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Calcium in PDB 3wv1: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid, PDB code: 3wv1 was solved by H.Oki, Y.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.65 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.372, 36.058, 95.298, 90.00, 130.90, 90.00
R / Rfree (%) 17.5 / 22

Other elements in 3wv1:

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Zinc (Zn) 4 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid (pdb code 3wv1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid, PDB code: 3wv1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3wv1

Go back to Calcium Binding Sites List in 3wv1
Calcium binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:19.7
occ:1.00
OE2 A:GLU205 2.1 23.8 1.0
OD2 A:ASP202 2.2 16.8 1.0
O A:GLY180 2.2 21.5 1.0
O A:LEU184 2.3 20.6 1.0
OD1 A:ASP179 2.3 23.1 1.0
O A:SER182 2.3 29.2 1.0
CG A:ASP202 3.4 14.5 1.0
CD A:GLU205 3.4 21.5 1.0
C A:LEU184 3.4 21.8 1.0
CG A:ASP179 3.5 28.8 1.0
C A:GLY180 3.5 21.7 1.0
C A:SER182 3.5 29.4 1.0
N A:LEU184 3.9 22.9 1.0
N A:SER182 4.0 27.1 1.0
OD2 A:ASP179 4.0 28.1 1.0
C A:PRO181 4.0 26.8 1.0
CB A:ASP202 4.1 13.7 1.0
N A:GLY180 4.1 22.7 1.0
CA A:LEU184 4.1 24.6 1.0
OE1 A:GLU205 4.2 22.0 1.0
C A:GLY183 4.2 24.9 1.0
N A:ASP179 4.3 24.3 1.0
OD1 A:ASP202 4.3 12.1 1.0
CG A:GLU205 4.3 18.0 1.0
CA A:SER182 4.3 30.5 1.0
C A:ASP179 4.4 26.4 1.0
N A:PRO181 4.4 22.7 1.0
O A:PRO181 4.4 28.8 1.0
CA A:GLY180 4.4 23.9 1.0
CA A:PRO181 4.4 24.1 1.0
CB A:LEU184 4.4 25.6 1.0
N A:GLY183 4.4 28.5 1.0
N A:LEU185 4.5 18.7 1.0
CA A:GLY183 4.5 26.1 1.0
CA A:ASP179 4.6 27.3 1.0
CB A:ASP179 4.6 28.2 1.0
O A:GLY183 4.8 24.2 1.0
CA A:LEU185 4.8 15.5 1.0
O A:ASP179 4.9 27.0 1.0
O A:HOH621 5.0 18.5 1.0

Calcium binding site 2 out of 4 in 3wv1

Go back to Calcium Binding Sites List in 3wv1
Calcium binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:23.6
occ:1.00
O A:ASP162 2.3 18.7 1.0
O A:GLY196 2.3 16.5 1.0
O A:HOH605 2.3 14.9 1.0
O A:HOH698 2.4 24.4 1.0
OD1 A:ASP198 2.4 17.7 1.0
O A:ASN194 2.4 27.4 1.0
C A:ASP162 3.4 17.5 1.0
CG A:ASP198 3.5 18.7 1.0
C A:GLY196 3.5 16.2 1.0
C A:ASN194 3.6 26.1 1.0
OD2 A:ASP198 3.9 20.3 1.0
O A:ALA161 4.0 23.6 1.0
C A:TYR195 4.0 21.8 1.0
N A:GLY196 4.0 20.6 1.0
O A:HOH678 4.1 32.2 1.0
N A:ASP198 4.2 18.5 1.0
CA A:ASP162 4.2 20.4 1.0
O A:TYR195 4.2 19.7 1.0
CA A:GLY196 4.2 16.6 1.0
O A:GLY192 4.4 24.0 1.0
N A:ILE163 4.4 18.6 1.0
O A:HOH602 4.4 25.9 1.0
N A:GLY197 4.4 17.0 1.0
N A:TYR195 4.5 26.3 1.0
N A:ASN194 4.5 28.2 1.0
CA A:TYR195 4.5 24.7 1.0
CA A:ASN194 4.5 30.0 1.0
CA A:GLY197 4.6 15.3 1.0
C A:GLY197 4.6 18.5 1.0
N A:MET164 4.6 16.6 1.0
CA A:ILE163 4.6 17.9 1.0
CB A:ASP198 4.7 19.9 1.0
O A:HOH739 4.7 37.9 1.0
CH2 A:TRP113 4.7 19.8 1.0
CA A:ASP198 4.8 18.0 1.0
CG A:MET164 4.8 18.4 1.0
C A:PRO193 4.8 27.8 1.0
C A:ALA161 4.9 22.5 1.0

