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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: Sun Jul 14 14:13:01 2024

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