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Zinc in PDB 4jpa: MMP13 in Complex with A Piperazine Hydantoin Ligand

Protein crystallography data

The structure of MMP13 in Complex with A Piperazine Hydantoin Ligand, PDB code: 4jpa was solved by S.Gerhardt, D.Hargreaves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.90 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.771, 35.986, 101.492, 90.00, 134.99, 90.00
R / Rfree (%) 17.7 / 23

Other elements in 4jpa:

The structure of MMP13 in Complex with A Piperazine Hydantoin Ligand also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the MMP13 in Complex with A Piperazine Hydantoin Ligand (pdb code 4jpa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the MMP13 in Complex with A Piperazine Hydantoin Ligand, PDB code: 4jpa:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4jpa

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Zinc binding site 1 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:14.5
occ:1.00
N7 A:AZ6306 2.0 12.9 1.0
NE2 A:HIS232 2.1 13.7 1.0
NE2 A:HIS226 2.1 9.3 1.0
NE2 A:HIS222 2.1 10.7 1.0
C20 A:AZ6306 2.9 13.7 1.0
CD2 A:HIS232 3.0 14.0 1.0
CE1 A:HIS226 3.0 10.6 1.0
CD2 A:HIS222 3.0 10.3 1.0
C21 A:AZ6306 3.1 13.4 1.0
CE1 A:HIS232 3.1 14.2 1.0
CD2 A:HIS226 3.1 10.2 1.0
O4 A:AZ6306 3.1 12.0 1.0
CE1 A:HIS222 3.1 9.0 1.0
O5 A:AZ6306 3.4 14.8 1.0
N6 A:AZ6306 4.1 12.8 1.0
ND1 A:HIS226 4.1 10.6 1.0
CG A:HIS232 4.2 13.3 1.0
CG A:HIS222 4.2 10.8 1.0
ND1 A:HIS232 4.2 13.2 1.0
ND1 A:HIS222 4.2 9.6 1.0
CG A:HIS226 4.2 9.9 1.0
C2 A:AZ6306 4.3 14.3 1.0
O A:HOH445 4.5 11.0 1.0
C7 A:AZ6306 4.6 14.4 1.0
CE A:MET240 4.6 11.7 1.0
N1 A:AZ6306 4.6 13.5 1.0
C4 A:AZ6306 4.7 12.8 1.0
O A:HOH465 4.9 28.8 1.0
CB A:PRO242 4.9 16.0 1.0
OE2 A:GLU223 4.9 9.4 1.0

Zinc binding site 2 out of 4 in 4jpa

Go back to Zinc Binding Sites List in 4jpa
Zinc binding site 2 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:15.1
occ:1.00
OD2 A:ASP174 2.0 10.2 1.0
NE2 A:HIS187 2.0 14.8 1.0
NE2 A:HIS172 2.1 15.0 1.0
ND1 A:HIS200 2.1 8.2 1.0
CE1 A:HIS187 2.8 16.7 1.0
CG A:ASP174 2.9 12.4 1.0
CD2 A:HIS172 2.9 13.7 1.0
CE1 A:HIS200 3.0 10.2 1.0
CG A:HIS200 3.1 10.0 1.0
OD1 A:ASP174 3.1 11.7 1.0
CE1 A:HIS172 3.1 14.4 1.0
CD2 A:HIS187 3.2 14.5 1.0
CB A:HIS200 3.4 9.5 1.0
ND1 A:HIS187 4.0 16.2 1.0
CG A:HIS172 4.1 13.6 1.0
ND1 A:HIS172 4.2 13.5 1.0
O A:TYR176 4.2 16.4 1.0
NE2 A:HIS200 4.2 9.8 1.0
CD2 A:HIS200 4.2 10.3 1.0
CG A:HIS187 4.2 13.3 1.0
CB A:ASP174 4.3 13.2 1.0
CZ A:PHE189 4.5 16.5 1.0
CE1 A:PHE189 4.6 16.1 1.0
CZ A:PHE178 4.7 14.1 1.0
CE2 A:PHE178 4.8 14.3 1.0
CB A:TYR176 4.9 17.8 1.0
CA A:HIS200 4.9 9.8 1.0

