Zinc in PDB 4u3d: Lpxc From A.Aaeolicus in Complex with 4-[[4-[2-[4-(Morpholinomethyl) Phenyl]Ethynyl]Phenoxy]Methyl]Tetrahydropyran-4-Carbohydroxamic Acid (Compound 9)

The structure of Lpxc From A.Aaeolicus in Complex with 4-[[4-[2-[4-(Morpholinomethyl) Phenyl]Ethynyl]Phenoxy]Methyl]Tetrahydropyran-4-Carbohydroxamic Acid (Compound 9), PDB code: 4u3d 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)	35.05 / 1.25
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	65.865, 65.865, 133.282, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 16.8

The structure of Lpxc From A.Aaeolicus in Complex with 4-[[4-[2-[4-(Morpholinomethyl) Phenyl]Ethynyl]Phenoxy]Methyl]Tetrahydropyran-4-Carbohydroxamic Acid (Compound 9) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Lpxc From A.Aaeolicus in Complex with 4-[[4-[2-[4-(Morpholinomethyl) Phenyl]Ethynyl]Phenoxy]Methyl]Tetrahydropyran-4-Carbohydroxamic Acid (Compound 9) (pdb code 4u3d). 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 4-[[4-[2-[4-(Morpholinomethyl) Phenyl]Ethynyl]Phenoxy]Methyl]Tetrahydropyran-4-Carbohydroxamic Acid (Compound 9), PDB code: 4u3d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Lpxc From A.Aaeolicus in Complex with 4-[[4-[2-[4-(Morpholinomethyl) Phenyl]Ethynyl]Phenoxy]Methyl]Tetrahydropyran-4-Carbohydroxamic Acid (Compound 9)


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 4-[[4-[2-[4-(Morpholinomethyl) Phenyl]Ethynyl]Phenoxy]Methyl]Tetrahydropyran-4-Carbohydroxamic Acid (Compound 9) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.6 occ:1.00 NE2 A:HIS74 2.0 8.3 0.5 OD1 A:ASP230 2.0 9.3 1.0 O31 A:3BX305 2.1 12.5 1.0 NE2 A:HIS226 2.1 7.8 1.0 O33 A:3BX305 2.2 12.4 1.0 NE2 A:HIS74 2.2 6.7 0.5 CG A:ASP230 2.7 8.6 1.0 OD2 A:ASP230 2.8 10.0 1.0 C30 A:3BX305 2.8 12.2 1.0 CD2 A:HIS74 2.9 9.1 0.5 N32 A:3BX305 3.0 13.0 1.0 CE1 A:HIS74 3.0 8.9 0.5 CE1 A:HIS226 3.0 7.9 1.0 CD2 A:HIS226 3.1 8.1 1.0 CD2 A:HIS74 3.1 7.2 0.5 CE1 A:HIS74 3.2 7.7 0.5 CG A:HIS74 4.1 8.6 0.5 ND1 A:HIS74 4.1 9.8 0.5 OG1 A:THR179 4.2 13.1 1.0 ND1 A:HIS226 4.2 7.7 1.0 CB A:ASP230 4.2 8.8 1.0 CG A:HIS226 4.2 7.9 1.0 CG A:GLU73 4.3 10.6 1.0 C24 A:3BX305 4.3 13.0 1.0 CG A:HIS74 4.3 8.4 0.5 OE2 A:GLU73 4.3 10.4 1.0 ND1 A:HIS74 4.3 8.5 0.5 CB A:THR179 4.5 11.1 1.0 C29 A:3BX305 4.8 16.8 1.0 O A:HOH526 4.8 0.8 1.0 CD A:GLU73 4.8 11.1 1.0 CA A:ASP230 4.8 7.4 1.0 CA A:THR179 4.8 8.6 1.0 C28 A:3BX305 4.9 17.9 1.0 O A:HIS226 4.9 7.8 1.0 CE1 A:HIS253 5.0 11.1 1.0 C23 A:3BX305 5.0 14.5 1.0

Zinc binding site 2 out of 2 in the Lpxc From A.Aaeolicus in Complex with 4-[[4-[2-[4-(Morpholinomethyl) Phenyl]Ethynyl]Phenoxy]Methyl]Tetrahydropyran-4-Carbohydroxamic Acid (Compound 9)


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 4-[[4-[2-[4-(Morpholinomethyl) Phenyl]Ethynyl]Phenoxy]Methyl]Tetrahydropyran-4-Carbohydroxamic Acid (Compound 9) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:16.9 occ:1.00 NE2 A:HIS188 2.0 14.3 1.0 NE2 A:HIS58 2.0 13.7 1.0 N1 A:IMD301 2.1 21.9 1.0 CL A:CL304 2.3 18.3 1.0 C5 A:IMD301 3.0 25.8 1.0 CE1 A:HIS188 3.0 14.5 1.0 CE1 A:HIS58 3.0 14.9 1.0 CD2 A:HIS188 3.0 15.3 1.0 CD2 A:HIS58 3.1 13.6 1.0 C2 A:IMD301 3.1 26.9 1.0 C4 A:IMD301 4.1 28.3 1.0 ND1 A:HIS188 4.1 15.3 1.0 CG A:HIS188 4.1 14.4 1.0 ND1 A:HIS58 4.2 15.2 1.0 N3 A:IMD301 4.2 27.8 1.0 CG A:HIS58 4.2 12.9 1.0 OD1 A:ASN57 4.4 29.6 1.0 CG2 A:VAL192 4.5 14.0 1.0 O A:HOH697 4.7 32.1 1.0 CB A:ASN57 4.8 14.5 1.0 O A:HOH742 4.8 48.5 1.0 CG1 A:VAL192 4.9 15.1 1.0 CD1 A:ILE189 4.9 18.1 0.5 O A:HOH469 5.0 28.9 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