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Calcium 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

Protein crystallography data

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

Other elements in 5bpa:

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:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5bpa

Go back to Calcium Binding Sites List in 5bpa
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca303

b:50.3
occ:1.00
 O A:ASP203 2.9 8.8 1.0
O A:GLU205 2.9 16.8 1.0
OD2 A:ASP128 2.9 20.8 1.0
OD2 A:ASP203 2.9 11.7 1.0
OD1 A:ASP128 3.1 26.2 1.0
CG A:ASP128 3.3 22.8 1.0
O A:HOH489 3.6 22.8 1.0
OG1 A:THR126 3.7 6.2 1.0
C A:ASP203 3.7 11.6 1.0
CG A:ASP203 3.8 15.0 1.0
C A:GLU205 4.1 10.3 1.0
CD A:PRO127 4.1 4.0 1.0
CA A:ASP203 4.2 3.8 1.0
CB A:ASP203 4.4 6.5 1.0
CG A:PRO127 4.5 5.5 1.0
CD1 A:TRP207 4.6 3.5 1.0
CB A:ASP128 4.6 6.8 1.0
OD1 A:ASP203 4.7 16.6 1.0
N A:GLU205 4.7 4.2 1.0
N A:ASP204 4.8 3.7 1.0
CA A:THR206 4.8 3.3 1.0
N A:ASP128 4.8 5.0 1.0
C A:ASP204 4.9 15.6 1.0
CB A:PRO127 4.9 4.5 1.0
N A:PRO127 4.9 3.7 1.0
N A:THR206 4.9 5.3 1.0
CA A:ASP204 5.0 7.0 1.0

Calcium binding site 2 out of 6 in 5bpa

Go back to Calcium Binding Sites List in 5bpa
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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:Ca304

b:6.1
occ:1.00
 O A:GLY180 2.3 9.7 1.0
OE2 A:GLU205 2.3 19.7 1.0
OD2 A:ASP202 2.4 4.9 1.0
OD1 A:ASP179 2.4 10.0 1.0
O A:SER182 2.4 10.2 1.0
O A:LEU184 2.4 8.5 1.0
CG A:ASP202 3.5 19.2 1.0
C A:GLY180 3.5 11.1 1.0
C A:SER182 3.5 24.2 1.0
CD A:GLU205 3.5 13.6 1.0
CG A:ASP179 3.5 17.3 1.0
C A:LEU184 3.6 15.9 1.0
N A:SER182 3.9 12.7 1.0
N A:LEU184 3.9 8.4 1.0
C A:PRO181 4.0 11.9 1.0
N A:GLY180 4.0 10.2 1.0
OD2 A:ASP179 4.1 15.3 1.0
C A:GLY183 4.2 8.1 1.0
C A:ASP179 4.2 21.2 1.0
N A:ASP179 4.2 6.3 1.0
CB A:ASP202 4.2 2.2 1.0
CG A:GLU205 4.3 12.6 1.0
CA A:LEU184 4.3 12.6 1.0
CA A:SER182 4.3 25.5 1.0
OD1 A:ASP202 4.3 3.0 1.0
O A:PRO181 4.4 21.0 1.0
CA A:GLY180 4.4 8.7 1.0
N A:PRO181 4.4 4.1 1.0
CA A:PRO181 4.4 3.7 1.0
N A:GLY183 4.5 13.3 1.0
OE1 A:GLU205 4.5 13.0 1.0
CA A:GLY183 4.5 11.9 1.0
O A:HOH494 4.6 37.3 1.0
CA A:ASP179 4.6 18.4 1.0
CB A:LEU184 4.6 12.8 1.0
N A:LEU185 4.6 6.1 1.0
O A:ASP179 4.7 8.8 1.0
CB A:ASP179 4.7 8.9 1.0
O A:GLY183 4.7 15.1 1.0
CA A:LEU185 4.8 2.2 1.0

