Atomistry » Zinc » PDB 3wlf-3wxc » 3wv3
Atomistry »
  Zinc »
    PDB 3wlf-3wxc »
      3wv3 »

Zinc in PDB 3wv3: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide, PDB code: 3wv3 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) 29.83 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.558, 36.352, 95.853, 90.00, 130.64, 90.00
R / Rfree (%) 16.3 / 21.2

Other elements in 3wv3:

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide (pdb code 3wv3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide, PDB code: 3wv3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3wv3

Go back to Zinc Binding Sites List in 3wv3
Zinc binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:14.3
occ:1.00
NE2 A:HIS232 2.0 15.3 1.0
NE2 A:HIS222 2.1 13.2 1.0
NE2 A:HIS226 2.1 13.4 1.0
O2 A:FMT306 2.1 23.4 1.0
O1 A:FMT306 2.4 19.0 1.0
C A:FMT306 2.5 20.7 1.0
CE1 A:HIS226 3.0 13.5 1.0
CD2 A:HIS232 3.0 15.6 1.0
CE1 A:HIS232 3.0 19.2 1.0
CE1 A:HIS222 3.0 13.8 1.0
CD2 A:HIS222 3.1 11.8 1.0
CD2 A:HIS226 3.1 11.3 1.0
ND1 A:HIS232 4.1 20.4 1.0
CG A:HIS232 4.1 15.6 1.0
O A:HOH433 4.1 28.1 1.0
ND1 A:HIS222 4.1 13.0 1.0
ND1 A:HIS226 4.1 14.5 1.0
CG A:HIS222 4.2 10.7 1.0
CG A:HIS226 4.2 11.8 1.0
O21 A:WLL308 4.5 17.7 1.0
OE2 A:GLU223 4.5 16.6 1.0
O A:HOH488 4.6 15.5 1.0
CE A:MET240 4.7 11.0 1.0
O A:HOH600 4.9 24.6 1.0
OE1 A:GLU223 5.0 16.1 1.0
C22 A:WLL308 5.0 23.6 1.0

Zinc binding site 2 out of 4 in 3wv3

Go back to Zinc Binding Sites List in 3wv3
Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:14.3
occ:1.00
NE2 A:HIS172 2.0 12.5 1.0
OD2 A:ASP174 2.0 12.8 1.0
NE2 A:HIS187 2.1 13.2 1.0
ND1 A:HIS200 2.1 12.7 1.0
CD2 A:HIS172 2.9 11.6 1.0
CG A:ASP174 2.9 17.1 1.0
CE1 A:HIS187 3.0 15.9 1.0
CE1 A:HIS200 3.0 14.8 1.0
CE1 A:HIS172 3.0 12.0 1.0
CD2 A:HIS187 3.1 11.0 1.0
CG A:HIS200 3.1 12.4 1.0
OD1 A:ASP174 3.2 16.2 1.0
CB A:HIS200 3.5 10.9 1.0
CG A:HIS172 4.1 10.9 1.0
ND1 A:HIS172 4.1 12.8 1.0
ND1 A:HIS187 4.1 15.7 1.0
NE2 A:HIS200 4.2 15.7 1.0
O A:TYR176 4.2 14.6 1.0
CG A:HIS187 4.2 12.2 1.0
CD2 A:HIS200 4.2 11.8 1.0
CB A:ASP174 4.3 13.9 1.0
CE1 A:PHE189 4.5 21.4 1.0
CB A:TYR176 4.6 15.3 1.0
CZ A:PHE189 4.7 23.2 1.0
CE2 A:PHE178 4.8 12.8 1.0
CZ A:PHE178 4.8 13.5 1.0
C A:TYR176 4.9 14.2 1.0
O A:HOH442 4.9 15.8 1.0
CA A:HIS200 5.0 10.2 1.0

Zinc binding site 3 out of 4 in 3wv3

Go back to Zinc Binding Sites List in 3wv3
Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:19.8
occ:1.00
O2 B:FMT306 1.8 39.5 1.0
NE2 B:HIS222 2.0 15.9 1.0
NE2 B:HIS232 2.1 19.3 1.0
NE2 B:HIS226 2.1 20.8 1.0
C B:FMT306 2.5 36.9 1.0
O1 B:FMT306 2.6 38.5 1.0
CD2 B:HIS222 3.0 17.6 1.0
CD2 B:HIS232 3.0 20.9 1.0
CE1 B:HIS222 3.0 19.8 1.0
CD2 B:HIS226 3.1 19.0 1.0
CE1 B:HIS232 3.1 30.1 1.0
CE1 B:HIS226 3.1 19.0 1.0
CG B:HIS222 4.1 14.3 1.0
ND1 B:HIS222 4.1 17.8 1.0
CG B:HIS232 4.1 25.8 1.0
ND1 B:HIS232 4.2 25.9 1.0
ND1 B:HIS226 4.2 20.5 1.0
CG B:HIS226 4.2 17.2 1.0
OE2 B:GLU223 4.5 22.3 1.0
O21 B:WLL308 4.7 24.0 1.0
O B:HOH464 4.7 23.4 1.0
O B:HOH602 4.8 47.4 1.0
CE B:MET240 4.8 17.2 1.0
OE1 B:GLU223 4.8 19.9 1.0
C22 B:WLL308 4.9 33.7 1.0
CD B:GLU223 5.0 20.1 1.0

Zinc binding site 4 out of 4 in 3wv3

Go back to Zinc Binding Sites List in 3wv3
Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:15.9
occ:1.00
OD2 B:ASP174 1.9 17.3 1.0
NE2 B:HIS172 2.0 15.5 1.0
ND1 B:HIS200 2.1 13.8 1.0
NE2 B:HIS187 2.1 14.4 1.0
CG B:ASP174 2.9 21.6 1.0
CD2 B:HIS172 2.9 16.2 1.0
CE1 B:HIS200 3.0 14.4 1.0
CE1 B:HIS172 3.0 13.0 1.0
CE1 B:HIS187 3.0 17.1 1.0
CG B:HIS200 3.1 14.9 1.0
CD2 B:HIS187 3.2 17.6 1.0
OD1 B:ASP174 3.2 17.4 1.0
CB B:HIS200 3.5 14.5 1.0
ND1 B:HIS172 4.1 12.8 1.0
CG B:HIS172 4.1 12.6 1.0
NE2 B:HIS200 4.1 15.5 1.0
ND1 B:HIS187 4.2 16.8 1.0
CD2 B:HIS200 4.2 16.5 1.0
CB B:ASP174 4.3 15.3 1.0
CG B:HIS187 4.3 14.4 1.0
O B:TYR176 4.3 16.2 1.0
CZ B:PHE178 4.6 13.7 1.0
CE2 B:PHE178 4.7 13.6 1.0
CE1 B:PHE189 4.8 20.8 1.0
O B:HOH443 4.8 17.6 1.0
CB B:TYR176 4.8 20.8 1.0
CZ B:PHE189 4.9 19.6 1.0
CA B:HIS200 5.0 13.9 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. Thieno[2,3-D]Pyrimidine-2-Carboxamides Bearing A Carboxybenzene Group at 5-Position: Highly Potent, Selective, and Orally Available Mmp-13 Inhibitors Interacting with the S1 Binding Site Bioorg.Med.Chem. 2014.
ISSN: ESSN 1464-3391
PubMed: 25192810
DOI: 10.1016/J.BMC.2014.07.025
Page generated: Wed Dec 16 04:58:07 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy