Calcium in PDB 4wki: Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11)

Enzymatic activity of Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11)

All present enzymatic activity of Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11):
3.4.24.82;

Protein crystallography data

The structure of Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11), PDB code: 4wki was solved by J.D.Durbin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.07 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.037, 68.193, 74.013, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.2

Other elements in 4wki:

The structure of Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11) 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 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11) (pdb code 4wki). 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 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11), PDB code: 4wki:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4wki

Go back to Calcium Binding Sites List in 4wki
Calcium binding site 1 out of 3 in the Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11)


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 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:29.2
occ:1.00
 OE1 A:GLU221 2.4 27.6 1.0
O A:CYS423 2.4 34.9 1.0
OD2 A:ASP304 2.4 35.5 1.0
O A:HOH700 2.4 30.4 1.0
OD2 A:ASP311 2.5 28.0 1.0
OD1 A:ASP426 2.5 38.4 1.0
OD1 A:ASP311 2.6 28.8 1.0
OD1 A:ASP304 2.8 35.0 1.0
CG A:ASP311 2.8 27.6 1.0
CG A:ASP304 3.0 33.2 1.0
CG A:ASP426 3.4 38.1 1.0
CD A:GLU221 3.5 27.1 1.0
OD2 A:ASP426 3.5 40.8 1.0
C A:CYS423 3.6 32.5 1.0
CA A:CA503 3.8 32.1 1.0
CG A:GLU221 4.1 26.6 1.0
O A:HOH650 4.3 36.8 1.0
CB A:ASP311 4.4 25.6 1.0
OE2 A:GLU221 4.4 27.3 1.0
CB A:ASP304 4.5 36.0 1.0
N A:LEU424 4.5 31.5 1.0
CA A:LEU424 4.5 32.3 1.0
CA A:CYS423 4.5 32.5 1.0
O A:PHE219 4.5 28.8 1.0
CB A:GLU221 4.6 26.9 1.0
CB A:CYS423 4.6 32.6 1.0
O A:ASP426 4.6 36.2 1.0
CB A:ASP426 4.8 38.0 1.0
O A:HOH695 4.8 28.7 1.0
N A:ASP426 4.9 36.9 1.0
C A:LEU424 5.0 33.4 1.0
SG A:CYS423 5.0 32.7 1.0
CD2 A:HIS309 5.0 30.3 1.0

Calcium binding site 2 out of 3 in 4wki

Go back to Calcium Binding Sites List in 4wki
Calcium binding site 2 out of 3 in the Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11)


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 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:32.1
occ:1.00
 OD2 A:ASP426 2.2 40.8 1.0
O A:HOH705 2.3 37.2 1.0
O A:HOH719 2.4 34.7 1.0
OE1 A:GLU221 2.4 27.6 1.0
OD1 A:ASP304 2.5 35.0 1.0
O A:ASP304 2.5 34.0 1.0
OE2 A:GLU221 2.5 27.3 1.0
CD A:GLU221 2.8 27.1 1.0
CG A:ASP426 3.3 38.1 1.0
CG A:ASP304 3.5 33.2 1.0
C A:ASP304 3.6 37.0 1.0
CA A:CA502 3.8 29.2 1.0
OD1 A:ASP426 3.9 38.4 1.0
CA A:ASP304 4.2 35.0 1.0
OD2 A:ASP304 4.2 35.5 1.0
O A:ASP306 4.3 37.2 1.0
CB A:ASP304 4.3 36.0 1.0
CG A:GLU221 4.4 26.6 1.0
O A:HOH732 4.4 39.4 1.0
O A:HIS309 4.4 26.8 1.0
CB A:ASP426 4.5 38.0 1.0
O A:HOH617 4.6 51.1 1.0
N A:SER305 4.7 38.3 1.0
OE1 A:GLU429 4.8 49.0 0.5
CB A:HIS309 4.8 30.4 1.0
O A:HOH700 4.9 30.4 1.0
CD2 A:HIS309 4.9 30.3 1.0

Calcium binding site 3 out of 3 in 4wki

Go back to Calcium Binding Sites List in 4wki
Calcium binding site 3 out of 3 in the Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11)


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 5- Chloro-N-{[(4S)-4-(1-Methyl-1H-Imidazol-2-Yl)-2,5-Dioxoimidazolidin- 4-Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:30.0
occ:1.00
 O A:CYS327 2.3 34.2 1.0
OD1 A:ASP320 2.3 33.4 1.0
O A:THR329 2.3 29.9 1.0
OE1 A:GLU349 2.4 30.2 1.0
O A:HOH707 2.4 33.3 1.0
O A:LEU321 2.4 32.8 1.0
CD A:GLU349 3.3 29.9 1.0
C A:CYS327 3.4 34.4 1.0
N A:LEU321 3.4 31.8 1.0
C A:LEU321 3.5 32.7 1.0
C A:THR329 3.5 30.7 1.0
OE2 A:GLU349 3.5 33.6 1.0
CG A:ASP320 3.6 36.5 1.0
N A:THR329 3.9 32.4 1.0
CA A:LEU321 4.0 31.9 1.0
C A:ASP320 4.0 34.3 1.0
C A:ASP328 4.1 33.4 1.0
O A:HOH780 4.1 49.7 1.0
CA A:CYS327 4.2 38.6 1.0
CA A:THR329 4.2 31.7 0.5
CA A:ASP320 4.2 34.4 1.0
OG1 A:THR329 4.3 34.7 0.5
CA A:THR329 4.3 32.0 0.5
CB A:CYS327 4.3 39.4 1.0
N A:ASP328 4.3 34.4 1.0
OD2 A:ASP320 4.4 37.9 1.0
CB A:LEU321 4.4 30.2 1.0
O A:ASP328 4.5 31.6 1.0
CB A:ASP320 4.5 34.5 1.0
CA A:ASP328 4.5 33.2 1.0
N A:LEU330 4.5 29.1 1.0
CB A:THR329 4.6 32.7 0.5
N A:CYS322 4.6 34.6 1.0
CG A:GLU349 4.7 27.8 1.0
CD2 A:LEU330 4.7 31.2 1.0
CA A:LEU330 4.7 27.3 1.0
O A:ASP320 4.8 33.2 1.0
O A:HOH706 4.9 46.2 1.0
CB A:THR329 4.9 33.5 0.5

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: Sat Dec 12 05:11:01 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy