Zinc in PDB 5dpx: 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases.

All present enzymatic activity of 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases.:
3.5.2.6;

The structure of 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases., PDB code: 5dpx was solved by L.Nauton, G.Garau, R.Khan, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 1.85
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.040, 105.040, 196.990, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.7

The binding sites of Zinc atom in the 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases. (pdb code 5dpx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases., PDB code: 5dpx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:14.6 occ:1.00 N5 A:L3B403 2.0 15.6 0.5 NE2 A:HIS181 2.0 11.6 1.0 N5 A:L3B403 2.1 16.2 0.5 ND1 A:HIS107 2.1 13.3 1.0 NE2 A:HIS105 2.2 8.6 1.0 C1 A:L3B403 2.9 17.8 0.5 C1 A:L3B403 2.9 17.7 0.5 CD2 A:HIS181 3.0 10.5 1.0 CE1 A:HIS107 3.0 13.3 1.0 CD2 A:HIS105 3.0 7.7 1.0 C4 A:L3B403 3.1 16.9 0.5 CE1 A:HIS181 3.1 11.6 1.0 CE1 A:HIS105 3.1 9.9 1.0 CG A:HIS107 3.1 10.6 1.0 C4 A:L3B403 3.2 15.7 0.5 S6 A:L3B403 3.3 18.0 0.5 S6 A:L3B403 3.3 18.0 0.5 CB A:HIS107 3.4 12.1 1.0 C7 A:L3B403 3.6 15.5 0.5 C7 A:L3B403 3.7 15.6 0.5 H133 A:L3B403 3.9 22.0 0.5 N2 A:L3B403 4.1 14.1 0.5 OD1 A:ASP109 4.1 12.4 1.0 H133 A:L3B403 4.1 20.7 0.5 ND1 A:HIS105 4.1 9.7 1.0 CG A:HIS105 4.1 8.5 1.0 N2 A:L3B403 4.1 18.1 0.5 CG A:HIS181 4.1 11.3 1.0 C12 A:L3B403 4.1 17.0 0.5 NE2 A:HIS107 4.2 10.4 1.0 ND1 A:HIS181 4.2 9.8 1.0 N3 A:L3B403 4.2 18.4 0.5 H12 A:L3B403 4.2 20.4 0.5 CD2 A:HIS107 4.2 9.4 1.0 H132 A:L3B403 4.2 22.0 0.5 ZN A:ZN402 4.3 13.9 1.0 N3 A:L3B403 4.3 15.5 0.5 C8 A:L3B403 4.3 17.5 0.5 C8 A:L3B403 4.3 16.9 0.5 C13 A:L3B403 4.4 18.4 0.5 C12 A:L3B403 4.4 15.9 0.5 H12 A:L3B403 4.5 19.1 0.5 H131 A:L3B403 4.5 20.7 0.5 C13 A:L3B403 4.5 17.3 0.5 CD2 A:HIS110 4.6 8.8 1.0 NE2 A:HIS110 4.8 10.8 1.0 CA A:HIS107 4.9 8.4 1.0 OD2 A:ASP109 4.9 10.9 1.0 CG A:ASP109 4.9 11.8 1.0 CG2 A:THR182 5.0 7.0 1.0 OH A:TYR212 5.0 8.6 1.0

Zinc binding site 2 out of 4 in the 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:13.9 occ:1.00 OD2 A:ASP109 2.0 10.9 1.0 NE2 A:HIS110 2.0 10.8 1.0 NE2 A:HIS246 2.1 9.3 1.0 S6 A:L3B403 2.2 18.0 0.5 S6 A:L3B403 2.3 18.0 0.5 CG A:ASP109 2.8 11.8 1.0 C1 A:L3B403 2.9 17.7 0.5 CE1 A:HIS110 2.9 9.1 1.0 CD2 A:HIS246 3.0 12.0 1.0 CD2 A:HIS110 3.0 8.8 1.0 C1 A:L3B403 3.1 17.8 0.5 CE1 A:HIS246 3.1 12.7 1.0 OD1 A:ASP109 3.1 12.4 1.0 N2 A:L3B403 3.6 18.1 0.5 N5 A:L3B403 3.7 16.2 0.5 N5 A:L3B403 3.8 15.6 0.5 N2 A:L3B403 3.9 14.1 0.5 ND1 A:HIS110 4.0 12.2 1.0 CG A:HIS110 4.1 15.1 1.0 CB A:ASP109 4.1 10.4 1.0 CG A:HIS246 4.1 10.5 1.0 ND1 A:HIS246 4.2 11.9 1.0 ZN A:ZN401 4.3 14.6 1.0 CE1 A:HIS105 4.3 9.9 1.0 NE2 A:HIS105 4.4 8.6 1.0 N3 A:L3B403 4.5 15.5 0.5 OG A:SER206 4.6 12.3 0.3 C4 A:L3B403 4.6 15.7 0.5 H133 A:L3B403 4.7 20.7 0.5 C4 A:L3B403 4.8 16.9 0.5 N3 A:L3B403 4.8 18.4 0.5 O A:HOH582 4.9 25.0 1.0