Calcium binding site 3 out of 6 in 5bpa

Go back to Calcium Binding Sites List in 5bpa
Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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
A:Ca305

b:27.3
occ:1.00
 O A:ASN194 2.5 21.9 1.0
O A:GLY196 2.5 10.6 1.0
O A:ASP162 2.6 7.5 1.0
OD1 A:ASP198 2.7 8.7 1.0
O A:HOH416 2.8 24.2 1.0
CG A:ASP198 3.5 11.9 1.0
C A:GLY196 3.5 15.0 1.0
C A:ASP162 3.6 4.9 1.0
C A:ASN194 3.6 10.2 1.0
C A:TYR195 3.7 12.2 1.0
O A:HOH411 3.8 17.9 1.0
OD2 A:ASP198 3.9 8.3 1.0
N A:GLY196 3.9 14.6 1.0
O A:TYR195 3.9 8.2 1.0
O A:ALA161 4.0 8.5 1.0
CA A:TYR195 4.1 14.2 1.0
O A:HOH522 4.1 35.1 1.0
N A:ASP198 4.2 2.2 1.0
CA A:GLY196 4.3 10.9 1.0
N A:TYR195 4.3 19.3 1.0
CA A:ASP162 4.4 3.2 1.0
N A:GLY197 4.5 1.1 1.0
N A:ILE163 4.6 10.0 1.0
CG A:MET164 4.6 17.7 1.0
CA A:GLY197 4.6 0.0 1.0
CB A:ASP198 4.7 4.1 1.0
N A:MET164 4.7 2.9 1.0
C A:GLY197 4.7 0.0 1.0
O A:HOH407 4.7 23.8 1.0
CA A:ILE163 4.7 6.3 1.0
CA A:ASN194 4.8 12.7 1.0
CA A:ASP198 4.8 2.0 1.0
O A:GLY192 4.9 12.9 1.0
C A:ALA161 5.0 3.5 1.0
CH2 A:TRP113 5.0 10.7 1.0

Calcium binding site 4 out of 6 in 5bpa

Go back to Calcium Binding Sites List in 5bpa
Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca 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:Ca303

b:48.2
occ:1.00
 OD2 B:ASP128 2.8 13.7 1.0
O B:GLU205 2.8 11.2 1.0
O B:ASP203 2.9 6.4 1.0
OD2 B:ASP203 3.0 15.8 1.0
CG B:ASP128 3.3 11.2 1.0
OD1 B:ASP128 3.3 17.3 1.0
C B:ASP203 3.7 0.0 1.0
OG1 B:THR126 3.7 7.0 1.0
CG B:ASP203 3.9 12.4 1.0
C B:GLU205 4.0 10.1 1.0
O B:HOH454 4.1 28.4 1.0
CA B:ASP203 4.1 3.0 1.0
CD B:PRO127 4.2 4.2 1.0
O B:HOH491 4.4 31.5 1.0
CD1 B:TRP207 4.4 4.0 1.0
CB B:ASP203 4.4 7.2 1.0
CB B:ASP128 4.6 6.3 1.0
CA B:THR206 4.6 2.4 1.0
N B:GLU205 4.6 8.5 1.0
N B:ASP204 4.6 3.1 1.0
OD1 B:ASP203 4.7 13.5 1.0
N B:THR206 4.7 4.9 1.0
C B:ASP204 4.8 16.8 1.0
CG B:PRO127 4.8 6.7 1.0
CA B:ASP204 4.9 7.9 1.0
N B:TRP207 4.9 9.2 1.0
NE1 B:TRP207 5.0 2.7 1.0
CA B:GLU205 5.0 9.9 1.0
N B:ASP128 5.0 7.8 1.0

Calcium binding site 5 out of 6 in 5bpa

Go back to Calcium Binding Sites List in 5bpa
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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:Ca304

b:13.2
occ:1.00
 O B:LEU184 2.3 11.6 1.0
O B:GLY180 2.3 18.6 1.0
OD2 B:ASP202 2.4 5.6 1.0
O B:SER182 2.5 20.9 1.0
OD1 B:ASP179 2.5 20.5 1.0
OE1 B:GLU205 2.5 32.6 1.0
C B:LEU184 3.5 17.2 1.0
CG B:ASP202 3.5 9.1 1.0
C B:GLY180 3.5 29.5 1.0
CD B:GLU205 3.6 19.0 1.0
C B:SER182 3.6 34.9 1.0
CG B:ASP179 3.7 21.6 1.0
N B:LEU184 3.9 17.4 1.0
N B:SER182 3.9 21.2 1.0
CG B:GLU205 4.1 10.2 1.0
N B:GLY180 4.1 14.7 1.0
C B:PRO181 4.1 14.1 1.0
CA B:LEU184 4.1 17.5 1.0
C B:GLY183 4.2 23.4 1.0
CB B:ASP202 4.2 2.3 1.0
N B:ASP179 4.2 12.6 1.0
C B:ASP179 4.3 19.2 1.0
OD2 B:ASP179 4.3 20.7 1.0
CA B:SER182 4.3 29.8 1.0
OD1 B:ASP202 4.4 4.0 1.0
CA B:GLY180 4.4 14.7 1.0
CB B:LEU184 4.4 14.6 1.0
CA B:PRO181 4.5 17.3 1.0
N B:PRO181 4.5 21.3 1.0
N B:GLY183 4.5 21.4 1.0
N B:LEU185 4.5 7.4 1.0
O B:PRO181 4.5 29.0 1.0
OE2 B:GLU205 4.6 20.7 1.0
O B:GLY183 4.6 17.0 1.0
CA B:ASP179 4.6 14.2 1.0
CA B:GLY183 4.6 23.5 1.0
O B:ASP179 4.7 21.3 1.0
CB B:ASP179 4.8 16.8 1.0
CA B:LEU185 4.8 9.9 1.0

Calcium binding site 6 out of 6 in 5bpa

Go back to Calcium Binding Sites List in 5bpa
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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:Ca305

b:31.6
occ:1.00
 O B:ASN194 2.6 37.8 1.0
O B:ASP162 2.6 10.5 1.0
O B:GLY196 2.6 16.6 1.0
OD1 B:ASP198 2.7 7.2 1.0
O B:HOH517 3.5 34.3 1.0
C B:ASP162 3.5 6.3 1.0
CG B:ASP198 3.6 19.9 1.0
C B:GLY196 3.7 11.2 1.0
O B:ALA161 3.7 11.2 1.0
C B:ASN194 3.8 29.0 1.0
O B:HOH418 3.8 15.9 1.0
C B:TYR195 3.9 20.5 1.0
O B:TYR195 4.0 15.2 1.0
OD2 B:ASP198 4.0 10.8 1.0
N B:GLY196 4.1 22.9 1.0
CA B:ASP162 4.2 6.6 1.0
N B:ASP198 4.3 8.1 1.0
CA B:TYR195 4.4 20.4 1.0
N B:ILE163 4.5 5.9 1.0
CA B:GLY196 4.5 10.4 1.0
N B:TYR195 4.6 20.8 1.0
CG B:MET164 4.6 6.8 1.0
N B:GLY197 4.7 11.1 1.0
N B:MET164 4.7 4.6 1.0
O B:GLY192 4.7 23.7 1.0
CA B:ILE163 4.7 4.7 1.0
C B:ALA161 4.8 10.4 1.0
O B:HOH470 4.8 29.1 1.0
CA B:GLY197 4.8 5.2 1.0
CB B:ASP198 4.8 7.3 1.0
N B:ASN194 4.8 35.7 1.0
CA B:ASN194 4.8 54.3 1.0
C B:GLY197 4.8 13.8 1.0
CA B:ASP198 4.9 5.3 1.0

Reference:

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
Page generated: Sun Jul 14 16:55:15 2024

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