Atomistry » Zinc » PDB 5b25-5bqk » 5b5o
Atomistry »
  Zinc »
    PDB 5b25-5bqk »
      5b5o »

Zinc in PDB 5b5o: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine, PDB code: 5b5o 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) 33.75 / 1.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.409, 36.060, 95.948, 90.00, 131.09, 90.00
R / Rfree (%) 16.4 / 18.5

Other elements in 5b5o:

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine 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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine (pdb code 5b5o). 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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine, PDB code: 5b5o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5b5o

Go back to Zinc Binding Sites List in 5b5o
Zinc binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:9.1
occ:1.00
N12 A:WMM307 1.9 18.9 1.0
NE2 A:HIS232 2.0 9.0 1.0
NE2 A:HIS222 2.0 7.9 1.0
NE2 A:HIS226 2.1 8.2 1.0
N11 A:WMM307 2.9 15.9 1.0
C8 A:WMM307 3.0 20.8 1.0
CD2 A:HIS232 3.0 9.3 1.0
CE1 A:HIS222 3.0 8.0 1.0
CE1 A:HIS232 3.0 11.3 1.0
CD2 A:HIS222 3.0 8.6 1.0
CE1 A:HIS226 3.1 8.1 1.0
CD2 A:HIS226 3.1 7.7 1.0
S7 A:WMM307 3.6 22.8 1.0
C10 A:WMM307 4.0 19.8 1.0
N9 A:WMM307 4.1 19.5 1.0
ND1 A:HIS232 4.1 11.4 1.0
CG A:HIS232 4.1 8.7 1.0
ND1 A:HIS222 4.1 7.2 1.0
CG A:HIS222 4.2 6.9 1.0
ND1 A:HIS226 4.2 8.7 1.0
CG A:HIS226 4.2 7.2 1.0
OE2 A:GLU223 4.3 11.0 1.0
O A:HOH568 4.5 16.5 1.0
N2 A:WMM307 4.6 22.3 1.0
OE1 A:GLU223 4.6 10.1 1.0
C3 A:WMM307 4.6 25.8 1.0
C6 A:WMM307 4.7 24.7 1.0
CD A:GLU223 4.8 8.3 1.0
CE A:MET240 4.8 8.1 1.0

Zinc binding site 2 out of 4 in 5b5o

Go back to Zinc Binding Sites List in 5b5o
Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:9.0
occ:1.00
OD2 A:ASP174 1.9 10.2 1.0
NE2 A:HIS172 2.0 8.1 1.0
ND1 A:HIS200 2.1 7.4 1.0
NE2 A:HIS187 2.1 11.4 1.0
CG A:ASP174 2.9 9.1 1.0
CD2 A:HIS172 3.0 8.0 1.0
CE1 A:HIS200 3.0 9.8 1.0
CE1 A:HIS187 3.0 14.1 1.0
CE1 A:HIS172 3.0 8.4 1.0
CG A:HIS200 3.1 7.3 1.0
CD2 A:HIS187 3.1 11.2 1.0
OD1 A:ASP174 3.1 9.2 1.0
CB A:HIS200 3.5 7.9 1.0
O A:TYR176 4.1 10.6 1.0
CG A:HIS172 4.1 7.6 1.0
ND1 A:HIS172 4.1 8.2 1.0
NE2 A:HIS200 4.1 9.0 1.0
ND1 A:HIS187 4.2 13.2 1.0
CD2 A:HIS200 4.2 8.4 1.0
CG A:HIS187 4.2 10.5 1.0
CB A:ASP174 4.3 10.9 1.0
CE1 A:PHE189 4.5 15.1 1.0
CZ A:PHE189 4.6 17.5 1.0
CB A:TYR176 4.6 11.8 1.0
CE2 A:PHE178 4.8 8.9 1.0
CZ A:PHE178 4.8 10.0 1.0
C A:TYR176 4.9 10.8 1.0
O A:HOH506 4.9 10.1 1.0
CA A:HIS200 5.0 6.8 1.0

