:LEU314 4.5 25.8 1.0
CB A:HIS319 4.7 47.4 1.0
CD A:GLU317 4.7 49.5 1.0
O A:HIS319 4.8 41.1 1.0
CG2 A:THR218 4.8 20.6 1.0
O A:GLU317 4.8 42.0 1.0
OG1 A:THR222 4.9 18.0 1.0
CA A:GLU317 4.9 40.7 1.0

Arsenic binding site 4 out of 4 in 3d3p

Go back to Arsenic Binding Sites List in 3d3p
Arsenic binding site 4 out of 4 in the Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As3

b:38.4
occ:1.00
 SG A:CYS432 2.1 32.7 1.0
CB A:CYS432 3.2 29.2 1.0
N A:CYS432 3.4 29.4 1.0
CA A:CYS432 3.7 25.5 1.0
C A:MET431 3.8 32.5 1.0
CB A:SER429 3.8 33.0 1.0
O A:HOH701 3.9 33.3 1.0
O A:MET431 4.3 30.7 1.0
CB A:MET431 4.4 34.4 1.0
O A:HOH723 4.4 51.5 1.0
CA A:MET431 4.4 36.5 1.0
N A:MET431 4.6 32.9 1.0
O A:SER429 4.6 29.7 1.0
O A:HOH724 4.6 36.6 1.0
OG A:SER429 4.6 31.1 1.0
NE2 A:GLN417 4.7 19.4 1.0
O A:HOH720 4.8 41.1 1.0
C A:SER429 4.8 30.8 1.0
CG A:PHE414 4.8 21.9 1.0
CD1 A:PHE414 4.9 23.6 1.0
CA A:SER429 5.0 32.3 1.0
CB A:PHE414 5.0 23.8 1.0

Reference:

J.N.Hamblin, T.D.Angell, S.P.Ballantine, C.M.Cook, A.W.Cooper, J.Dawson, C.J.Delves, P.S.Jones, M.Lindvall, F.S.Lucas, C.J.Mitchell, M.Y.Neu, L.E.Ranshaw, Y.E.Solanke, D.O.Somers, J.O.Wiseman. Pyrazolopyridines As A Novel Structural Class of Potent and Selective PDE4 Inhibitors. Bioorg.Med.Chem.Lett. V. 18 4237 2008.
ISSN: ISSN 0960-894X
PubMed: 18539455
DOI: 10.1016/J.BMCL.2008.05.052
Page generated: Sun Jul 6 23:20:24 2025

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