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Fluorine 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:

Zinc (Zn) 4 atoms
Calcium (Ca) 4 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 2 in 3wv1

Go back to Fluorine Binding Sites List in 3wv1
Fluorine 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 Fluorine with other atoms in the F 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:F307

b:25.4
occ:1.00
F36 A:WHH307 0.0 25.4 1.0
C1 A:WHH307 1.3 25.6 1.0
C6 A:WHH307 2.4 24.5 1.0
C2 A:WHH307 2.4 21.1 1.0
O7 A:WHH307 2.7 29.0 1.0
C8 A:WHH307 2.9 32.0 1.0
N A:MET253 3.3 28.6 1.0
O A:MET253 3.4 24.4 1.0
CD A:LYS249 3.5 63.6 1.0
O A:HOH643 3.5 32.4 1.0
C3 A:WHH307 3.6 21.7 1.0
C5 A:WHH307 3.6 24.8 1.0
CD2 A:PHE252 3.8 21.9 1.0
CA A:PHE252 3.8 33.4 1.0
C A:PHE252 4.1 31.4 1.0
O A:HIS251 4.1 45.3 1.0
C4 A:WHH307 4.1 22.3 1.0
C A:MET253 4.1 26.9 1.0
CE A:LYS249 4.2 65.6 1.0
CE2 A:PHE252 4.2 21.4 1.0
CG A:PHE252 4.2 25.2 1.0
CA A:MET253 4.2 30.3 1.0
C9 A:WHH307 4.3 31.5 1.0
CB A:PHE252 4.5 30.3 1.0
CB A:MET253 4.6 33.3 1.0
CG A:LYS249 4.7 64.1 1.0
CB A:LYS249 4.8 63.2 1.0
N A:PHE252 4.8 39.2 1.0
NZ A:LYS249 4.9 68.8 1.0
C19 A:WHH307 4.9 23.6 1.0
C A:HIS251 4.9 46.3 1.0
CZ A:PHE252 5.0 21.3 1.0
CD1 A:PHE252 5.0 21.2 1.0
OG1 A:THR247 5.0 48.5 1.0

Fluorine binding site 2 out of 2 in 3wv1

Go back to Fluorine Binding Sites List in 3wv1
Fluorine 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 Fluorine with other atoms in the F 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:F307

b:37.9
occ:1.00
F36 B:WHH307 0.0 37.9 1.0
C1 B:WHH307 1.3 37.1 1.0
C2 B:WHH307 2.3 36.4 1.0
C6 B:WHH307 2.3 37.0 1.0
O7 B:WHH307 2.7 39.2 1.0
C8 B:WHH307 3.1 37.8 1.0
O B:MET253 3.3 31.1 1.0
N B:MET253 3.5 36.5 1.0
O B:HOH649 3.6 39.3 1.0
CD2 B:PHE252 3.6 28.8 1.0
C3 B:WHH307 3.6 38.5 1.0
C5 B:WHH307 3.6 38.4 1.0
CE B:LYS249 3.7 55.1 1.0
CE2 B:PHE252 3.9 22.5 1.0
CA B:PHE252 4.0 36.8 1.0
CD B:LYS249 4.1 53.9 1.0
C4 B:WHH307 4.1 38.4 1.0
C B:MET253 4.2 33.8 1.0
CG B:PHE252 4.2 31.9 1.0
C9 B:WHH307 4.2 38.2 1.0
C B:PHE252 4.3 36.8 1.0
O B:HIS251 4.3 40.7 1.0
CA B:MET253 4.4 37.0 1.0
CB B:PHE252 4.6 35.7 1.0
CZ B:PHE252 4.7 23.4 1.0
OG1 B:THR247 4.8 46.9 1.0
CB B:MET253 4.8 39.5 1.0
C19 B:WHH307 4.8 33.7 1.0
CD1 B:PHE252 4.9 31.0 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: Sun Dec 13 11:57:49 2020

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