Zinc in PDB 1hy7: A Carboxylic Acid Based Inhibitor in Complex with MMP3

All present enzymatic activity of A Carboxylic Acid Based Inhibitor in Complex with MMP3:
3.4.24.17;

The structure of A Carboxylic Acid Based Inhibitor in Complex with MMP3, PDB code: 1hy7 was solved by M.G.Natchus, R.G.Bookland, M.J.Laufersweiler, S.Pikul, N.G.Almstead, B.De, M.J.Janusz, L.C.Hsieh, F.Gu, M.E.Pokross, V.S.Patel, S.M.Garver, S.X.Peng, T.M.Branch, S.L.King, T.R.Baker, D.J.Foltz, G.E.Mieling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.25 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.918, 78.059, 105.801, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22

The structure of A Carboxylic Acid Based Inhibitor in Complex with MMP3 also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the A Carboxylic Acid Based Inhibitor in Complex with MMP3 (pdb code 1hy7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the A Carboxylic Acid Based Inhibitor in Complex with MMP3, PDB code: 1hy7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Carboxylic Acid Based Inhibitor in Complex with MMP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.3 occ:1.00 NE2 A:HIS201 2.0 10.7 1.0 NE2 A:HIS211 2.1 12.3 1.0 NE2 A:HIS205 2.1 9.1 1.0 O A:HOH379 2.8 20.7 1.0 CE1 A:HIS201 3.0 10.4 1.0 CE1 A:HIS211 3.0 12.8 1.0 CD2 A:HIS201 3.0 10.0 1.0 CE1 A:HIS205 3.1 10.3 1.0 CD2 A:HIS211 3.1 14.5 1.0 CD2 A:HIS205 3.1 10.5 1.0 ND1 A:HIS201 4.1 11.0 1.0 ND1 A:HIS211 4.1 12.7 1.0 CG A:HIS201 4.2 9.9 1.0 CG A:HIS211 4.2 12.7 1.0 ND1 A:HIS205 4.2 9.9 1.0 CG A:HIS205 4.2 9.0 1.0 CE A:MET219 4.7 12.1 1.0 OE1 A:GLU202 4.8 12.3 1.0 OE2 A:GLU202 4.8 11.4 1.0

Zinc binding site 2 out of 4 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Carboxylic Acid Based Inhibitor in Complex with MMP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.1 occ:1.00 OD2 A:ASP153 2.0 10.3 1.0 NE2 A:HIS166 2.0 10.2 1.0 ND1 A:HIS179 2.1 11.5 1.0 NE2 A:HIS151 2.1 9.9 1.0 CG A:ASP153 2.9 12.3 1.0 CE1 A:HIS166 2.9 8.7 1.0 CE1 A:HIS179 3.0 9.7 1.0 CD2 A:HIS151 3.0 11.2 1.0 CD2 A:HIS166 3.1 9.0 1.0 CE1 A:HIS151 3.1 11.6 1.0 CG A:HIS179 3.1 7.4 1.0 OD1 A:ASP153 3.2 14.1 1.0 CB A:HIS179 3.5 8.1 1.0 ND1 A:HIS166 4.1 9.5 1.0 NE2 A:HIS179 4.1 9.8 1.0 CG A:HIS151 4.1 12.2 1.0 CG A:HIS166 4.2 8.5 1.0 ND1 A:HIS151 4.2 11.7 1.0 CD2 A:HIS179 4.2 10.2 1.0 OH A:TYR168 4.2 14.1 1.0 O A:TYR155 4.3 14.1 1.0 CB A:ASP153 4.3 13.6 1.0 CE1 A:TYR168 4.5 12.0 1.0 CZ A:PHE157 4.6 9.0 1.0 CE1 A:PHE157 4.7 10.8 1.0 CZ A:TYR168 4.9 14.3 1.0

Zinc binding site 3 out of 4 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Carboxylic Acid Based Inhibitor in Complex with MMP3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:18.6 occ:1.00 O2 B:MBS901 1.9 20.1 1.0 NE2 B:HIS711 2.1 30.5 1.0 NE2 B:HIS701 2.1 14.9 1.0 NE2 B:HIS705 2.2 24.9 1.0 C1 B:MBS901 2.8 20.9 1.0 CE1 B:HIS705 2.8 20.8 1.0 CD2 B:HIS711 2.9 26.4 1.0 O1 B:MBS901 2.9 20.3 1.0 CD2 B:HIS701 3.0 14.8 1.0 CE1 B:HIS701 3.1 19.1 1.0 CE1 B:HIS711 3.2 26.9 1.0 CD2 B:HIS705 3.3 23.6 1.0 ND1 B:HIS705 4.1 17.6 1.0 CG B:HIS711 4.1 27.0 1.0 CG B:HIS701 4.2 12.5 1.0 C2 B:MBS901 4.2 28.1 1.0 ND1 B:HIS701 4.2 17.0 1.0 ND1 B:HIS711 4.2 28.0 1.0 CG B:HIS705 4.3 17.1 1.0 C22 B:MBS901 4.5 25.7 1.0 N1 B:MBS901 4.6 27.1 1.0 C23 B:MBS901 4.6 24.0 1.0 C21 B:MBS901 4.6 24.0 1.0 OE2 B:GLU702 4.7 15.6 1.0 O B:HOH76 4.7 16.9 1.0 C3 B:MBS901 4.7 30.3 1.0 CE B:MET719 4.8 17.1 1.0 C24 B:MBS901 4.9 23.3 1.0 C26 B:MBS901 4.9 23.4 1.0

Zinc binding site 4 out of 4 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Carboxylic Acid Based Inhibitor in Complex with MMP3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:12.7 occ:1.00 NE2 B:HIS666 2.0 12.5 1.0 NE2 B:HIS651 2.0 13.0 1.0 OD2 B:ASP653 2.0 11.6 1.0 ND1 B:HIS679 2.1 10.7 1.0 CE1 B:HIS679 2.9 12.5 1.0 CE1 B:HIS666 2.9 12.8 1.0 CG B:ASP653 3.0 13.6 1.0 CD2 B:HIS651 3.0 11.6 1.0 CE1 B:HIS651 3.0 13.5 1.0 CD2 B:HIS666 3.1 12.7 1.0 CG B:HIS679 3.1 11.5 1.0 OD1 B:ASP653 3.2 12.5 1.0 CB B:HIS679 3.5 10.6 1.0 OH B:TYR668 4.1 15.8 1.0 ND1 B:HIS666 4.1 12.6 1.0 NE2 B:HIS679 4.1 10.5 1.0 ND1 B:HIS651 4.1 14.6 1.0 CG B:HIS651 4.1 12.8 1.0 CG B:HIS666 4.2 10.8 1.0 CD2 B:HIS679 4.2 13.0 1.0 O B:TYR655 4.2 13.2 1.0 CB B:ASP653 4.3 13.1 1.0 CE1 B:TYR668 4.5 13.9 1.0 CE1 B:PHE657 4.6 11.1 1.0 CZ B:PHE657 4.7 12.0 1.0 CZ B:TYR668 4.8 16.1 1.0

M.G.Natchus, R.G.Bookland, M.J.Laufersweiler, S.Pikul, N.G.Almstead, B.De, M.J.Janusz, L.C.Hsieh, F.Gu, M.E.Pokross, V.S.Patel, S.M.Garver, S.X.Peng, T.M.Branch, S.L.King, T.R.Baker, D.J.Foltz, G.E.Mieling. Development of New Carboxylic Acid-Based Mmp Inhibitors Derived From Functionalized Propargylglycines. J.Med.Chem. V. 44 1060 2001.
ISSN: ISSN 0022-2623
PubMed: 11297453
DOI: 10.1021/JM000477L