Atomistry » Sodium » PDB 3wc3-3wxo » 3wv1
Atomistry »
  Sodium »
    PDB 3wc3-3wxo »
      3wv1 »

Sodium 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
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3wv1

Go back to Sodium Binding Sites List in 3wv1
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na305

b:28.5
occ:1.00
OD2 A:ASP128 2.4 27.9 1.0
O A:GLU205 2.4 17.8 1.0
O A:ASP203 2.8 21.9 1.0
OD1 A:ASP203 2.9 26.0 1.0
O A:HOH696 3.2 42.7 1.0
CG A:ASP128 3.2 28.9 1.0
OD1 A:ASP128 3.3 40.6 1.0
O A:HOH688 3.3 38.7 1.0
C A:GLU205 3.6 18.2 1.0
C A:ASP203 3.6 18.5 1.0
OG1 A:THR126 3.8 16.3 1.0
CG A:ASP203 3.9 25.8 1.0
CA A:ASP203 4.1 15.9 1.0
CD1 A:TRP207 4.3 14.0 1.0
N A:GLU205 4.3 17.0 1.0
CA A:THR206 4.4 20.8 1.0
N A:THR206 4.4 19.4 1.0
CB A:ASP203 4.4 19.8 1.0
C A:ASP204 4.5 18.5 1.0
CD A:PRO127 4.5 16.6 1.0
CB A:ASP128 4.6 21.4 1.0
N A:ASP204 4.6 17.0 1.0
CA A:GLU205 4.6 17.7 1.0
CA A:ASP204 4.7 19.1 1.0
N A:TRP207 4.8 16.6 1.0
OD2 A:ASP203 4.8 29.9 1.0
NE1 A:TRP207 4.9 15.0 1.0
O A:ASP204 5.0 21.0 1.0

Sodium binding site 2 out of 2 in 3wv1

Go back to Sodium Binding Sites List in 3wv1
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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
B:Na305

b:27.6
occ:1.00
O B:GLU205 2.3 20.1 1.0
OD2 B:ASP128 2.5 28.0 1.0
O B:HOH657 2.7 35.4 1.0
O B:ASP203 2.7 26.9 1.0
OD1 B:ASP203 3.0 29.8 1.0
CG B:ASP128 3.2 26.3 1.0
OD1 B:ASP128 3.2 32.3 1.0
C B:GLU205 3.5 21.5 1.0
C B:ASP203 3.6 22.7 1.0
OG1 B:THR126 4.0 22.1 1.0
CG B:ASP203 4.1 25.1 1.0
N B:GLU205 4.1 21.7 1.0
CA B:ASP203 4.2 22.5 1.0
CA B:THR206 4.3 20.2 1.0
CD1 B:TRP207 4.3 16.9 1.0
N B:THR206 4.3 20.8 1.0
C B:ASP204 4.3 24.8 1.0
CA B:GLU205 4.4 21.5 1.0
N B:ASP204 4.5 21.5 1.0
CB B:ASP203 4.6 21.6 1.0
CD B:PRO127 4.6 20.7 1.0
CA B:ASP204 4.6 22.1 1.0
CB B:ASP128 4.6 24.0 1.0
N B:TRP207 4.7 20.2 1.0
O B:ASP204 4.8 23.5 1.0
NE1 B:TRP207 4.9 19.9 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: Tue Dec 15 06:30:21 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy