Zinc in PDB 8r5t: Crystal Structure of Ndm-1 in Complex with Benzobisheterocycle Compound 14.

All present enzymatic activity of Crystal Structure of Ndm-1 in Complex with Benzobisheterocycle Compound 14.:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 in Complex with Benzobisheterocycle Compound 14., PDB code: 8r5t 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)	34.36 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.1, 73.768, 77.647, 90, 90, 90
R / Rfree (%)	16.9 / 21.3

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with Benzobisheterocycle Compound 14. (pdb code 8r5t). 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 Ndm-1 in Complex with Benzobisheterocycle Compound 14., PDB code: 8r5t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 in Complex with Benzobisheterocycle Compound 14.


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 Ndm-1 in Complex with Benzobisheterocycle Compound 14. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:18.4 occ:1.00 OD2 A:ASP124 2.0 18.7 1.0 NE2 A:HIS250 2.1 18.9 1.0 SG A:CYS208 2.2 17.5 1.0 S01 A:Y4E301 2.3 20.9 1.0 H011 A:Y4E301 2.6 25.1 1.0 CG A:ASP124 3.0 17.3 1.0 CE1 A:HIS250 3.0 18.7 1.0 CD2 A:HIS250 3.1 18.0 1.0 HE1 A:HIS250 3.2 22.4 1.0 HD2 A:HIS250 3.3 21.6 1.0 HB3 A:CYS208 3.3 20.3 1.0 OD1 A:ASP124 3.3 18.6 1.0 H022 A:Y4E301 3.4 29.3 1.0 CB A:CYS208 3.5 16.9 1.0 C02 A:Y4E301 3.5 24.4 1.0 H091 A:Y4E301 3.6 40.3 1.0 H031 A:Y4E301 3.6 34.8 1.0 ZN A:ZN303 3.7 19.2 1.0 HB3 A:SER249 3.7 20.0 1.0 HE1 A:HIS120 3.9 23.5 1.0 HE3 A:LYS125 3.9 25.3 1.0 HB2 A:CYS208 3.9 20.3 1.0 HG A:SER249 3.9 20.4 1.0 HB2 A:SER249 3.9 20.0 1.0 C03 A:Y4E301 4.0 29.0 1.0 ND1 A:HIS250 4.2 16.7 1.0 O A:HOH567 4.2 38.4 1.0 CG A:HIS250 4.2 18.9 1.0 CB A:SER249 4.2 16.7 1.0 CB A:ASP124 4.3 15.5 1.0 H021 A:Y4E301 4.3 29.3 1.0 HB2 A:ASP124 4.4 18.6 1.0 HG2 A:LYS125 4.4 23.4 1.0 NE2 A:HIS120 4.4 17.7 1.0 CE1 A:HIS120 4.4 19.6 1.0 C09 A:Y4E301 4.5 33.6 1.0 HB3 A:ASP124 4.5 18.6 1.0 HE1 A:HIS189 4.5 25.4 1.0 HD2 A:LYS125 4.5 24.5 1.0 OG A:SER249 4.5 17.0 1.0 NE2 A:HIS189 4.5 20.7 1.0 HA A:CYS208 4.6 20.5 1.0 CA A:CYS208 4.6 17.1 1.0 CE1 A:HIS189 4.7 21.1 1.0 N07 A:Y4E301 4.8 31.6 1.0 CE A:LYS125 4.8 21.1 1.0 HD1 A:HIS250 4.9 20.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 in Complex with Benzobisheterocycle Compound 14.


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 Ndm-1 in Complex with Benzobisheterocycle Compound 14. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:19.2 occ:1.00 NE2 A:HIS189 2.0 20.7 1.0 NE2 A:HIS120 2.1 17.7 1.0 ND1 A:HIS122 2.1 18.4 1.0 S01 A:Y4E301 2.3 20.9 1.0 CD2 A:HIS120 3.0 17.7 1.0 CE1 A:HIS189 3.0 21.1 1.0 H021 A:Y4E301 3.0 29.3 1.0 CE1 A:HIS122 3.0 19.5 1.0 H022 A:Y4E301 3.0 29.3 1.0 HB2 A:HIS122 3.0 19.1 1.0 CE1 A:HIS120 3.0 19.6 1.0 CD2 A:HIS189 3.1 19.5 1.0 C02 A:Y4E301 3.1 24.4 1.0 CG A:HIS122 3.1 16.9 1.0 HE1 A:HIS122 3.1 23.4 1.0 HD2 A:HIS120 3.2 21.2 1.0 HE1 A:HIS189 3.2 25.4 1.0 HD2 A:HIS189 3.3 23.4 1.0 HE1 A:HIS120 3.3 23.5 1.0 H011 A:Y4E301 3.4 25.1 1.0 CB A:HIS122 3.5 15.9 1.0 ZN A:ZN302 3.7 18.4 1.0 HB3 A:HIS122 3.7 19.1 1.0 HB2 A:CYS208 3.7 20.3 1.0 SG A:CYS208 4.0 17.5 1.0 HB3 A:CYS208 4.0 20.3 1.0 ND1 A:HIS120 4.1 19.1 1.0 ND1 A:HIS189 4.1 20.4 1.0 CB A:CYS208 4.1 16.9 1.0 CG A:HIS120 4.1 16.8 1.0 OD1 A:ASP124 4.1 18.6 1.0 NE2 A:HIS122 4.1 21.5 1.0 HG21 A:THR190 4.2 22.2 1.0 HG23 A:THR190 4.2 22.2 1.0 CG A:HIS189 4.2 17.8 1.0 CD2 A:HIS122 4.2 19.1 1.0 C03 A:Y4E301 4.6 29.0 1.0 CG2 A:THR190 4.6 18.5 1.0 OD2 A:ASP124 4.8 18.7 1.0 HG2 A:LYS125 4.9 23.4 1.0 CG A:ASP124 4.9 17.3 1.0 HG3 A:LYS125 4.9 23.4 1.0 HD1 A:HIS189 4.9 24.4 1.0 HD1 A:HIS120 4.9 22.9 1.0 HE2 A:HIS122 4.9 25.8 1.0 CA A:HIS122 4.9 14.9 1.0 H031 A:Y4E301 5.0 34.8 1.0 HG22 A:THR190 5.0 22.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 in Complex with Benzobisheterocycle Compound 14.


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 Ndm-1 in Complex with Benzobisheterocycle Compound 14. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:24.0 occ:1.00 ND1 B:HIS122 1.9 13.3 1.0 NE2 B:HIS189 2.0 25.5 1.0 NE2 B:HIS120 2.1 22.9 1.0 O B:HOH518 2.3 12.8 1.0 CE1 B:HIS122 2.8 20.1 1.0 CE1 B:HIS189 2.9 25.6 1.0 HE1 B:HIS122 2.9 24.1 1.0 CE1 B:HIS120 3.0 25.2 1.0 CD2 B:HIS189 3.0 23.6 1.0 CG B:HIS122 3.0 19.6 1.0 HE1 B:HIS189 3.1 30.7 1.0 CD2 B:HIS120 3.1 24.1 1.0 HB2 B:HIS122 3.1 26.0 1.0 HE1 B:HIS120 3.2 30.3 1.0 HD2 B:HIS189 3.2 28.3 1.0 HD2 B:HIS120 3.3 28.9 1.0 CB B:HIS122 3.5 21.6 1.0 HB3 B:HIS122 3.7 26.0 1.0 ZN B:ZN302 3.7 24.8 1.0 HB2 B:CYS208 3.8 22.9 1.0 NE2 B:HIS122 4.0 22.4 1.0 ND1 B:HIS189 4.0 24.1 1.0 SG B:CYS208 4.1 21.8 1.0 CD2 B:HIS122 4.1 21.9 1.0 ND1 B:HIS120 4.1 24.1 1.0 HB3 B:CYS208 4.1 22.9 1.0 CG B:HIS189 4.1 23.5 1.0 HG21 B:THR190 4.1 25.4 1.0 HG23 B:THR190 4.1 25.4 1.0 CG B:HIS120 4.2 22.5 1.0 CB B:CYS208 4.2 19.1 1.0 OD1 B:ASP124 4.2 24.1 1.0 CG2 B:THR190 4.6 21.1 1.0 HE2 B:HIS122 4.7 26.9 1.0 HG3 B:LYS125 4.8 30.6 1.0 HD1 B:HIS189 4.8 28.9 1.0 OD2 B:ASP124 4.8 21.4 1.0 HD1 B:HIS120 4.9 28.9 1.0 HG2 B:LYS125 4.9 30.6 1.0 CG B:ASP124 4.9 23.1 1.0 HD2 B:HIS122 5.0 26.3 1.0 CA B:HIS122 5.0 22.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 in Complex with Benzobisheterocycle Compound 14.


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 Ndm-1 in Complex with Benzobisheterocycle Compound 14. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:24.8 occ:1.00 OD2 B:ASP124 2.0 21.4 1.0 NE2 B:HIS250 2.1 19.9 1.0 SG B:CYS208 2.2 21.8 1.0 O B:HOH518 2.3 12.8 1.0 CE1 B:HIS250 3.0 22.0 1.0 CG B:ASP124 3.0 23.1 1.0 HE1 B:HIS250 3.1 26.4 1.0 CD2 B:HIS250 3.2 20.5 1.0 HB3 B:CYS208 3.3 22.9 1.0 OD1 B:ASP124 3.4 24.1 1.0 HD2 B:HIS250 3.4 24.6 1.0 CB B:CYS208 3.4 19.1 1.0 HB3 B:SER249 3.7 28.5 1.0 ZN B:ZN301 3.7 24.0 1.0 HE1 B:HIS120 3.8 30.3 1.0 HB2 B:CYS208 3.9 22.9 1.0 HG B:SER249 3.9 30.2 1.0 HE3 B:LYS125 3.9 33.1 1.0 HB2 B:SER249 4.0 28.5 1.0 ND1 B:HIS250 4.1 22.8 1.0 CB B:SER249 4.2 23.8 1.0 CG B:HIS250 4.2 22.3 1.0 CB B:ASP124 4.3 23.0 1.0 HD2 B:LYS125 4.3 33.9 1.0 HG2 B:LYS125 4.3 30.6 1.0 CE1 B:HIS120 4.4 25.2 1.0 HB2 B:ASP124 4.5 27.6 1.0 NE2 B:HIS120 4.5 22.9 1.0 OG B:SER249 4.5 25.2 1.0 HA B:CYS208 4.5 24.1 1.0 HE1 B:HIS189 4.5 30.7 1.0 NE2 B:HIS189 4.5 25.5 1.0 HB3 B:ASP124 4.6 27.6 1.0 CA B:CYS208 4.6 20.1 1.0 CE1 B:HIS189 4.7 25.6 1.0 CE B:LYS125 4.8 27.6 1.0 HD1 B:HIS250 4.9 27.3 1.0 CD B:LYS125 4.9 28.2 1.0 CG B:LYS125 4.9 25.5 1.0 HG3 B:LYS125 5.0 30.6 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