Calcium binding site 3 out of 4 in 3wv1

Go back to Calcium Binding Sites List in 3wv1
Calcium binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:25.7
occ:1.00
OE2 B:GLU205 2.2 23.6 1.0
O B:LEU184 2.2 30.6 1.0
O B:GLY180 2.3 29.6 1.0
OD2 B:ASP202 2.3 24.9 1.0
OD1 B:ASP179 2.3 25.1 1.0
O B:SER182 2.5 34.5 1.0
CG B:ASP202 3.4 22.7 1.0
C B:LEU184 3.4 28.8 1.0
CD B:GLU205 3.5 27.8 1.0
CG B:ASP179 3.5 31.8 1.0
C B:SER182 3.5 35.4 1.0
C B:GLY180 3.5 29.0 1.0
N B:SER182 3.9 35.1 1.0
N B:LEU184 3.9 30.2 1.0
N B:GLY180 3.9 29.7 1.0
CB B:ASP202 4.0 20.3 1.0
C B:PRO181 4.0 33.4 1.0
OD2 B:ASP179 4.1 38.6 1.0
CA B:LEU184 4.1 31.3 1.0
CA B:SER182 4.2 36.9 1.0
N B:ASP179 4.2 31.7 1.0
C B:GLY183 4.3 30.2 1.0
OD1 B:ASP202 4.3 22.4 1.0
C B:ASP179 4.3 31.3 1.0
CA B:GLY180 4.3 28.8 1.0
OE1 B:GLU205 4.3 33.0 1.0
CG B:GLU205 4.3 25.1 1.0
O B:PRO181 4.4 34.5 1.0
N B:LEU185 4.5 26.2 1.0
N B:PRO181 4.5 31.2 1.0
N B:GLY183 4.5 31.4 1.0
CA B:PRO181 4.5 31.8 1.0
CB B:LEU184 4.5 32.2 1.0
CA B:ASP179 4.6 31.8 1.0
CB B:ASP179 4.6 33.3 1.0
CA B:LEU185 4.7 28.0 1.0
CA B:GLY183 4.7 29.9 1.0
O B:GLY183 4.8 28.2 1.0
O B:ASP179 4.9 32.9 1.0

Calcium binding site 4 out of 4 in 3wv1

Go back to Calcium Binding Sites List in 3wv1
Calcium binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:27.8
occ:1.00
O B:GLY196 2.3 28.4 1.0
O B:ASP162 2.3 22.2 1.0
O B:HOH611 2.3 27.5 1.0
O B:ASN194 2.3 32.3 1.0
O B:HOH604 2.4 20.3 1.0
OD1 B:ASP198 2.5 22.0 1.0
C B:ASP162 3.4 22.4 1.0
C B:GLY196 3.4 29.7 1.0
CG B:ASP198 3.5 20.2 1.0
C B:ASN194 3.5 32.6 1.0
N B:GLY196 3.9 31.0 1.0
O B:ALA161 4.0 23.6 1.0
C B:TYR195 4.0 31.1 1.0
CA B:ASP162 4.0 22.1 1.0
OD2 B:ASP198 4.0 17.9 1.0
N B:ASP198 4.1 23.6 1.0
CA B:GLY196 4.2 29.0 1.0
O B:TYR195 4.2 32.4 1.0
O B:HOH674 4.2 37.4 1.0
N B:ASN194 4.3 34.5 1.0
O B:GLY192 4.4 31.5 1.0
N B:GLY197 4.4 28.5 1.0
CA B:ASN194 4.4 33.4 1.0
N B:ILE163 4.4 20.1 1.0
N B:TYR195 4.4 29.7 1.0
CA B:TYR195 4.5 31.8 1.0
CA B:GLY197 4.6 28.7 1.0
C B:GLY197 4.6 26.7 1.0
O B:HOH648 4.6 34.7 1.0
CB B:ASP198 4.7 19.5 1.0
N B:MET164 4.7 20.9 1.0
C B:PRO193 4.7 35.2 1.0
CA B:ILE163 4.7 19.5 1.0
CA B:ASP198 4.8 22.2 1.0
C B:ALA161 4.9 23.4 1.0
CH2 B:TRP113 4.9 36.6 1.0
O B:PRO193 4.9 32.2 1.0
CG B:MET164 4.9 17.6 1.0
N B:ASP162 5.0 23.1 1.0

Reference:

H.Nara, K.Sato, T.Naito, H.Mototani, H.Oki, Y.Yamamoto, H.Kuno, T.Santou, N.Kanzaki, J.Terauchi, O.Uchikawa, M.Kori. Discovery of Novel, Highly Potent, and Selective Quinazoline-2-Carboxamide-Based Matrix Metalloproteinase (Mmp)-13 Inhibitors Without A Zinc Binding Group Using A Structure-Based Design Approach J.Med.Chem. V. 57 8886 2014.
ISSN: ISSN 0022-2623
PubMed: 25264600
DOI: 10.1021/JM500981K
Page generated: Sat Dec 12 04:36:12 2020

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