Zinc in PDB 6tld: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2, PDB code: 6tld was solved by T.B.Shaik, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.61
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.640, 70.720, 98.050, 78.08, 75.69, 85.72
R / Rfree (%)	16.6 / 19.5

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2 also contains other interesting chemical elements:

Potassium

(K)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2 (pdb code 6tld). 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 Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2, PDB code: 6tld:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2


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 Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:36.8 occ:1.00 OD1 A:ASP186 2.0 26.3 1.0 OD2 A:ASP285 2.0 24.5 1.0 ND1 A:HIS188 2.1 23.9 1.0 O19 A:NK5504 2.3 35.0 1.0 O20 A:NK5504 2.6 53.6 1.0 N18 A:NK5504 2.7 50.1 1.0 CG A:ASP186 2.9 22.5 1.0 CE1 A:HIS188 2.9 31.6 1.0 C17 A:NK5504 2.9 56.0 1.0 CG A:ASP285 3.0 27.6 1.0 OD2 A:ASP186 3.1 25.1 1.0 CG A:HIS188 3.2 20.3 1.0 OD1 A:ASP285 3.4 25.2 1.0 CB A:HIS188 3.7 20.6 1.0 N A:HIS188 3.8 19.3 1.0 NE2 A:HIS188 4.1 25.3 1.0 CA A:GLY339 4.1 25.4 1.0 CD2 A:HIS188 4.3 25.8 1.0 CB A:ASP186 4.3 20.2 1.0 N A:LEU187 4.3 20.8 1.0 C15 A:NK5504 4.3 57.1 1.0 CB A:ASP285 4.3 22.9 1.0 O A:HOH630 4.4 49.4 1.0 CA A:HIS188 4.4 20.6 1.0 NE2 A:HIS141 4.5 26.4 1.0 OH A:TYR341 4.5 40.8 1.0 CB A:LEU187 4.5 20.5 1.0 N A:GLY339 4.5 25.1 1.0 C A:LEU187 4.7 21.0 1.0 CA A:LEU187 4.7 21.2 1.0 CE2 A:TYR341 4.8 43.1 1.0 NE2 A:HIS142 4.8 23.1 1.0 CE1 A:HIS141 4.9 24.3 1.0 C A:ASP186 4.9 22.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2


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 Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:35.0 occ:1.00 OD1 B:ASP186 1.9 23.4 1.0 OD2 B:ASP285 2.0 21.5 1.0 ND1 B:HIS188 2.2 23.0 1.0 O19 B:NK5504 2.4 38.0 1.0 O20 B:NK5504 2.6 49.6 1.0 N18 B:NK5504 2.6 47.9 1.0 CG B:ASP186 2.8 24.1 1.0 C17 B:NK5504 2.9 55.5 1.0 CG B:ASP285 3.0 25.7 1.0 CE1 B:HIS188 3.0 26.4 1.0 OD2 B:ASP186 3.0 20.8 1.0 CG B:HIS188 3.3 20.2 1.0 OD1 B:ASP285 3.4 24.6 1.0 CB B:HIS188 3.7 20.4 1.0 N B:HIS188 3.8 17.8 1.0 CA B:GLY339 4.1 19.5 1.0 NE2 B:HIS188 4.2 27.2 1.0 CB B:ASP186 4.2 17.9 1.0 CD2 B:HIS188 4.3 25.7 1.0 CB B:ASP285 4.3 19.8 1.0 C15 B:NK5504 4.3 57.2 1.0 N B:LEU187 4.3 19.4 1.0 CA B:HIS188 4.4 18.6 1.0 CB B:LEU187 4.5 18.5 1.0 NE2 B:HIS141 4.5 20.5 1.0 OH B:TYR341 4.5 50.1 1.0 O B:HOH612 4.5 43.1 1.0 N B:GLY339 4.5 24.9 1.0 C B:LEU187 4.7 22.0 1.0 CA B:LEU187 4.7 19.8 1.0 CE2 B:TYR341 4.8 39.4 1.0 NE2 B:HIS142 4.8 21.4 1.0 CE1 B:HIS141 4.8 19.6 1.0 C B:ASP186 4.9 20.6 1.0 CA B:ASP186 5.0 15.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2


