Zinc in PDB 4u3b: Lpxc From A.Aaeolicus in Complex with the Mmp Inhibitor 4-[[4-(4- Chlorophenoxy)Phenyl]Sulfanylmethyl]Tetrahydropyran-4-Carbohydroxamic Acid - Compound 2

The structure of Lpxc From A.Aaeolicus in Complex with the Mmp Inhibitor 4-[[4-(4- Chlorophenoxy)Phenyl]Sulfanylmethyl]Tetrahydropyran-4-Carbohydroxamic Acid - Compound 2, PDB code: 4u3b was solved by N.B.Olivier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.80 / 1.34
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	65.929, 65.929, 133.556, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 18.4

The structure of Lpxc From A.Aaeolicus in Complex with the Mmp Inhibitor 4-[[4-(4- Chlorophenoxy)Phenyl]Sulfanylmethyl]Tetrahydropyran-4-Carbohydroxamic Acid - Compound 2 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Lpxc From A.Aaeolicus in Complex with the Mmp Inhibitor 4-[[4-(4- Chlorophenoxy)Phenyl]Sulfanylmethyl]Tetrahydropyran-4-Carbohydroxamic Acid - Compound 2 (pdb code 4u3b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Lpxc From A.Aaeolicus in Complex with the Mmp Inhibitor 4-[[4-(4- Chlorophenoxy)Phenyl]Sulfanylmethyl]Tetrahydropyran-4-Carbohydroxamic Acid - Compound 2, PDB code: 4u3b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Lpxc From A.Aaeolicus in Complex with the Mmp Inhibitor 4-[[4-(4- Chlorophenoxy)Phenyl]Sulfanylmethyl]Tetrahydropyran-4-Carbohydroxamic Acid - Compound 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lpxc From A.Aaeolicus in Complex with the Mmp Inhibitor 4-[[4-(4- Chlorophenoxy)Phenyl]Sulfanylmethyl]Tetrahydropyran-4-Carbohydroxamic Acid - Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.4 occ:1.00 OD1 A:ASP230 2.0 13.2 1.0 NE2 A:HIS226 2.0 10.8 1.0 NE2 A:HIS74 2.1 13.8 1.0 O24 A:3BW306 2.1 17.3 1.0 O26 A:3BW306 2.2 18.8 1.0 CG A:ASP230 2.7 14.5 1.0 C23 A:3BW306 2.8 17.2 1.0 OD2 A:ASP230 2.8 13.9 1.0 N25 A:3BW306 3.0 19.4 1.0 CE1 A:HIS226 3.0 10.6 1.0 CD2 A:HIS74 3.1 13.0 1.0 CD2 A:HIS226 3.1 11.1 1.0 CE1 A:HIS74 3.1 16.6 1.0 ND1 A:HIS226 4.2 11.3 1.0 OG1 A:THR179 4.2 19.0 1.0 CG A:HIS226 4.2 11.0 1.0 CB A:ASP230 4.2 12.2 1.0 CG A:HIS74 4.2 14.6 1.0 ND1 A:HIS74 4.2 18.8 1.0 CG A:GLU73 4.2 15.1 1.0 OE2 A:GLU73 4.3 15.8 1.0 O A:HOH688 4.3 27.6 1.0 C17 A:3BW306 4.3 17.7 1.0 CB A:THR179 4.3 17.1 1.0 CA A:THR179 4.8 11.6 1.0 C21 A:3BW306 4.8 19.7 1.0 C22 A:3BW306 4.8 21.8 1.0 CD A:GLU73 4.8 15.0 1.0 CA A:ASP230 4.8 10.6 1.0 NE2 A:HIS253 4.9 16.1 1.0 CE1 A:HIS253 4.9 15.8 1.0 O A:HIS226 5.0 10.5 1.0 O A:HOH583 5.0 24.9 1.0

Zinc binding site 2 out of 2 in the Lpxc From A.Aaeolicus in Complex with the Mmp Inhibitor 4-[[4-(4- Chlorophenoxy)Phenyl]Sulfanylmethyl]Tetrahydropyran-4-Carbohydroxamic Acid - Compound 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lpxc From A.Aaeolicus in Complex with the Mmp Inhibitor 4-[[4-(4- Chlorophenoxy)Phenyl]Sulfanylmethyl]Tetrahydropyran-4-Carbohydroxamic Acid - Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:22.7 occ:1.00 NE2 A:HIS188 2.0 17.4 1.0 N3 A:IMD301 2.0 24.9 1.0 NE2 A:HIS58 2.0 17.8 1.0 CL A:CL304 2.4 23.1 1.0 C2 A:IMD301 2.9 27.1 1.0 CD2 A:HIS188 3.0 19.5 1.0 CE1 A:HIS58 3.0 19.1 1.0 CE1 A:HIS188 3.0 18.6 1.0 C4 A:IMD301 3.1 28.0 1.0 CD2 A:HIS58 3.1 18.0 1.0 N1 A:IMD301 4.1 30.1 1.0 CG A:HIS188 4.1 18.4 1.0 ND1 A:HIS188 4.1 20.1 1.0 ND1 A:HIS58 4.2 19.3 1.0 C5 A:IMD301 4.2 27.3 1.0 CG A:HIS58 4.2 17.4 1.0 OD1 A:ASN57 4.5 35.4 1.0 CG2 A:VAL192 4.5 18.4 1.0 O A:HOH643 4.7 32.6 1.0 CB A:ASN57 4.7 19.4 1.0 O A:HOH479 4.8 30.8 1.0 CG A:ASN57 5.0 39.1 1.0

K.Murphy-Benenato, N.B.Olivier, A.Choy, P.Ross, M.Miller, M.Hale. Synthesis, Structure and Sar of Pyran-Based Lpxc Inhibitors Acs Med.Chem.Lett. 2014.
ISSN: ISSN 1948-5875
DOI: 10.1021/ML500210X