Atomistry » Calcium » PDB 4wa3-4wn0 » 4wk7
Atomistry »
  Calcium »
    PDB 4wa3-4wn0 »
      4wk7 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy