Zinc in PDB 5bpa: X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate

The structure of X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate, PDB code: 5bpa was solved by N.A.Farrow, S.M.Margarit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.54 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.281, 36.141, 96.097, 90.00, 131.48, 90.00
R / Rfree (%)	23.7 / 28

The structure of X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate (pdb code 5bpa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate, PDB code: 5bpa:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:5.4 occ:1.00 NE2 A:HIS222 2.0 1.7 1.0 NE2 A:HIS226 2.2 5.0 1.0 NE2 A:HIS232 2.2 3.8 1.0 CE1 A:HIS222 2.9 2.1 1.0 CD2 A:HIS232 2.9 7.0 1.0 CD2 A:HIS222 3.0 4.8 1.0 CD2 A:HIS226 3.1 12.8 1.0 CE1 A:HIS226 3.2 17.5 1.0 CE1 A:HIS232 3.3 6.9 1.0 ND1 A:HIS222 4.1 5.7 1.0 CG A:HIS222 4.1 3.2 1.0 CG A:HIS232 4.2 0.0 1.0 OE2 A:GLU223 4.2 3.4 1.0 ND1 A:HIS232 4.3 4.0 1.0 CG A:HIS226 4.3 7.8 1.0 ND1 A:HIS226 4.3 10.3 1.0 O12 A:4UF306 4.6 11.9 1.0 OE1 A:GLU223 4.6 9.3 1.0 O A:HOH516 4.7 26.1 1.0 CD A:GLU223 4.7 4.9 1.0 CE A:MET240 4.8 2.6 1.0 C13 A:4UF306 4.9 11.8 1.0

Zinc binding site 2 out of 4 in the X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:5.3 occ:1.00 OD2 A:ASP174 1.9 4.5 1.0 NE2 A:HIS172 2.1 3.7 1.0 NE2 A:HIS187 2.1 6.9 1.0 ND1 A:HIS200 2.2 2.4 1.0 CG A:ASP174 2.9 7.8 1.0 CD2 A:HIS172 3.0 5.6 1.0 CE1 A:HIS187 3.0 10.5 1.0 CE1 A:HIS200 3.1 9.0 1.0 CG A:HIS200 3.2 1.8 1.0 CE1 A:HIS172 3.2 7.8 1.0 CD2 A:HIS187 3.2 5.0 1.0 OD1 A:ASP174 3.3 4.2 1.0 CB A:HIS200 3.5 0.0 1.0 O A:TYR176 4.1 4.0 1.0 CG A:HIS172 4.2 5.9 1.0 ND1 A:HIS187 4.2 7.1 1.0 ND1 A:HIS172 4.2 3.2 1.0 NE2 A:HIS200 4.2 5.6 1.0 CB A:ASP174 4.2 6.2 1.0 CG A:HIS187 4.3 9.3 1.0 CD2 A:HIS200 4.3 7.0 1.0 CE1 A:PHE189 4.4 8.2 1.0 CZ A:PHE178 4.7 9.3 1.0 CZ A:PHE189 4.7 17.3 1.0 CB A:TYR176 4.8 8.7 1.0 CE2 A:PHE178 4.8 6.1 1.0 O A:HOH434 4.9 5.4 1.0 C A:TYR176 5.0 0.0 1.0 CA A:HIS200 5.0 0.5 1.0

Zinc binding site 3 out of 4 in the X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:9.8 occ:1.00 NE2 B:HIS232 2.0 11.3 1.0 NE2 B:HIS222 2.1 6.5 1.0 NE2 B:HIS226 2.2 7.9 1.0 CD2 B:HIS232 2.8 8.0 1.0 CD2 B:HIS222 3.0 5.9 1.0 CD2 B:HIS226 3.1 13.8 1.0 CE1 B:HIS232 3.1 12.0 1.0 CE1 B:HIS222 3.1 3.8 1.0 CE1 B:HIS226 3.2 15.6 1.0 CG B:HIS232 4.0 12.3 1.0 ND1 B:HIS232 4.1 13.8 1.0 CG B:HIS222 4.2 7.5 1.0 ND1 B:HIS222 4.2 2.6 1.0 OE2 B:GLU223 4.2 11.8 1.0 CG B:HIS226 4.3 13.0 1.0 ND1 B:HIS226 4.3 11.2 1.0 OE1 B:GLU223 4.7 11.4 1.0 CE B:MET240 4.8 8.8 1.0 O12 B:4UF306 4.8 7.5 1.0 CD B:GLU223 4.8 13.9 1.0 O B:HOH502 4.9 18.0 1.0

Zinc binding site 4 out of 4 in the X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Co-Structure of Mmp-13 with 4-[({5-[2-(Ethoxycarbonyl)-1H-Indol- 5-Yl]-1-Methyl-1H-Pyrazol-3-Yl}Formamido)Methyl]Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:5.5 occ:1.00 OD2 B:ASP174 2.0 8.5 1.0 ND1 B:HIS200 2.1 5.6 1.0 NE2 B:HIS172 2.1 3.0 1.0 NE2 B:HIS187 2.1 6.6 1.0 CG B:ASP174 2.9 13.4 1.0 CE1 B:HIS200 3.0 9.3 1.0 CD2 B:HIS172 3.0 2.7 1.0 CE1 B:HIS187 3.1 7.3 1.0 CE1 B:HIS172 3.1 11.2 1.0 CG B:HIS200 3.1 3.5 1.0 CD2 B:HIS187 3.2 13.4 1.0 OD1 B:ASP174 3.2 4.6 1.0 CB B:HIS200 3.5 1.1 1.0 NE2 B:HIS200 4.1 5.8 1.0 CG B:HIS172 4.1 6.9 1.0 ND1 B:HIS172 4.2 4.6 1.0 CD2 B:HIS200 4.2 11.2 1.0 ND1 B:HIS187 4.2 5.8 1.0 O B:TYR176 4.2 6.9 1.0 CB B:ASP174 4.3 3.6 1.0 CG B:HIS187 4.3 7.2 1.0 CE1 B:PHE189 4.6 13.7 1.0 O B:HOH414 4.7 7.4 1.0 CB B:TYR176 4.7 7.5 1.0 CZ B:PHE178 4.8 4.1 1.0 CE2 B:PHE178 4.8 4.9 1.0 CZ B:PHE189 4.9 16.6 1.0 CA B:HIS200 5.0 3.5 1.0

S.J.Taylor, A.Abeywardane, S.Liang, I.Muegge, A.K.Padyana, Z.Xiong, M.Hill-Drzewi, B.Farmer, X.Li, B.Collins, J.X.Li, A.Heim-Riether, J.Proudfoot, Q.Zhang, D.Goldberg, L.Zuvela-Jelaska, H.Zaher, J.Li, N.A.Farrow. Fragment-Based Discovery of Indole Inhibitors of Matrix Metalloproteinase-13. J. Med. Chem. V. 54 8174 2011.
ISSN: ISSN 1520-4804
PubMed: 22017539
DOI: 10.1021/JM201129M