Zinc in PDB 4a7b: MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22, PDB code: 4a7b was solved by D.Hargreaves, S.Gerhardt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.02 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.854, 36.220, 95.568, 90.00, 131.10, 90.00
R / Rfree (%)	19.3 / 25.3

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 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 Novel Selective Non Zinc Binding Inhibitor CMPD22 (pdb code 4a7b). 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 Novel Selective Non Zinc Binding Inhibitor CMPD22, PDB code: 4a7b:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22


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 Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1276 b:24.3 occ:1.00 O A:HAE1273 1.8 28.0 1.0 NE2 A:HIS232 2.0 24.2 1.0 NE2 A:HIS226 2.1 17.5 1.0 NE2 A:HIS222 2.2 17.8 1.0 N A:HAE1273 2.7 28.1 1.0 O2 A:HAE1273 2.7 35.5 1.0 CD2 A:HIS232 2.8 20.4 1.0 C2 A:HAE1273 2.9 33.5 1.0 CD2 A:HIS222 3.0 17.9 1.0 CE1 A:HIS226 3.1 17.6 1.0 CD2 A:HIS226 3.1 16.8 1.0 CE1 A:HIS232 3.2 22.7 1.0 CE1 A:HIS222 3.3 18.4 1.0 CG A:HIS232 4.0 20.9 1.0 ND1 A:HIS232 4.2 23.4 1.0 C1 A:HAE1273 4.2 40.2 1.0 OE2 A:GLU223 4.2 18.7 1.0 ND1 A:HIS226 4.2 18.2 1.0 CG A:HIS226 4.2 18.2 1.0 CG A:HIS222 4.2 18.3 1.0 ND1 A:HIS222 4.3 17.9 1.0 C18 A:3W51000 4.7 26.3 1.0 OE1 A:GLU223 4.7 22.1 1.0 CE A:MET240 4.8 17.2 1.0 CD A:GLU223 4.8 20.3 1.0 O A:HOH2086 5.0 39.2 1.0 C17 A:3W51000 5.0 25.5 1.0 CA A:PRO242 5.0 23.9 1.0

Zinc binding site 2 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22


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 Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1278 b:24.2 occ:1.00 ND1 A:HIS200 2.0 21.6 1.0 NE2 A:HIS172 2.0 19.5 1.0 NE2 A:HIS187 2.0 27.6 1.0 OD2 A:ASP174 2.1 24.7 1.0 CE1 A:HIS187 2.6 25.9 1.0 CG A:ASP174 2.9 25.1 1.0 CD2 A:HIS172 3.0 19.5 1.0 CE1 A:HIS200 3.0 20.9 1.0 CG A:HIS200 3.0 21.5 1.0 CE1 A:HIS172 3.1 21.1 1.0 OD1 A:ASP174 3.2 23.5 1.0 CD2 A:HIS187 3.3 25.5 1.0 CB A:HIS200 3.4 20.4 1.0 ND1 A:HIS187 3.9 26.2 1.0 O A:TYR176 4.1 30.1 1.0 NE2 A:HIS200 4.1 20.3 1.0 CG A:HIS172 4.1 20.6 1.0 ND1 A:HIS172 4.1 20.7 1.0 CD2 A:HIS200 4.2 21.5 1.0 CG A:HIS187 4.2 24.5 1.0 CB A:ASP174 4.4 24.6 1.0 CB A:TYR176 4.5 35.4 1.0 CZ A:PHE178 4.6 21.1 1.0 CE2 A:PHE178 4.6 21.6 1.0 CE1 A:PHE189 4.7 26.0 1.0 CA A:HIS200 4.9 20.1 1.0 C A:TYR176 4.9 30.2 1.0 O A:HOH2058 5.0 25.4 1.0 O A:HOH2062 5.0 29.9 1.0

Zinc binding site 3 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22


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 Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1273 b:29.4 occ:1.00 NE2 B:HIS226 2.1 27.6 1.0 NE2 B:HIS222 2.1 24.9 1.0 NE2 B:HIS232 2.1 24.6 1.0 O B:HAE1270 2.4 34.9 1.0 CD2 B:HIS222 3.0 23.4 1.0 CD2 B:HIS232 3.0 26.3 1.0 CD2 B:HIS226 3.0 25.1 1.0 N B:HAE1270 3.0 44.1 1.0 CE1 B:HIS226 3.1 26.7 1.0 CE1 B:HIS222 3.1 24.1 1.0 CE1 B:HIS232 3.2 27.1 1.0 C2 B:HAE1270 3.9 46.8 1.0 CG B:HIS222 4.2 24.1 1.0 CG B:HIS232 4.2 26.8 1.0 ND1 B:HIS222 4.2 25.2 1.0 ND1 B:HIS226 4.2 27.1 1.0 CG B:HIS226 4.2 25.8 1.0 ND1 B:HIS232 4.2 28.3 1.0 OE2 B:GLU223 4.4 25.7 1.0 O2 B:HAE1270 4.4 50.2 1.0 OE1 B:GLU223 4.7 25.2 1.0 C20 B:3W41000 4.7 31.9 1.0 CE B:MET240 4.8 23.1 1.0 C21 B:3W41000 4.8 30.1 1.0 C1 B:HAE1270 4.8 40.4 1.0 CD B:GLU223 4.9 26.6 1.0 O B:HOH2070 5.0 28.4 1.0

Zinc binding site 4 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22


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 Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1274 b:26.1 occ:1.00 NE2 B:HIS172 2.0 23.1 1.0 OD2 B:ASP174 2.1 24.7 1.0 NE2 B:HIS187 2.1 22.5 1.0 ND1 B:HIS200 2.1 22.3 1.0 CG B:ASP174 2.9 25.9 1.0 CD2 B:HIS172 3.0 23.2 1.0 CE1 B:HIS187 3.0 23.8 1.0 CE1 B:HIS200 3.0 22.9 1.0 CE1 B:HIS172 3.0 24.8 1.0 OD1 B:ASP174 3.1 26.8 1.0 CD2 B:HIS187 3.1 23.2 1.0 CG B:HIS200 3.2 22.9 1.0 CB B:HIS200 3.6 22.6 1.0 NE2 B:HIS200 4.1 22.8 1.0 ND1 B:HIS172 4.1 24.6 1.0 CG B:HIS172 4.2 24.5 1.0 ND1 B:HIS187 4.2 23.6 1.0 CD2 B:HIS200 4.2 22.4 1.0 CG B:HIS187 4.3 23.6 1.0 CB B:ASP174 4.3 24.7 1.0 O B:TYR176 4.3 28.0 1.0 CZ B:PHE178 4.5 23.8 1.0 CE2 B:PHE178 4.6 24.3 1.0 CE1 B:PHE189 4.7 27.0 1.0 O B:HOH2056 4.8 22.1 1.0 CZ B:PHE189 4.8 29.1 1.0

C.De Savi, A.D.Morley, I.Nash, G.Karoutchi, K.Page, A.Ting, S.Gerhardt. Lead Optimisation of Selective Non-Zinc Binding Inhibitors of MMP13. Part 2. Bioorg.Med.Chem.Lett. V. 22 271 2012.
ISSN: ISSN 0960-894X
PubMed: 22153941
DOI: 10.1016/J.BMCL.2011.11.034