Zinc in PDB 7yhd: Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(4-(2- Aminoethoxy)Phenyl)-1H-1,2,3-Triazol-1-Yl)Phthalic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(4-(2- Aminoethoxy)Phenyl)-1H-1,2,3-Triazol-1-Yl)Phthalic Acid, PDB code: 7yhd was solved by G.-B.Li, Y.-H.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.39 / 1.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.407, 77.566, 79.019, 90, 90, 90
R / Rfree (%)	27.3 / 34

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(4-(2- Aminoethoxy)Phenyl)-1H-1,2,3-Triazol-1-Yl)Phthalic Acid (pdb code 7yhd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(4-(2- Aminoethoxy)Phenyl)-1H-1,2,3-Triazol-1-Yl)Phthalic Acid, PDB code: 7yhd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(4-(2- Aminoethoxy)Phenyl)-1H-1,2,3-Triazol-1-Yl)Phthalic Acid


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 Vim-2 Mbl in Complex with 3-(4-(4-(2- Aminoethoxy)Phenyl)-1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.9 occ:1.00 OD2 A:ASP118 2.1 20.8 1.0 NE2 A:HIS240 2.1 21.7 1.0 O08 A:IU7303 2.2 22.4 1.0 SG A:CYS198 2.2 20.2 1.0 O03 A:IU7303 2.3 26.2 1.0 C02 A:IU7303 3.0 32.2 1.0 C06 A:IU7303 3.0 24.2 1.0 CE1 A:HIS240 3.1 19.4 1.0 CG A:ASP118 3.2 27.5 1.0 CD2 A:HIS240 3.2 31.9 1.0 C05 A:IU7303 3.2 30.7 1.0 C04 A:IU7303 3.3 35.6 1.0 NH2 A:ARG119 3.3 22.4 1.0 CB A:CYS198 3.3 20.7 1.0 ZN A:ZN302 3.6 23.2 1.0 OD1 A:ASP118 3.7 26.5 1.0 O01 A:IU7303 4.0 26.8 1.0 NE A:ARG119 4.1 21.4 1.0 CZ A:ARG119 4.2 19.6 1.0 O07 A:IU7303 4.2 37.0 1.0 ND1 A:HIS240 4.2 23.4 1.0 C09 A:IU7303 4.2 33.8 1.0 C12 A:IU7303 4.3 36.7 1.0 CG A:HIS240 4.3 25.8 1.0 CB A:ASP118 4.3 21.1 1.0 NE2 A:HIS179 4.4 19.2 1.0 O A:HOH425 4.4 20.1 1.0 CE1 A:HIS179 4.5 19.6 1.0 CA A:CYS198 4.5 19.3 1.0 CE1 A:HIS114 4.5 19.3 1.0 NE2 A:HIS114 4.7 23.1 1.0 N13 A:IU7303 5.0 46.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(4-(2- Aminoethoxy)Phenyl)-1H-1,2,3-Triazol-1-Yl)Phthalic Acid


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 Vim-2 Mbl in Complex with 3-(4-(4-(2- Aminoethoxy)Phenyl)-1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:23.2 occ:1.00 O03 A:IU7303 1.9 26.2 1.0 NE2 A:HIS179 2.0 19.2 1.0 ND1 A:HIS116 2.1 18.4 1.0 NE2 A:HIS114 2.2 23.1 1.0 C02 A:IU7303 2.6 32.2 1.0 O01 A:IU7303 2.8 26.8 1.0 CE1 A:HIS179 2.9 19.6 1.0 CE1 A:HIS114 3.0 19.3 1.0 CG A:HIS116 3.0 26.8 1.0 CD2 A:HIS179 3.0 10.9 1.0 CE1 A:HIS116 3.2 19.7 1.0 CB A:HIS116 3.2 25.8 1.0 CD2 A:HIS114 3.3 21.8 1.0 ZN A:ZN301 3.6 22.9 1.0 OD1 A:ASP118 3.8 26.5 1.0 ND1 A:HIS179 4.0 16.3 1.0 CB A:CYS198 4.1 20.7 1.0 C04 A:IU7303 4.1 35.6 1.0 CG A:HIS179 4.1 17.3 1.0 ND1 A:HIS114 4.1 21.6 1.0 CD2 A:HIS116 4.2 27.9 1.0 NE2 A:HIS116 4.2 28.2 1.0 SG A:CYS198 4.2 20.2 1.0 O08 A:IU7303 4.2 22.4 1.0 OD2 A:ASP118 4.3 20.8 1.0 CG A:HIS114 4.3 20.0 1.0 CG A:ASP118 4.5 27.5 1.0 CA A:HIS116 4.7 20.4 1.0 C06 A:IU7303 4.7 24.2 1.0 N13 A:IU7303 4.8 46.6 1.0 ND2 A:ASN210 4.9 41.2 1.0 C05 A:IU7303 4.9 30.7 1.0 C12 A:IU7303 4.9 36.7 1.0

Y.H.Yan, H.S.Ding, K.R.Zhu, B.S.Mu, Y.Zheng, M.Y.Huang, C.Zhou, W.F.Li, Z.Wang, Y.Wu, G.B.Li. Metal Binding Pharmacophore Click-Derived Discovery of New Broad-Spectrum Metallo-Beta-Lactamase Inhibitors. Eur.J.Med.Chem. V. 257 15473 2023.
ISSN: ISSN 0223-5234
PubMed: 37209449
DOI: 10.1016/J.EJMECH.2023.115473