Zinc binding site 3 out of 4 in 5b5o

Go back to Zinc Binding Sites List in 5b5o
Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:9.9
occ:1.00
N12 B:WMM306 2.0 12.6 1.0
NE2 B:HIS232 2.0 10.1 1.0
NE2 B:HIS222 2.0 9.3 1.0
NE2 B:HIS226 2.1 9.3 1.0
C8 B:WMM306 2.9 13.3 1.0
N11 B:WMM306 2.9 14.1 1.0
CD2 B:HIS232 3.0 10.0 1.0
CD2 B:HIS222 3.0 9.5 1.0
CE1 B:HIS232 3.0 12.5 1.0
CE1 B:HIS226 3.0 10.0 1.0
CE1 B:HIS222 3.1 9.6 1.0
CD2 B:HIS226 3.1 8.8 1.0
S7 B:WMM306 3.5 18.7 1.0
C10 B:WMM306 4.0 16.0 1.0
N9 B:WMM306 4.1 17.5 1.0
ND1 B:HIS232 4.1 11.9 1.0
CG B:HIS232 4.1 10.7 1.0
CG B:HIS222 4.1 9.3 1.0
ND1 B:HIS222 4.2 9.4 1.0
ND1 B:HIS226 4.2 10.4 1.0
OE2 B:GLU223 4.2 16.2 1.0
CG B:HIS226 4.2 9.3 1.0
N2 B:WMM306 4.6 19.2 1.0
C3 B:WMM306 4.6 17.1 1.0
O B:HOH549 4.7 31.1 1.0
O B:HOH552 4.7 13.5 1.0
CE B:MET240 4.7 10.8 1.0
C6 B:WMM306 4.8 20.4 1.0

Zinc binding site 4 out of 4 in 5b5o

Go back to Zinc Binding Sites List in 5b5o
Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:8.1
occ:1.00
OD2 B:ASP174 2.0 9.2 1.0
NE2 B:HIS172 2.0 7.9 1.0
NE2 B:HIS187 2.0 7.9 1.0
ND1 B:HIS200 2.0 7.1 1.0
CG B:ASP174 2.9 8.5 1.0
CE1 B:HIS200 2.9 8.3 1.0
CE1 B:HIS187 3.0 10.1 1.0
CD2 B:HIS172 3.0 8.0 1.0
CE1 B:HIS172 3.0 7.4 1.0
CD2 B:HIS187 3.1 8.8 1.0
CG B:HIS200 3.1 6.8 1.0
OD1 B:ASP174 3.2 8.8 1.0
CB B:HIS200 3.5 8.6 1.0
NE2 B:HIS200 4.1 8.2 1.0
ND1 B:HIS187 4.1 9.7 1.0
ND1 B:HIS172 4.1 7.8 1.0
CG B:HIS172 4.1 8.2 1.0
CG B:HIS187 4.2 8.2 1.0
CD2 B:HIS200 4.2 8.1 1.0
CB B:ASP174 4.2 9.6 1.0
O B:TYR176 4.4 10.1 1.0
CZ B:PHE178 4.7 9.4 1.0
CE1 B:PHE189 4.7 12.7 1.0
CB B:TYR176 4.7 11.8 1.0
CE2 B:PHE178 4.8 9.9 1.0
O B:HOH499 4.8 10.2 1.0
CZ B:PHE189 4.8 15.3 1.0

Reference:

H.Nara, A.Kaieda, 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 Matrix Metalloproteinase (Mmp)-13 Inhibitors with A 1,2,4-Triazol-3-Yl Moiety As A Zinc Binding Group Using A Structure-Based Design Approach J. Med. Chem. V. 60 608 2017.
ISSN: ISSN 1520-4804
PubMed: 27966948
DOI: 10.1021/ACS.JMEDCHEM.6B01007
Page generated: Wed Dec 16 06:04:35 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