Zinc binding site 3 out of 4 in the 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:15.1 occ:1.00 N5 B:L3B403 1.9 18.4 0.5 NE2 B:HIS181 2.1 14.6 1.0 N5 B:L3B403 2.1 19.0 0.5 NE2 B:HIS105 2.1 13.3 1.0 ND1 B:HIS107 2.1 13.3 1.0 C1 B:L3B403 2.7 18.4 0.5 CD2 B:HIS181 2.9 12.9 1.0 CD2 B:HIS105 2.9 10.6 1.0 C1 B:L3B403 3.0 17.6 0.5 C4 B:L3B403 3.1 16.2 0.5 CE1 B:HIS107 3.1 14.1 1.0 CG B:HIS107 3.1 14.5 1.0 S6 B:L3B403 3.1 15.9 0.5 CE1 B:HIS105 3.1 9.7 1.0 C4 B:L3B403 3.2 17.8 0.5 CE1 B:HIS181 3.2 13.8 1.0 CB B:HIS107 3.4 10.8 1.0 S6 B:L3B403 3.4 16.9 0.5 C7 B:L3B403 3.7 18.1 0.5 C7 B:L3B403 3.7 17.1 0.5 N2 B:L3B403 3.9 16.2 0.5 H133 B:L3B403 4.0 18.2 0.5 H133 B:L3B403 4.0 23.1 0.5 CG B:HIS105 4.1 10.2 1.0 OD1 B:ASP109 4.1 11.3 1.0 CG B:HIS181 4.1 12.4 1.0 N3 B:L3B403 4.1 19.0 0.5 ND1 B:HIS105 4.1 9.5 1.0 NE2 B:HIS107 4.2 13.3 1.0 N2 B:L3B403 4.2 16.5 0.5 ND1 B:HIS181 4.2 9.3 1.0 ZN B:ZN402 4.2 15.6 1.0 C8 B:L3B403 4.2 17.9 0.5 CD2 B:HIS107 4.2 10.9 1.0 C12 B:L3B403 4.2 17.2 0.5 C12 B:L3B403 4.3 19.5 0.5 H132 B:L3B403 4.3 18.2 0.5 H12 B:L3B403 4.3 20.6 0.5 N3 B:L3B403 4.3 19.3 0.5 C8 B:L3B403 4.3 20.6 0.5 H12 B:L3B403 4.3 23.4 0.5 C13 B:L3B403 4.4 15.2 0.5 CD2 B:HIS110 4.5 12.3 1.0 H131 B:L3B403 4.5 23.1 0.5 C13 B:L3B403 4.5 19.2 0.5 NE2 B:HIS110 4.7 12.8 1.0 CA B:HIS107 4.9 9.0 1.0 CG2 B:THR182 4.9 9.4 1.0 OD2 B:ASP109 4.9 12.9 1.0 OH B:TYR212 4.9 11.3 1.0 CG B:ASP109 4.9 12.6 1.0

Zinc binding site 4 out of 4 in the 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 1,2,4-Triazole-3-Thione Compounds As Inhibitors of L1, Di-Zinc Metallo-Beta-Lactamases. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:15.6 occ:1.00 OD2 B:ASP109 2.0 12.9 1.0 NE2 B:HIS110 2.0 12.8 1.0 NE2 B:HIS246 2.0 13.7 1.0 S6 B:L3B403 2.3 15.9 0.5 S6 B:L3B403 2.3 16.9 0.5 C1 B:L3B403 2.7 17.6 0.5 CG B:ASP109 2.8 12.6 1.0 CE1 B:HIS110 2.8 11.2 1.0 CE1 B:HIS246 2.9 14.4 1.0 C1 B:L3B403 3.0 18.4 0.5 CD2 B:HIS246 3.0 15.6 1.0 CD2 B:HIS110 3.1 12.3 1.0 OD1 B:ASP109 3.2 11.3 1.0 N2 B:L3B403 3.4 16.5 0.5 N5 B:L3B403 3.5 19.0 0.5 N2 B:L3B403 3.8 16.2 0.5 N5 B:L3B403 3.8 18.4 0.5 ND1 B:HIS110 4.0 10.1 1.0 ND1 B:HIS246 4.1 11.3 1.0 CG B:HIS110 4.1 11.6 1.0 CB B:ASP109 4.1 10.9 1.0 CG B:HIS246 4.1 14.1 1.0 ZN B:ZN401 4.2 15.1 1.0 CE1 B:HIS105 4.2 9.7 1.0 NE2 B:HIS105 4.3 13.3 1.0 N3 B:L3B403 4.3 19.3 0.5 C4 B:L3B403 4.4 17.8 0.5 H133 B:L3B403 4.5 23.1 0.5 OG B:SER206 4.6 11.6 0.3 C4 B:L3B403 4.7 16.2 0.5 N3 B:L3B403 4.8 19.0 0.5 CH2 B:TRP38 4.9 15.8 1.0

L.Sevaille, L.Gavara, C.Bebrone, F.De Luca, L.Nauton, M.Achard, P.Mercuri, S.Tanfoni, L.Borgianni, C.Guyon, P.Lonjon, G.Turan-Zitouni, J.Dzieciolowski, K.Becker, L.Benard, C.Condon, L.Maillard, J.Martinez, J.M.Frere, O.Dideberg, M.Galleni, J.D.Docquier, J.F.Hernandez. 1,2,4-Triazole-3-Thione Compounds As Inhibitors of Dizinc Metallo-Beta-Lactamases. Chemmedchem V. 12 972 2017.
ISSN: ESSN 1860-7187
PubMed: 28505394
DOI: 10.1002/CMDC.201700186