Zinc in PDB 5lch: Vim-2 Metallo-Beta-Lactamase in Complex with (S)-1-Allyl-2-(3- Methoxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 42)

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with (S)-1-Allyl-2-(3- Methoxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 42), PDB code: 5lch was solved by G.-B.Li, J.Brem, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.17 / 1.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.870, 67.840, 40.350, 90.00, 91.75, 90.00
R / Rfree (%)	12.5 / 16.1

The binding sites of Zinc atom in the Vim-2 Metallo-Beta-Lactamase in Complex with (S)-1-Allyl-2-(3- Methoxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 42) (pdb code 5lch). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Vim-2 Metallo-Beta-Lactamase in Complex with (S)-1-Allyl-2-(3- Methoxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 42), PDB code: 5lch:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Vim-2 Metallo-Beta-Lactamase in Complex with (S)-1-Allyl-2-(3- Methoxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 42)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-2 Metallo-Beta-Lactamase in Complex with (S)-1-Allyl-2-(3- Methoxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 42) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:7.8 occ:1.00 O A:HOH771 1.8 5.0 1.0 ND1 A:HIS116 2.1 5.8 1.0 NE2 A:HIS179 2.1 5.3 1.0 NE2 A:HIS114 2.1 5.2 1.0 CD2 A:HIS179 3.0 4.9 1.0 CE1 A:HIS114 3.0 4.7 1.0 CE1 A:HIS116 3.0 8.9 1.0 CG A:HIS116 3.1 6.4 1.0 CE1 A:HIS179 3.1 5.6 1.0 CD2 A:HIS114 3.1 5.5 1.0 CB A:HIS116 3.4 6.3 1.0 ZN A:ZN502 3.5 9.4 1.0 O A:HOH681 3.7 47.2 1.0 OD1 A:ASP118 3.9 9.3 1.0 CB A:CYS198 4.1 7.3 1.0 ND1 A:HIS114 4.1 4.6 1.0 NE2 A:HIS116 4.1 10.2 1.0 CG A:HIS179 4.1 5.2 1.0 ND1 A:HIS179 4.1 5.7 1.0 CD2 A:HIS116 4.2 7.1 1.0 CG A:HIS114 4.2 3.8 1.0 SG A:CYS198 4.3 4.5 1.0 O11 A:6TU503 4.3 15.7 1.0 OD2 A:ASP118 4.5 6.8 1.0 C17 A:6TU503 4.6 19.7 1.0 C22 A:6TU503 4.6 18.7 1.0 CG A:ASP118 4.6 7.9 1.0 CA A:HIS116 4.8 5.2 1.0 C10 A:6TU503 4.9 14.7 1.0 C21 A:6TU503 4.9 25.2 1.0 C18 A:6TU503 4.9 24.4 1.0 N12 A:6TU503 5.0 20.3 1.0

Zinc binding site 2 out of 2 in the Vim-2 Metallo-Beta-Lactamase in Complex with (S)-1-Allyl-2-(3- Methoxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 42)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-2 Metallo-Beta-Lactamase in Complex with (S)-1-Allyl-2-(3- Methoxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 42) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:9.4 occ:1.00 O A:HOH771 2.0 5.0 1.0 OD2 A:ASP118 2.0 6.8 1.0 NE2 A:HIS240 2.1 7.2 1.0 SG A:CYS198 2.3 4.5 1.0 O A:HOH681 2.4 47.2 1.0 CE1 A:HIS240 3.0 6.7 1.0 CG A:ASP118 3.0 7.9 1.0 CD2 A:HIS240 3.1 5.9 1.0 CB A:CYS198 3.3 7.3 1.0 OD1 A:ASP118 3.4 9.3 1.0 ZN A:ZN501 3.5 7.8 1.0 NH2 A:ARG119 3.8 5.5 1.0 NE A:ARG119 4.0 4.7 1.0 ND1 A:HIS240 4.1 6.5 1.0 CE1 A:HIS114 4.2 4.7 1.0 CG A:HIS240 4.2 7.9 1.0 C10 A:6TU503 4.2 14.7 1.0 N12 A:6TU503 4.2 20.3 1.0 CZ A:ARG119 4.3 5.5 1.0 NE2 A:HIS114 4.3 5.2 1.0 CB A:ASP118 4.4 6.5 1.0 NE2 A:HIS179 4.4 5.3 1.0 O11 A:6TU503 4.5 15.7 1.0 C05 A:6TU503 4.5 15.1 1.0 C13 A:6TU503 4.5 25.8 1.0 C18 A:6TU503 4.6 24.4 1.0 C17 A:6TU503 4.6 19.7 1.0 O A:HOH693 4.6 6.7 1.0 CA A:CYS198 4.6 5.7 1.0 C04 A:6TU503 4.7 17.3 1.0 CE1 A:HIS179 4.7 5.6 1.0

G.B.Li, M.I.Abboud, J.Brem, H.Someya, C.T.Lohans, S.Y.Yang, J.Spencer, D.W.Wareham, M.A.Mcdonough, C.J.Schofield. uc(Nmr)-Filtered Virtual Screening Leads to Non-Metal Chelating Metallo-Beta-Lactamase Inhibitors. Chem Sci V. 8 928 2017.
ISSN: ISSN 2041-6520
PubMed: 28451231
DOI: 10.1039/C6SC04524C