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Zinc in PDB 4wk7: Crystal Structure of Human Adamts-4 in Complex with Inhibitor (Compound 1, 2-(4-Chlorophenoxy)-N-{[(4R)-4-Methyl-2,5- Dioxoimidazolidin-4-Yl]Methyl} Acetamide)

Enzymatic activity of Crystal Structure of Human Adamts-4 in Complex with Inhibitor (Compound 1, 2-(4-Chlorophenoxy)-N-{[(4R)-4-Methyl-2,5- Dioxoimidazolidin-4-Yl]Methyl} Acetamide)

All present enzymatic activity of Crystal Structure of Human Adamts-4 in Complex with Inhibitor (Compound 1, 2-(4-Chlorophenoxy)-N-{[(4R)-4-Methyl-2,5- Dioxoimidazolidin-4-Yl]Methyl} Acetamide):
3.4.24.82;

Protein crystallography data

The structure of Crystal Structure of Human Adamts-4 in Complex with Inhibitor (Compound 1, 2-(4-Chlorophenoxy)-N-{[(4R)-4-Methyl-2,5- Dioxoimidazolidin-4-Yl]Methyl} Acetamide), PDB code: 4wk7 was solved by J.D.Durbin, S.L.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.72 / 1.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.506, 67.923, 74.581, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 21.3

Other elements in 4wk7:

The structure of Crystal Structure of Human Adamts-4 in Complex with Inhibitor (Compound 1, 2-(4-Chlorophenoxy)-N-{[(4R)-4-Methyl-2,5- Dioxoimidazolidin-4-Yl]Methyl} Acetamide) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Adamts-4 in Complex with Inhibitor (Compound 1, 2-(4-Chlorophenoxy)-N-{[(4R)-4-Methyl-2,5- Dioxoimidazolidin-4-Yl]Methyl} Acetamide) (pdb code 4wk7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human Adamts-4 in Complex with Inhibitor (Compound 1, 2-(4-Chlorophenoxy)-N-{[(4R)-4-Methyl-2,5- Dioxoimidazolidin-4-Yl]Methyl} Acetamide), PDB code: 4wk7:

Zinc binding site 1 out of 1 in 4wk7

Go back to Zinc Binding Sites List in 4wk7
Zinc binding site 1 out of 1 in the Crystal Structure of Human Adamts-4 in Complex with Inhibitor (Compound 1, 2-(4-Chlorophenoxy)-N-{[(4R)-4-Methyl-2,5- Dioxoimidazolidin-4-Yl]Methyl} Acetamide)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Adamts-4 in Complex with Inhibitor (Compound 1, 2-(4-Chlorophenoxy)-N-{[(4R)-4-Methyl-2,5- Dioxoimidazolidin-4-Yl]Methyl} Acetamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:12.9
occ:1.00
 N1 A:3PQ505 2.0 16.8 1.0
NE2 A:HIS361 2.1 10.8 1.0
NE2 A:HIS371 2.1 14.8 1.0
NE2 A:HIS365 2.1 11.1 1.0
C2 A:3PQ505 2.8 16.7 1.0
O3 A:3PQ505 2.9 15.9 1.0
CE1 A:HIS361 3.0 10.8 1.0
CE1 A:HIS365 3.0 11.2 1.0
CD2 A:HIS371 3.0 14.7 1.0
CE1 A:HIS371 3.1 15.0 1.0
C7 A:3PQ505 3.1 17.7 1.0
CD2 A:HIS361 3.1 10.4 1.0
CD2 A:HIS365 3.1 10.8 1.0
O8 A:3PQ505 3.5 18.3 1.0
N4 A:3PQ505 4.0 17.3 1.0
ND1 A:HIS361 4.1 10.7 1.0
ND1 A:HIS371 4.2 15.4 1.0
ND1 A:HIS365 4.2 11.1 1.0
CG A:HIS371 4.2 14.7 1.0
CG A:HIS361 4.2 10.4 1.0
CG A:HIS365 4.2 10.9 1.0
C5 A:3PQ505 4.3 17.6 1.0
O A:HOH685 4.5 18.2 1.0
N10 A:3PQ505 4.6 17.6 1.0
CE A:MET391 4.7 10.9 1.0
O A:HOH668 4.8 38.5 1.0
O A:PRO393 5.0 19.0 1.0

Reference:

T.B.Durham, V.J.Klimkowski, C.J.Rito, J.Marimuthu, J.L.Toth, C.Liu, J.D.Durbin, S.L.Stout, L.Adams, C.Swearingen, C.Lin, M.G.Chambers, K.Thirunavukkarasu, M.R.Wiley. Identification of Potent and Selective Hydantoin Inhibitors of Aggrecanase-1 and Aggrecanase-2 That Are Efficacious in Both Chemical and Surgical Models of Osteoarthritis. J.Med.Chem. 2014.
ISSN: ISSN 0022-2623
PubMed: 25415648
DOI: 10.1021/JM501522N
Page generated: Sun Oct 27 09:57:19 2024

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