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Calcium in PDB 4wke: Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10)

Enzymatic activity of Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10)

All present enzymatic activity of Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10):
3.4.24.82;

Protein crystallography data

The structure of Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10), PDB code: 4wke 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) 21.70 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.275, 68.035, 74.765, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 20.9

Other elements in 4wke:

The structure of Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10) 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-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10) (pdb code 4wke). 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-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10), PDB code: 4wke:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4wke

Go back to Calcium Binding Sites List in 4wke
Calcium binding site 1 out of 3 in the Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10)


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-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:17.3
occ:1.00
 O A:CYS423 2.4 18.3 1.0
O A:HOH672 2.4 19.0 1.0
OE1 A:GLU221 2.4 19.2 1.0
OD2 A:ASP311 2.5 16.3 1.0
OD1 A:ASP426 2.5 23.5 1.0
OD2 A:ASP304 2.5 22.7 1.0
OD1 A:ASP311 2.5 17.1 1.0
OD1 A:ASP304 2.8 22.0 1.0
CG A:ASP311 2.8 16.1 1.0
CG A:ASP304 3.0 21.6 1.0
CG A:ASP426 3.4 24.9 1.0
CD A:GLU221 3.5 18.6 1.0
C A:CYS423 3.6 18.9 1.0
OD2 A:ASP426 3.6 26.9 1.0
CA A:CA503 3.8 19.6 1.0
CG A:GLU221 4.1 17.7 1.0
O A:HOH601 4.2 44.4 1.0
CB A:ASP311 4.4 16.0 1.0
CA A:CYS423 4.5 19.5 1.0
OE2 A:GLU221 4.5 18.8 1.0
N A:LEU424 4.5 17.8 1.0
CB A:CYS423 4.5 19.9 1.0
CB A:ASP304 4.5 21.4 1.0
CA A:LEU424 4.5 18.0 1.0
O A:PHE219 4.5 18.0 1.0
O A:ASP426 4.6 24.4 1.0
CB A:GLU221 4.6 16.8 1.0
O A:HOH616 4.7 30.4 1.0
CB A:ASP426 4.8 23.9 1.0
SG A:CYS423 4.9 20.4 1.0
O A:HOH675 4.9 18.4 1.0
N A:ASP426 4.9 23.7 1.0
N A:GLU221 5.0 16.1 1.0

Calcium binding site 2 out of 3 in 4wke

Go back to Calcium Binding Sites List in 4wke
Calcium binding site 2 out of 3 in the Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10)


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-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:19.6
occ:1.00
 OD2 A:ASP426 2.2 26.9 1.0
OE1 A:GLU221 2.4 19.2 1.0
O A:HOH690 2.4 28.2 1.0
O A:HOH681 2.4 20.9 1.0
O A:ASP304 2.4 22.4 1.0
OD1 A:ASP304 2.5 22.0 1.0
OE2 A:GLU221 2.6 18.8 1.0
CD A:GLU221 2.8 18.6 1.0
CG A:ASP426 3.4 24.9 1.0
CG A:ASP304 3.5 21.6 1.0
C A:ASP304 3.5 22.4 1.0
CA A:CA502 3.8 17.3 1.0
OD1 A:ASP426 3.9 23.5 1.0
CA A:ASP304 4.1 21.9 1.0
OD2 A:ASP304 4.3 22.7 1.0
CB A:ASP304 4.3 21.4 1.0
CG A:GLU221 4.4 17.7 1.0
O A:ASP306 4.4 23.6 1.0
O A:HOH698 4.5 31.6 1.0
O A:HIS309 4.5 17.5 1.0
N A:SER305 4.6 22.5 1.0
CB A:ASP426 4.6 23.9 1.0
CB A:HIS309 4.8 17.5 1.0
CA A:SER305 4.8 23.5 1.0
O A:HOH672 4.9 19.0 1.0
CD2 A:HIS309 4.9 17.9 1.0

Calcium binding site 3 out of 3 in 4wke

Go back to Calcium Binding Sites List in 4wke
Calcium binding site 3 out of 3 in the Crystal Structure of Human Adamts-4 in Complex with Inhibitor 5- Chloro-N-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10)


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-{[(4R)-2,5-Dioxo-4-(1,3-Thiazol-2-Yl)Imidazolidin-4- Yl]Methyl}-1-Benzofuran-2-Carboxamide (Compound 10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:21.2
occ:1.00
 OD1 A:ASP320 2.3 25.3 1.0
O A:CYS327 2.3 25.5 1.0
O A:HOH674 2.3 25.0 1.0
O A:LEU321 2.4 22.8 1.0
OE1 A:GLU349 2.4 21.9 1.0
O A:THR329 2.4 20.8 1.0
CD A:GLU349 3.3 22.2 1.0
C A:CYS327 3.4 26.8 1.0
N A:LEU321 3.4 23.4 1.0
C A:LEU321 3.5 24.3 1.0
CG A:ASP320 3.5 26.9 1.0
OE2 A:GLU349 3.6 26.2 1.0
C A:THR329 3.6 21.4 1.0
C A:ASP320 3.9 25.1 1.0
CA A:LEU321 4.0 23.1 1.0
N A:THR329 4.1 24.6 1.0
C A:ASP328 4.1 25.7 1.0
O A:HOH742 4.1 35.5 1.0
CA A:CYS327 4.2 30.3 1.0
CA A:ASP320 4.2 25.3 1.0
CB A:CYS327 4.3 31.0 1.0
O A:ASP328 4.3 24.6 1.0
OD2 A:ASP320 4.3 28.4 1.0
N A:ASP328 4.4 26.8 1.0
CA A:THR329 4.4 23.3 1.0
CB A:LEU321 4.4 22.8 1.0
CG2 A:THR329 4.5 25.8 1.0
CB A:ASP320 4.5 26.0 1.0
CA A:ASP328 4.5 27.2 1.0
N A:LEU330 4.6 19.4 1.0
N A:CYS322 4.6 26.0 1.0
O A:ASP320 4.7 26.8 1.0
CG A:GLU349 4.7 21.0 1.0
CD2 A:LEU330 4.8 23.3 1.0
CA A:LEU330 4.8 19.5 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 Jul 14 14:12:21 2024

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