Zinc in PDB 6odb: Crystal Structure of HDAC8 in Complex with Compound 3

All present enzymatic activity of Crystal Structure of HDAC8 in Complex with Compound 3:
3.5.1.98;

The structure of Crystal Structure of HDAC8 in Complex with Compound 3, PDB code: 6odb was solved by X.Zheng, C.Conti, J.Caravella, M.-M.Zablocki, K.Bair, N.Barczak, B.Han, D.Lancia Jr., C.Liu, M.Martin, P.Y.Ng, A.Rudnitskaya, J.J.Thomason, R.Garcia-Dancey, C.Hardy, J.Lahdenranta, C.Leng, P.Li, E.Pardo, A.Saldahna, T.Tan, A.V.Toms, L.Yao, C.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.915, 90.950, 93.067, 90.00, 94.10, 90.00
R / Rfree (%)	19.5 / 24.1

The structure of Crystal Structure of HDAC8 in Complex with Compound 3 also contains other interesting chemical elements:

Potassium

(K)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of HDAC8 in Complex with Compound 3 (pdb code 6odb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of HDAC8 in Complex with Compound 3, PDB code: 6odb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of HDAC8 in Complex with Compound 3


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 HDAC8 in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:36.2 occ:1.00 OD2 A:ASP267 2.0 31.3 1.0 O45 A:M8G401 2.0 42.2 1.0 O42 A:M8G401 2.0 43.1 1.0 OD1 A:ASP178 2.0 34.4 1.0 ND1 A:HIS180 2.1 43.1 1.0 N43 A:M8G401 2.5 45.6 1.0 C41 A:M8G401 2.5 45.1 1.0 CG A:ASP178 2.9 32.1 1.0 CE1 A:HIS180 2.9 40.8 1.0 CG A:ASP267 3.0 33.1 1.0 OD2 A:ASP178 3.1 31.6 1.0 CG A:HIS180 3.1 38.8 1.0 OD1 A:ASP267 3.4 35.0 1.0 CB A:HIS180 3.6 34.9 1.0 N A:HIS180 3.7 32.9 1.0 C39 A:M8G401 3.9 45.4 1.0 NE2 A:HIS180 4.0 38.9 1.0 CD2 A:HIS180 4.1 37.1 1.0 N A:LEU179 4.2 33.9 1.0 CB A:ASP267 4.3 31.1 1.0 CB A:ASP178 4.3 31.1 1.0 CA A:HIS180 4.3 33.5 1.0 CB A:LEU179 4.3 33.7 1.0 CA A:GLY304 4.3 38.0 1.0 NE2 A:HIS142 4.5 32.2 1.0 C37 A:M8G401 4.6 48.6 1.0 OH A:TYR306 4.6 40.6 1.0 C A:LEU179 4.6 33.0 1.0 CA A:LEU179 4.7 32.8 1.0 N A:GLY304 4.8 38.3 1.0 CE2 A:TYR306 4.8 38.2 1.0 CE1 A:HIS142 4.9 32.2 1.0 C A:ASP178 4.9 30.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of HDAC8 in Complex with Compound 3


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 HDAC8 in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:40.8 occ:1.00 OD2 B:ASP267 2.0 35.8 1.0 O45 B:M8G401 2.0 51.7 1.0 OD1 B:ASP178 2.0 45.3 1.0 O42 B:M8G401 2.0 55.0 1.0 ND1 B:HIS180 2.1 41.5 1.0 C41 B:M8G401 2.7 53.6 1.0 N43 B:M8G401 2.7 53.5 1.0 CG B:ASP178 2.8 40.9 1.0 CE1 B:HIS180 2.9 41.8 1.0 CG B:ASP267 3.0 41.2 1.0 OD2 B:ASP178 3.0 34.5 1.0 CG B:HIS180 3.1 38.0 1.0 OD1 B:ASP267 3.4 45.2 1.0 CB B:HIS180 3.6 37.2 1.0 N B:HIS180 3.8 36.0 1.0 NE2 B:HIS180 4.0 42.0 1.0 C39 B:M8G401 4.1 50.6 1.0 CD2 B:HIS180 4.1 40.0 1.0 N B:LEU179 4.2 38.7 1.0 CB B:ASP267 4.3 40.5 1.0 CB B:ASP178 4.3 40.2 1.0 CA B:GLY304 4.3 38.6 1.0 CA B:HIS180 4.3 37.0 1.0 CB B:LEU179 4.4 33.5 1.0 NE2 B:HIS142 4.5 39.3 1.0 OH B:TYR306 4.6 45.8 1.0 C B:LEU179 4.7 36.5 1.0 C37 B:M8G401 4.7 48.4 1.0 CA B:LEU179 4.7 35.7 1.0 N B:GLY304 4.7 38.8 1.0 CE2 B:TYR306 4.7 40.0 1.0 CE1 B:HIS142 4.9 37.4 1.0 C B:ASP178 4.9 37.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of HDAC8 in Complex with Compound 3


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 HDAC8 in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:53.5 occ:1.00 OD1 C:ASP178 2.0 42.8 1.0 O45 C:M8G401 2.0 69.9 1.0 OD2 C:ASP267 2.0 59.5 1.0 O42 C:M8G401 2.0 63.2 1.0 ND1 C:HIS180 2.1 54.1 1.0 C41 C:M8G401 2.7 69.8 1.0 N43 C:M8G401 2.7 71.0 1.0 CG C:ASP178 2.8 38.2 1.0 CE1 C:HIS180 2.9 55.0 1.0 OD2 C:ASP178 3.0 35.5 1.0 CG C:ASP267 3.0 57.9 1.0 CG C:HIS180 3.0 54.9 1.0 OD1 C:ASP267 3.4 53.5 1.0 CB C:HIS180 3.5 51.2 1.0 N C:HIS180 3.7 52.0 1.0 NE2 C:HIS180 4.0 57.2 1.0 CD2 C:HIS180 4.0 57.9 1.0 C39 C:M8G401 4.1 67.3 1.0 N C:LEU179 4.2 48.3 1.0 CB C:ASP178 4.2 42.3 1.0 CA C:HIS180 4.3 51.5 1.0 CB C:ASP267 4.4 53.6 1.0 CA C:GLY304 4.4 48.0 1.0 CB C:LEU179 4.4 49.6 1.0 NE2 C:HIS142 4.4 61.1 1.0 C37 C:M8G401 4.5 71.8 1.0 C C:LEU179 4.6 50.4 1.0 OH C:TYR306 4.6 65.6 1.0 CA C:LEU179 4.7 49.1 1.0 N C:GLY304 4.7 48.7 1.0 CE2 C:TYR306 4.8 62.5 1.0 CE1 C:HIS142 4.8 61.4 1.0 C C:ASP178 4.9 47.0 1.0 CA C:ASP178 5.0 44.1 1.0

X.Zheng, C.Conti, J.Caravella, M.-M.Zablocki, K.Bair, N.Barczak, B.Han, D.Lancia Jr., C.Liu, M.Martin, P.Y.Ng, A.Rudnitskaya, J.J.Thomason, R.Garcia-Dancey, C.Hardy, J.Lahdenranta, C.Leng, P.Li, E.Pardo, A.Saldahna, T.Tan, A.V.Toms, L.Yao, C.Zhang. Structure-Based Discovery of Novel N-(E)-N-Hydroxy-3-(2-(2-Oxoimidazolidin-1-Yl)Phenyl) Acrylamides As Potent and Selective HDAC8 Inhibitors To Be Published.