Zinc in PDB 8r5u: Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14, PDB code: 8r5u was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.79 / 1.56
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.636, 79.375, 67.585, 90, 130.43, 90
R / Rfree (%)	16.1 / 19.9

The binding sites of Zinc atom in the Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14 (pdb code 8r5u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14, PDB code: 8r5u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14


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 Benzebisheterocycle Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:15.9 occ:1.00 H011 A:Y4E306 1.9 23.2 1.0 ND1 A:HIS116 2.0 16.8 1.0 NE2 A:HIS179 2.0 13.4 1.0 NE2 A:HIS114 2.1 14.8 1.0 S01 A:Y4E306 2.4 19.4 1.0 H022 A:Y4E306 2.9 27.9 1.0 CE1 A:HIS116 2.9 18.2 1.0 HB2 A:HIS116 2.9 17.6 1.0 CE1 A:HIS179 3.0 14.8 1.0 CG A:HIS116 3.0 15.8 1.0 CE1 A:HIS114 3.0 15.2 1.0 H021 A:Y4E306 3.0 27.9 1.0 CD2 A:HIS179 3.0 12.0 1.0 C02 A:Y4E306 3.1 23.2 1.0 CD2 A:HIS114 3.1 14.2 1.0 HE1 A:HIS116 3.1 21.8 1.0 HE1 A:HIS179 3.1 17.7 1.0 HE1 A:HIS114 3.2 18.2 1.0 HD2 A:HIS179 3.3 14.4 1.0 HD2 A:HIS114 3.3 17.0 1.0 CB A:HIS116 3.4 14.8 1.0 HB3 A:HIS116 3.6 17.6 1.0 HB2 A:CYS198 3.7 15.9 1.0 ZN A:ZN304 3.7 19.7 1.0 HB3 A:CYS198 4.0 15.9 1.0 NE2 A:HIS116 4.0 19.8 1.0 HD22 A:ASN210 4.0 57.1 1.0 CD2 A:HIS116 4.1 16.4 1.0 ND1 A:HIS179 4.1 11.7 1.0 OD1 A:ASP118 4.1 19.2 1.0 ND1 A:HIS114 4.1 14.5 1.0 CB A:CYS198 4.1 13.2 1.0 CG A:HIS179 4.2 10.6 1.0 CG A:HIS114 4.2 13.8 1.0 SG A:CYS198 4.3 16.1 1.0 HD21 A:ASN210 4.4 57.1 1.0 ND2 A:ASN210 4.4 47.6 1.0 H A:HIS116 4.6 16.2 1.0 C03 A:Y4E306 4.6 26.9 1.0 OD2 A:ASP118 4.7 21.2 1.0 HE2 A:HIS116 4.8 23.7 1.0 CA A:HIS116 4.8 13.9 1.0 CG A:ASP118 4.8 18.9 1.0 HD1 A:HIS179 4.9 14.1 1.0 HG2 A:ARG119 4.9 20.7 1.0 HD1 A:HIS114 4.9 17.5 1.0 HB3 A:SER180 4.9 16.5 1.0 H A:FMT307 4.9 42.8 1.0 HE A:ARG119 4.9 26.3 1.0 HD2 A:HIS116 4.9 19.7 1.0 H031 A:Y4E306 5.0 32.2 1.0

Zinc binding site 2 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14


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 Benzebisheterocycle Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:19.7 occ:1.00 H011 A:Y4E306 1.8 23.2 1.0 OD2 A:ASP118 2.1 21.2 1.0 NE2 A:HIS240 2.1 17.6 1.0 S01 A:Y4E306 2.2 19.4 1.0 SG A:CYS198 2.3 16.1 1.0 HH21 A:ARG119 2.9 27.9 1.0 CE1 A:HIS240 3.1 18.9 1.0 CD2 A:HIS240 3.1 14.9 1.0 CG A:ASP118 3.1 18.9 1.0 H021 A:Y4E306 3.2 27.9 1.0 HE1 A:HIS240 3.2 22.7 1.0 C02 A:Y4E306 3.3 23.2 1.0 HD2 A:HIS240 3.3 17.9 1.0 HB3 A:CYS198 3.4 15.9 1.0 HE A:ARG119 3.4 26.3 1.0 H A:FMT307 3.5 42.8 1.0 OD1 A:ASP118 3.5 19.2 1.0 H031 A:Y4E306 3.5 32.2 1.0 CB A:CYS198 3.5 13.2 1.0 HE1 A:HIS114 3.6 18.2 1.0 H091 A:Y4E306 3.7 37.1 1.0 NH2 A:ARG119 3.7 23.2 1.0 ZN A:ZN303 3.7 15.9 1.0 C03 A:Y4E306 3.9 26.9 1.0 HB2 A:CYS198 3.9 15.9 1.0 H022 A:Y4E306 4.1 27.9 1.0 NE A:ARG119 4.1 21.9 1.0 ND1 A:HIS240 4.2 14.2 1.0 CG A:HIS240 4.2 14.3 1.0 HH22 A:ARG119 4.3 27.9 1.0 CE1 A:HIS114 4.3 15.2 1.0 C A:FMT307 4.3 35.6 1.0 CZ A:ARG119 4.4 20.6 1.0 CB A:ASP118 4.4 19.1 1.0 HE1 A:HIS179 4.5 17.7 1.0 NE2 A:HIS114 4.5 14.8 1.0 O1 A:FMT307 4.5 34.0 1.0 NE2 A:HIS179 4.5 13.4 1.0 C09 A:Y4E306 4.6 30.9 1.0 HB2 A:ASP118 4.6 23.0 1.0 HA A:CYS198 4.6 16.4 1.0 HB3 A:ASP118 4.6 23.0 1.0 HA3 A:GLY239 4.7 17.1 1.0 O A:HOH420 4.7 21.1 1.0 CE1 A:HIS179 4.7 14.8 1.0 CA A:CYS198 4.7 13.6 1.0 N07 A:Y4E306 4.7 28.7 1.0 HG2 A:ARG119 4.9 20.7 1.0 HD1 A:HIS240 5.0 17.1 1.0

Zinc binding site 3 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:18.4 occ:1.00 O2 A:FMT302 1.9 22.1 1.0 O1 A:FMT301 2.0 18.6 1.0 NE2 A:HIS153 2.0 19.2 1.0 C A:FMT302 2.6 23.7 1.0 O1 A:FMT302 2.6 25.2 1.0 CE1 A:HIS153 2.9 22.9 1.0 C A:FMT301 2.9 19.8 1.0 HE1 A:HIS153 3.0 27.5 1.0 CD2 A:HIS153 3.1 15.0 1.0 O2 A:FMT301 3.2 21.8 1.0 HD2 A:HIS153 3.4 17.9 1.0 H A:FMT302 3.6 28.5 1.0 HB1 A:ALA132 3.7 19.5 1.0 H A:FMT301 3.9 23.7 1.0 HB2 A:ALA132 4.0 19.5 1.0 ND1 A:HIS153 4.1 17.5 1.0 HG22 A:THR152 4.2 21.8 1.0 CG A:HIS153 4.2 15.1 1.0 HG21 A:THR152 4.2 21.8 1.0 CB A:ALA132 4.3 16.2 1.0 HA A:ALA132 4.3 18.5 1.0 O A:HOH403 4.5 44.4 1.0 CG2 A:THR152 4.7 18.1 1.0 HD1 A:HIS153 4.8 21.0 1.0 CA A:ALA132 4.9 15.4 1.0 HB A:THR152 4.9 17.6 1.0

Zinc binding site 4 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:16.3 occ:1.00 ND1 B:HIS116 2.0 15.1 1.0 H011 B:Y4E306 2.0 23.8 0.8 NE2 B:HIS114 2.0 13.3 1.0 NE2 B:HIS179 2.1 14.8 1.0 S01 B:Y4E306 2.4 19.8 0.8 H022 B:Y4E306 2.6 32.4 0.8 C02 B:Y4E306 2.9 27.0 0.8 HB2 B:HIS116 2.9 17.2 1.0 CE1 B:HIS116 2.9 15.6 1.0 H021 B:Y4E306 2.9 32.4 0.8 CE1 B:HIS114 3.0 18.8 1.0 CG B:HIS116 3.0 15.4 1.0 CD2 B:HIS114 3.0 15.5 1.0 CE1 B:HIS179 3.0 12.3 1.0 CD2 B:HIS179 3.0 13.0 1.0 HE1 B:HIS116 3.1 18.6 1.0 HE1 B:HIS114 3.1 22.6 1.0 HD2 B:HIS114 3.2 18.6 1.0 HE1 B:HIS179 3.2 14.8 1.0 HD2 B:HIS179 3.2 15.6 1.0 CB B:HIS116 3.4 14.4 1.0 HB3 B:HIS116 3.6 17.2 1.0 ZN B:ZN304 3.7 19.9 1.0 HB2 B:CYS198 3.8 15.6 1.0 HB3 B:CYS198 4.0 15.6 1.0 NE2 B:HIS116 4.0 21.8 1.0 OD1 B:ASP118 4.0 20.2 1.0 ND1 B:HIS114 4.1 14.4 1.0 CD2 B:HIS116 4.1 18.2 1.0 CG B:HIS114 4.1 15.1 1.0 ND1 B:HIS179 4.1 13.0 1.0 HD22 B:ASN210 4.2 86.7 1.0 CG B:HIS179 4.2 10.5 1.0 CB B:CYS198 4.2 13.0 1.0 SG B:CYS198 4.3 15.2 1.0 C03 B:Y4E306 4.4 28.9 0.8 H B:HIS116 4.5 15.9 1.0 ND2 B:ASN210 4.7 72.2 1.0 OD2 B:ASP118 4.7 23.3 1.0 HD21 B:ASN210 4.8 86.7 1.0 CA B:HIS116 4.8 15.8 1.0 HE2 B:HIS116 4.8 26.1 1.0 CG B:ASP118 4.8 20.6 1.0 HD1 B:HIS114 4.8 17.3 1.0 HG2 B:ARG119 4.9 15.9 1.0 HB3 B:SER180 4.9 17.3 1.0 HD1 B:HIS179 4.9 15.6 1.0 HD2 B:HIS116 4.9 21.9 1.0 H031 B:Y4E306 4.9 34.7 0.8 HE B:ARG119 5.0 24.2 1.0 N07 B:Y4E306 5.0 30.1 0.8

Zinc binding site 5 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:19.9 occ:1.00 H011 B:Y4E306 1.8 23.8 0.8 OD2 B:ASP118 2.0 23.3 1.0 NE2 B:HIS240 2.1 14.8 1.0 S01 B:Y4E306 2.2 19.8 0.8 SG B:CYS198 2.3 15.2 1.0 HH21 B:ARG119 3.0 27.0 1.0 CG B:ASP118 3.1 20.6 1.0 CD2 B:HIS240 3.1 15.6 1.0 CE1 B:HIS240 3.1 16.8 1.0 H021 B:Y4E306 3.2 32.4 0.8 HD2 B:HIS240 3.2 18.8 1.0 HE1 B:HIS240 3.3 20.1 1.0 C02 B:Y4E306 3.3 27.0 0.8 HB3 B:CYS198 3.3 15.6 1.0 HE B:ARG119 3.3 24.2 1.0 OD1 B:ASP118 3.4 20.2 1.0 CB B:CYS198 3.5 13.0 1.0 H091 B:Y4E306 3.6 34.8 0.8 HE1 B:HIS114 3.6 22.6 1.0 H031 B:Y4E306 3.7 34.7 0.8 ZN B:ZN303 3.7 16.3 1.0 NH2 B:ARG119 3.8 22.5 1.0 HB2 B:CYS198 3.9 15.6 1.0 C03 B:Y4E306 4.0 28.9 0.8 NE B:ARG119 4.0 20.2 1.0 H022 B:Y4E306 4.1 32.4 0.8 ND1 B:HIS240 4.2 15.7 1.0 CG B:HIS240 4.2 15.0 1.0 CE1 B:HIS114 4.3 18.8 1.0 HH22 B:ARG119 4.3 27.0 1.0 CZ B:ARG119 4.3 19.4 1.0 CB B:ASP118 4.4 18.6 1.0 C09 B:Y4E306 4.4 29.0 0.8 NE2 B:HIS114 4.5 13.3 1.0 HB2 B:ASP118 4.5 22.3 1.0 HA3 B:GLY239 4.6 17.3 1.0 HE1 B:HIS179 4.6 14.8 1.0 NE2 B:HIS179 4.6 14.8 1.0 O B:HOH581 4.6 31.4 1.0 HB3 B:ASP118 4.6 22.3 1.0 HA B:CYS198 4.6 15.2 1.0 O B:HOH502 4.6 19.2 1.0 CA B:CYS198 4.7 12.7 1.0 N07 B:Y4E306 4.8 30.1 0.8 CE1 B:HIS179 4.8 12.3 1.0 HG2 B:ARG119 4.8 15.9 1.0 HD1 B:HIS240 4.9 18.8 1.0

Zinc binding site 6 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Vim-2 Metallo-Beta-Lactamase in Complex with Benzebisheterocycle Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:15.7 occ:1.00 O1 B:FMT301 1.9 16.4 1.0 O2 B:FMT302 1.9 17.2 1.0 NE2 B:HIS153 2.0 19.5 1.0 C B:FMT301 2.6 19.6 1.0 O2 B:FMT301 2.7 19.6 1.0 C B:FMT302 2.9 17.7 1.0 CE1 B:HIS153 2.9 20.4 1.0 HE1 B:HIS153 3.0 24.4 1.0 CD2 B:HIS153 3.2 16.0 1.0 O1 B:FMT302 3.2 19.0 1.0 HD2 B:HIS153 3.4 19.2 1.0 H B:FMT301 3.6 23.6 1.0 HB1 B:ALA132 3.7 18.2 1.0 HB2 B:ALA132 3.8 18.2 1.0 H B:FMT302 3.9 21.3 1.0 ND1 B:HIS153 4.1 17.0 1.0 HA B:ALA132 4.2 18.1 1.0 CB B:ALA132 4.2 15.3 1.0 CG B:HIS153 4.2 15.2 1.0 HG22 B:THR152 4.4 23.3 1.0 HG21 B:THR152 4.7 23.3 1.0 CA B:ALA132 4.7 15.1 1.0 HD1 B:HIS153 4.8 20.4 1.0 O B:HOH475 4.8 20.7 1.0

V.Villamil, M.A.Rossi, M.F.Mojica, P.Hinchliffe, V.Martinez, V.Castillo, C.Saiz, C.Banchio, M.A.Macias, J.Spencer, R.A.Bonomo, A.Vila, D.M.Moreno, G.Mahler. Rational Design of Benzobisheterocycle Metallo-Beta-Lactamase Inhibitors: A Tricyclic Scaffold Enhances Potency Against Target Enzymes. J.Med.Chem. V. 67 3795 2024.
ISSN: ISSN 0022-2623
PubMed: 38373290
DOI: 10.1021/ACS.JMEDCHEM.3C02209