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

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

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

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 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 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 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 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

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