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 Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:34.0 occ:1.00 OD1 C:ASP186 1.9 19.9 1.0 OD2 C:ASP285 2.0 21.8 1.0 ND1 C:HIS188 2.2 22.6 1.0 O19 C:NK5504 2.2 27.5 1.0 N18 C:NK5504 2.7 46.3 1.0 O20 C:NK5504 2.7 48.5 1.0 CG C:ASP186 2.9 25.0 1.0 C17 C:NK5504 3.0 52.7 1.0 CG C:ASP285 3.0 23.1 1.0 CE1 C:HIS188 3.0 27.9 1.0 OD2 C:ASP186 3.1 20.3 1.0 CG C:HIS188 3.2 19.6 1.0 OD1 C:ASP285 3.4 22.6 1.0 CB C:HIS188 3.6 17.4 1.0 N C:HIS188 3.9 16.7 1.0 CA C:GLY339 4.1 21.4 1.0 NE2 C:HIS188 4.2 25.6 1.0 CB C:ASP186 4.2 16.3 1.0 N C:LEU187 4.3 18.7 1.0 CD2 C:HIS188 4.3 22.2 1.0 CB C:ASP285 4.3 17.7 1.0 CA C:HIS188 4.4 18.9 1.0 OH C:TYR341 4.4 38.2 1.0 C15 C:NK5504 4.4 54.6 1.0 CB C:LEU187 4.5 18.4 1.0 NE2 C:HIS141 4.5 23.6 1.0 N C:GLY339 4.5 23.6 1.0 C C:LEU187 4.7 19.1 1.0 CE2 C:TYR341 4.7 29.9 1.0 O C:HOH787 4.7 46.5 1.0 CA C:LEU187 4.7 18.8 1.0 NE2 C:HIS142 4.9 23.6 1.0 CE1 C:HIS141 4.9 20.2 1.0 C C:ASP186 4.9 17.1 1.0 CA C:ASP186 5.0 17.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2


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 Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:37.1 occ:1.00 OD1 D:ASP186 1.9 26.5 1.0 OD2 D:ASP285 2.0 23.3 1.0 ND1 D:HIS188 2.2 25.6 1.0 O19 D:NK5505 2.4 35.8 1.0 N18 D:NK5505 2.5 53.4 1.0 O20 D:NK5505 2.5 60.4 1.0 C17 D:NK5505 2.8 61.8 1.0 CG D:ASP186 2.8 25.0 1.0 CE1 D:HIS188 3.0 32.4 1.0 CG D:ASP285 3.0 26.5 1.0 OD2 D:ASP186 3.0 22.2 1.0 CG D:HIS188 3.2 24.1 1.0 OD1 D:ASP285 3.4 24.9 1.0 CB D:HIS188 3.7 20.4 1.0 N D:HIS188 3.9 23.7 1.0 CA D:GLY339 4.1 25.8 1.0 NE2 D:HIS188 4.2 28.7 1.0 C15 D:NK5505 4.2 65.3 1.0 CB D:ASP186 4.2 17.8 1.0 O D:HOH604 4.3 48.1 1.0 CD2 D:HIS188 4.3 27.4 1.0 N D:LEU187 4.3 19.0 1.0 CB D:ASP285 4.4 20.6 1.0 CA D:HIS188 4.4 20.7 1.0 OH D:TYR341 4.4 38.5 1.0 NE2 D:HIS141 4.5 26.4 1.0 CB D:LEU187 4.5 19.8 1.0 N D:GLY339 4.5 23.1 1.0 C D:LEU187 4.7 20.6 1.0 CE2 D:TYR341 4.8 35.8 1.0 CA D:LEU187 4.8 18.2 1.0 NE2 D:HIS142 4.8 24.0 1.0 CE1 D:HIS141 4.9 24.0 1.0 C16 D:NK5505 4.9 65.6 1.0 C D:ASP186 5.0 21.0 1.0 CA D:ASP186 5.0 22.8 1.0

R.Holl, D.V.Kalinin, S.K.Jana, M.Pfafenrot, A.Chakrabarti, J.Melesina, T.B.Shaik, J.Lancelot, R.J.Pierce, W.Sippl, C.Romier, M.Jung. Structure-Based Design, Synthesis, and Biological Evaluation of Triazole-Based SMHDAC8 Inhibitors. Chemmedchem 2019.
ISSN: ESSN 1860-7187
PubMed: 31816172
DOI: 10.1002/CMDC.201900583