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Calcium 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
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where 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:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4wk7

Go back to Calcium Binding Sites List in 4wk7
Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca502

b:11.1
occ:1.00
 O A:CYS423 2.3 12.0 1.0
OE1 A:GLU221 2.4 12.5 1.0
O A:HOH686 2.4 13.4 1.0
OD2 A:ASP304 2.5 13.5 1.0
OD1 A:ASP426 2.5 14.4 1.0
OD2 A:ASP311 2.5 10.8 1.0
OD1 A:ASP311 2.6 10.6 1.0
OD1 A:ASP304 2.8 13.5 1.0
CG A:ASP311 2.9 10.3 1.0
CG A:ASP304 3.0 13.3 1.0
CG A:ASP426 3.4 14.6 1.0
CD A:GLU221 3.5 11.7 1.0
OD2 A:ASP426 3.6 14.8 1.0
C A:CYS423 3.6 12.2 1.0
CA A:CA503 3.9 11.4 1.0
CG A:GLU221 4.1 11.3 1.0
O A:HOH602 4.2 24.5 1.0
CB A:ASP311 4.4 10.3 1.0
OE2 A:GLU221 4.5 12.5 1.0
CA A:CYS423 4.5 12.4 1.0
N A:LEU424 4.5 12.2 1.0
CB A:CYS423 4.5 12.2 1.0
CB A:ASP304 4.5 13.5 1.0
CA A:LEU424 4.5 12.3 1.0
O A:PHE219 4.5 13.0 1.0
O A:ASP426 4.5 16.0 1.0
CB A:GLU221 4.6 11.0 1.0
O A:HOH626 4.7 17.9 1.0
CB A:ASP426 4.8 15.0 1.0
SG A:CYS423 4.9 12.3 1.0
O A:HOH682 4.9 11.4 1.0
N A:ASP426 4.9 14.9 1.0

Calcium binding site 2 out of 3 in 4wk7

Go back to Calcium Binding Sites List in 4wk7
Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca binding site number 2 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:Ca503

b:11.4
occ:1.00
 OD2 A:ASP426 2.3 14.8 1.0
O A:HOH691 2.3 12.7 1.0
O A:HOH696 2.4 17.3 1.0
O A:ASP304 2.4 13.3 1.0
OE1 A:GLU221 2.4 12.5 1.0
OD1 A:ASP304 2.4 13.5 1.0
OE2 A:GLU221 2.6 12.5 1.0
CD A:GLU221 2.9 11.7 1.0
CG A:ASP426 3.4 14.6 1.0
CG A:ASP304 3.4 13.3 1.0
C A:ASP304 3.5 13.3 1.0
CA A:CA502 3.9 11.1 1.0
OD1 A:ASP426 3.9 14.4 1.0
CA A:ASP304 4.1 13.5 1.0
OD2 A:ASP304 4.2 13.5 1.0
CB A:ASP304 4.2 13.5 1.0
O A:ASP306 4.4 14.9 1.0
CG A:GLU221 4.4 11.3 1.0
O A:HIS309 4.5 11.1 1.0
O A:HOH718 4.5 22.6 1.0
N A:SER305 4.6 13.5 1.0
CB A:ASP426 4.6 15.0 1.0
O A:HOH787 4.6 31.3 1.0
CB A:HIS309 4.8 11.9 1.0
O A:HOH658 4.8 33.5 1.0
CA A:SER305 4.9 14.2 1.0
O A:HOH632 4.9 35.1 1.0
CD2 A:HIS309 5.0 11.8 1.0
O A:HOH686 5.0 13.4 1.0

Calcium binding site 3 out of 3 in 4wk7

Go back to Calcium Binding Sites List in 4wk7
Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca binding site number 3 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:Ca504

b:15.4
occ:1.00
 OD1 A:ASP320 2.3 18.3 1.0
O A:CYS327 2.3 19.4 1.0
O A:LEU321 2.4 17.5 1.0
OE1 A:GLU349 2.4 15.4 1.0
O A:THR329 2.4 15.0 1.0
O A:HOH699 2.4 18.2 1.0
CD A:GLU349 3.3 15.1 1.0
N A:LEU321 3.4 17.1 1.0
C A:CYS327 3.4 20.3 1.0
C A:LEU321 3.4 17.7 1.0
CG A:ASP320 3.5 18.9 1.0
OE2 A:GLU349 3.6 16.6 1.0
C A:THR329 3.6 15.5 1.0
CA A:LEU321 3.9 16.9 1.0
C A:ASP320 3.9 18.0 1.0
N A:THR329 4.0 17.0 1.0
C A:ASP328 4.1 18.1 1.0
O A:HOH764 4.1 30.3 1.0
CA A:CYS327 4.2 21.6 1.0
OG1 A:THR329 4.2 17.1 0.3
CA A:ASP320 4.2 18.1 1.0
CB A:CYS327 4.2 21.8 1.0
OD2 A:ASP320 4.3 20.2 1.0
N A:ASP328 4.4 19.7 1.0
CA A:THR329 4.4 16.3 0.3
O A:ASP328 4.4 17.6 1.0
CA A:THR329 4.4 16.3 0.7
CB A:LEU321 4.4 16.3 1.0
CB A:ASP320 4.5 18.6 1.0
CG2 A:THR329 4.5 17.1 0.7
CA A:ASP328 4.5 19.7 1.0
N A:LEU330 4.6 14.4 1.0
N A:CYS322 4.6 19.0 1.0
CD2 A:LEU330 4.7 14.9 1.0
CG A:GLU349 4.7 14.7 1.0
O A:ASP320 4.8 18.6 1.0
CA A:LEU330 4.8 13.8 1.0
CB A:THR329 4.9 16.6 0.3

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 Jul 14 14:11:30 2024

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