Zinc binding site 3 out of 4 in 4jpa

Go back to Zinc Binding Sites List in 4jpa
Zinc binding site 3 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:13.5
occ:1.00
NE2 B:HIS232 2.0 13.0 1.0
N7 B:AZ6306 2.1 13.6 1.0
NE2 B:HIS226 2.1 12.2 1.0
NE2 B:HIS222 2.1 8.6 1.0
CD2 B:HIS222 3.0 9.6 1.0
C20 B:AZ6306 3.0 13.6 1.0
CD2 B:HIS232 3.0 13.1 1.0
CE1 B:HIS226 3.0 12.2 1.0
CE1 B:HIS232 3.0 13.1 1.0
C21 B:AZ6306 3.1 13.4 1.0
CD2 B:HIS226 3.1 12.3 1.0
CE1 B:HIS222 3.2 10.7 1.0
O4 B:AZ6306 3.2 12.2 1.0
O5 B:AZ6306 3.4 13.3 1.0
ND1 B:HIS232 4.1 12.3 1.0
CG B:HIS232 4.1 12.9 1.0
ND1 B:HIS226 4.1 12.4 1.0
N6 B:AZ6306 4.2 12.7 1.0
CG B:HIS222 4.2 10.2 1.0
ND1 B:HIS222 4.2 11.0 1.0
CG B:HIS226 4.2 11.6 1.0
C2 B:AZ6306 4.3 13.1 1.0
N1 B:AZ6306 4.6 13.0 1.0
C4 B:AZ6306 4.6 12.6 1.0
CE B:MET240 4.7 8.8 1.0
C7 B:AZ6306 4.8 13.0 1.0
O B:HOH513 4.8 9.2 1.0
CB B:PRO242 4.9 13.6 1.0
O B:HOH527 4.9 44.7 1.0
OE2 B:GLU223 5.0 12.2 1.0

Zinc binding site 4 out of 4 in 4jpa

Go back to Zinc Binding Sites List in 4jpa
Zinc binding site 4 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:14.3
occ:1.00
OD2 B:ASP174 1.9 9.5 1.0
NE2 B:HIS172 2.0 10.2 1.0
ND1 B:HIS200 2.1 8.3 1.0
NE2 B:HIS187 2.2 10.2 1.0
CG B:ASP174 2.9 12.0 1.0
CE1 B:HIS172 3.0 10.6 1.0
CD2 B:HIS172 3.0 9.6 1.0
CE1 B:HIS200 3.1 9.7 1.0
CG B:HIS200 3.1 8.7 1.0
CE1 B:HIS187 3.2 10.8 1.0
CD2 B:HIS187 3.2 11.5 1.0
OD1 B:ASP174 3.2 11.7 1.0
CB B:HIS200 3.4 9.8 1.0
ND1 B:HIS172 4.1 11.4 1.0
CG B:HIS172 4.2 11.1 1.0
NE2 B:HIS200 4.2 9.1 1.0
CD2 B:HIS200 4.2 9.1 1.0
CB B:ASP174 4.2 12.1 1.0
ND1 B:HIS187 4.3 10.8 1.0
CG B:HIS187 4.3 11.8 1.0
O B:TYR176 4.3 14.1 1.0
CZ B:PHE178 4.6 14.0 1.0
CE2 B:PHE178 4.7 14.1 1.0
CB B:TYR176 4.7 15.5 1.0
CE1 B:PHE189 4.8 14.4 1.0
O B:HOH434 4.8 10.8 1.0
CA B:HIS200 4.9 10.1 1.0
CZ B:PHE189 4.9 15.1 1.0

Reference:

C.De Savi, D.Waterson, A.Pape, S.Lamont, E.Hadley, M.Mills, K.M.Page, J.Bowyer, R.A.Maciewicz. Hydantoin Based Inhibitors of MMP13--Discovery of AZD6605. Bioorg.Med.Chem.Lett. V. 23 4705 2013.
ISSN: ISSN 0960-894X
PubMed: 23810497
DOI: 10.1016/J.BMCL.2013.05.089
Page generated: Wed Dec 16 05:26:49 2020

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