Zinc in PDB 6odc: Crystal Structure of HDAC8 in Complex with Compound 30

All present enzymatic activity of Crystal Structure of HDAC8 in Complex with Compound 30:
3.5.1.98;

The structure of Crystal Structure of HDAC8 in Complex with Compound 30, PDB code: 6odc 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 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.540, 91.161, 92.574, 90.00, 94.07, 90.00
R / Rfree (%)	19.4 / 23.6

The structure of Crystal Structure of HDAC8 in Complex with Compound 30 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 30 (pdb code 6odc). 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 30, PDB code: 6odc:
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 30


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 30 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:58.1 occ:1.00 OD2 A:ASP267 2.0 51.9 1.0 OD2 A:ASP178 2.0 62.4 1.0 O11 A:M7Y404 2.0 76.4 1.0 O12 A:M7Y404 2.0 73.2 1.0 ND1 A:HIS180 2.2 62.8 1.0 N10 A:M7Y404 2.7 78.0 1.0 C9 A:M7Y404 2.7 70.3 1.0 CG A:ASP178 2.8 63.2 1.0 CG A:ASP267 3.0 61.9 1.0 OD1 A:ASP178 3.0 65.2 1.0 CE1 A:HIS180 3.0 59.1 1.0 CG A:HIS180 3.1 59.2 1.0 OD1 A:ASP267 3.4 65.8 1.0 CB A:HIS180 3.5 55.6 1.0 N A:HIS180 3.7 51.9 1.0 NE2 A:HIS180 4.1 63.5 1.0 C8 A:M7Y404 4.1 65.3 1.0 CD2 A:HIS180 4.2 59.3 1.0 CB A:ASP178 4.2 60.4 1.0 CA A:HIS180 4.2 52.7 1.0 CB A:ASP267 4.3 59.2 1.0 CA A:GLY304 4.3 58.3 1.0 N A:LEU179 4.3 57.4 1.0 NE2 A:HIS142 4.4 51.4 1.0 CB A:LEU179 4.4 49.8 1.0 N A:GLY304 4.6 57.4 1.0 C A:LEU179 4.6 51.4 1.0 CE2 A:TYR306 4.7 68.3 1.0 OH A:TYR306 4.7 65.4 1.0 CE1 A:HIS142 4.7 53.3 1.0 CA A:LEU179 4.7 51.0 1.0 C7 A:M7Y404 4.8 66.7 1.0 C A:ASP178 5.0 55.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of HDAC8 in Complex with Compound 30


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 30 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:51.9 occ:1.00 OD2 B:ASP267 2.0 41.4 1.0 O11 B:M7Y404 2.0 73.0 1.0 O12 B:M7Y404 2.0 61.9 1.0 OD2 B:ASP178 2.0 52.6 1.0 ND1 B:HIS180 2.2 60.4 1.0 N10 B:M7Y404 2.6 69.3 1.0 C9 B:M7Y404 2.6 67.3 1.0 CG B:ASP178 2.9 50.5 1.0 CG B:ASP267 3.0 45.8 1.0 CE1 B:HIS180 3.0 62.4 1.0 OD1 B:ASP178 3.1 47.5 1.0 CG B:HIS180 3.1 57.3 1.0 OD1 B:ASP267 3.4 50.5 1.0 CB B:HIS180 3.6 51.1 1.0 N B:HIS180 3.8 46.9 1.0 C8 B:M7Y404 4.0 66.9 1.0 NE2 B:HIS180 4.1 63.2 1.0 CD2 B:HIS180 4.2 59.8 1.0 CA B:GLY304 4.3 56.1 1.0 CB B:ASP267 4.3 47.1 1.0 CA B:HIS180 4.3 49.4 1.0 CB B:ASP178 4.3 49.5 1.0 N B:LEU179 4.4 55.6 1.0 NE2 B:HIS142 4.4 55.4 1.0 OH B:TYR306 4.4 67.5 1.0 O B:HOH514 4.5 57.1 1.0 CB B:LEU179 4.5 60.5 1.0 CE2 B:TYR306 4.6 56.9 1.0 N B:GLY304 4.6 56.2 1.0 C B:LEU179 4.7 50.0 1.0 CE1 B:HIS142 4.7 57.6 1.0 CA B:LEU179 4.8 57.1 1.0 C7 B:M7Y404 4.8 70.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of HDAC8 in Complex with Compound 30


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 30 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:72.2 occ:1.00 OD2 C:ASP178 2.0 59.2 1.0 O11 C:M7Y404 2.0 84.0 1.0 OD2 C:ASP267 2.0 87.0 1.0 O12 C:M7Y404 2.0 78.3 1.0 ND1 C:HIS180 2.1 63.3 1.0 N10 C:M7Y404 2.7 84.6 1.0 C9 C:M7Y404 2.7 86.9 1.0 CG C:ASP178 2.8 56.4 1.0 CE1 C:HIS180 3.0 69.3 1.0 OD1 C:ASP178 3.0 52.9 1.0 CG C:ASP267 3.0 78.2 1.0 CG C:HIS180 3.1 67.3 1.0 OD1 C:ASP267 3.4 85.8 1.0 CB C:HIS180 3.5 61.9 1.0 N C:HIS180 3.7 63.4 1.0 NE2 C:HIS180 4.1 67.2 1.0 C8 C:M7Y404 4.1 85.4 1.0 CD2 C:HIS180 4.1 71.4 1.0 CA C:HIS180 4.2 61.9 1.0 CB C:ASP178 4.2 57.0 1.0 CA C:GLY304 4.3 63.3 1.0 N C:LEU179 4.3 64.7 1.0 CB C:ASP267 4.3 68.7 1.0 NE2 C:HIS142 4.3 67.5 1.0 CB C:LEU179 4.5 61.9 1.0 OH C:TYR306 4.5 70.4 1.0 N C:GLY304 4.6 64.0 1.0 C C:LEU179 4.7 68.0 1.0 CE1 C:HIS142 4.7 72.9 1.0 CE2 C:TYR306 4.7 67.1 1.0 CA C:LEU179 4.7 64.8 1.0 C7 C:M7Y404 4.9 91.0 1.0 C C:ASP178 5.0 60.5 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.