Sodium in PDB 8a0b: Inhibitor Binding to HDAC2

Enzymatic activity of Inhibitor Binding to HDAC2

All present enzymatic activity of Inhibitor Binding to HDAC2:
3.5.1.98;

Protein crystallography data

The structure of Inhibitor Binding to HDAC2, PDB code: 8a0b was solved by A.Cleasby, D.Tisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.17 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.221, 98.018, 139.402, 90, 90, 90
R / Rfree (%) 16.5 / 18.8

Other elements in 8a0b:

The structure of Inhibitor Binding to HDAC2 also contains other interesting chemical elements:

Calcium (Ca) 3 atoms
Zinc (Zn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Inhibitor Binding to HDAC2 (pdb code 8a0b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Inhibitor Binding to HDAC2, PDB code: 8a0b:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8a0b

Go back to Sodium Binding Sites List in 8a0b
Sodium binding site 1 out of 3 in the Inhibitor Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Inhibitor Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:27.8
occ:1.00
 O A:PHE192 2.2 25.2 1.0
O A:VAL198 2.3 26.8 1.0
O A:HOH799 2.4 27.6 1.0
O A:THR195 2.4 27.7 1.0
O A:HOH821 3.0 36.4 1.0
C A:PHE192 3.3 24.9 1.0
C A:VAL198 3.6 26.3 1.0
O A:TYR227 3.6 26.0 1.0
C A:THR195 3.6 29.0 1.0
CB A:TYR227 3.7 26.2 1.0
CB A:PHE192 3.9 25.4 1.0
C A:TYR227 4.2 26.2 1.0
N A:THR195 4.2 29.8 1.0
CG2 A:THR195 4.2 28.7 1.0
CA A:PHE192 4.2 24.6 1.0
N A:TYR193 4.3 25.6 1.0
CA A:TYR193 4.3 26.2 1.0
C A:TYR193 4.3 27.4 1.0
CA A:THR195 4.4 29.5 1.0
O A:TYR193 4.4 27.7 1.0
N A:MET199 4.5 24.8 1.0
CA A:VAL198 4.5 24.3 1.0
CA A:MET199 4.5 22.8 1.0
CA A:TYR227 4.6 25.7 1.0
N A:VAL198 4.6 24.7 1.0
CA A:GLY224 4.6 29.5 1.0
CB A:VAL198 4.6 23.4 1.0
N A:ASP196 4.7 30.1 1.0
O A:GLY224 4.7 26.0 1.0
N A:THR194 4.9 27.3 1.0
CA A:ASP196 4.9 29.1 1.0
N A:THR200 4.9 23.3 1.0
CB A:THR195 4.9 31.1 1.0
N A:ALA228 4.9 25.5 1.0
CG A:TYR227 4.9 27.7 1.0

Sodium binding site 2 out of 3 in 8a0b

Go back to Sodium Binding Sites List in 8a0b
Sodium binding site 2 out of 3 in the Inhibitor Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Inhibitor Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:26.5
occ:1.00
 O B:PHE192 2.3 24.9 1.0
O B:VAL198 2.3 25.1 1.0
O B:HOH803 2.4 23.1 1.0
O B:THR195 2.4 26.0 1.0
O B:HOH795 2.8 31.9 1.0
C B:PHE192 3.4 24.3 1.0
O B:TYR227 3.5 26.6 1.0
C B:VAL198 3.6 24.1 1.0
C B:THR195 3.7 26.1 1.0
CB B:TYR227 3.7 25.6 1.0
CB B:PHE192 4.0 24.1 1.0
C B:TYR227 4.1 26.3 1.0
N B:THR195 4.2 27.2 1.0
CG2 B:THR195 4.2 27.4 1.0
N B:TYR193 4.3 24.6 1.0
CA B:PHE192 4.3 23.6 1.0
CA B:TYR193 4.3 24.2 1.0
C B:TYR193 4.3 25.8 1.0
O B:TYR193 4.3 26.7 1.0
CA B:THR195 4.4 26.6 1.0
N B:MET199 4.5 22.3 1.0
CA B:MET199 4.5 22.0 1.0
CA B:VAL198 4.5 22.9 1.0
CA B:TYR227 4.5 25.2 1.0
N B:VAL198 4.6 24.4 1.0
CA B:GLY224 4.6 28.8 1.0
O B:GLY224 4.7 26.5 1.0
CB B:VAL198 4.7 22.5 1.0
N B:ASP196 4.7 24.7 1.0
N B:THR194 4.8 26.6 1.0
N B:ALA228 4.9 24.1 1.0
N B:THR200 4.9 21.1 1.0
CA B:ASP196 4.9 26.0 1.0
CG B:TYR227 4.9 25.9 1.0
CB B:THR195 5.0 27.7 1.0

Sodium binding site 3 out of 3 in 8a0b

Go back to Sodium Binding Sites List in 8a0b
Sodium binding site 3 out of 3 in the Inhibitor Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Inhibitor Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na603

b:30.3
occ:1.00
 O C:VAL198 2.3 29.4 1.0
O C:PHE192 2.3 26.9 1.0
O C:THR195 2.3 29.4 1.0
O C:HOH772 2.3 27.0 1.0
O C:HOH788 2.9 41.3 1.0
C C:PHE192 3.4 26.1 1.0
C C:VAL198 3.5 28.7 1.0
C C:THR195 3.5 29.6 1.0
O C:TYR227 3.6 31.1 1.0
CB C:TYR227 3.7 31.3 1.0
CB C:PHE192 4.0 25.8 1.0
N C:THR195 4.1 29.3 1.0
C C:TYR227 4.1 31.9 1.0
CG2 C:THR195 4.2 28.3 1.0
CA C:PHE192 4.3 25.4 1.0
CA C:THR195 4.3 28.8 1.0
C C:TYR193 4.4 28.0 1.0
N C:TYR193 4.4 25.4 1.0
CA C:TYR193 4.4 26.1 1.0
O C:TYR193 4.4 29.0 1.0
N C:MET199 4.4 27.8 1.0
CA C:MET199 4.4 27.7 0.5
CA C:MET199 4.4 27.2 0.5
CA C:VAL198 4.5 27.4 1.0
CA C:TYR227 4.5 30.7 1.0
N C:VAL198 4.5 28.1 1.0
CA C:GLY224 4.5 29.6 1.0
N C:ASP196 4.6 28.9 1.0
O C:GLY224 4.6 29.0 1.0
CB C:VAL198 4.7 26.5 1.0
CA C:ASP196 4.8 30.1 1.0
CG C:TYR227 4.8 32.6 1.0
N C:THR194 4.9 26.5 1.0
CB C:THR195 4.9 29.9 1.0
N C:ALA228 4.9 31.1 1.0
N C:THR200 4.9 26.5 1.0

Reference:

E.Tamanini, S.Miyamura, I.M.Buck, B.D.Cons, L.Dawson, C.East, T.Futamura, S.Goto, C.Griffiths-Jones, T.Hashimoto, T.D.Heightman, S.Ishikawa, H.Ito, Y.Kaneko, T.Kawato, K.Kondo, N.Kurihara, J.M.Mccarthy, Y.Mori, T.Nagase, Y.Nakaishi, J.Reeks, A.Sato, P.Schopf, K.Tai, T.Tamai, D.Tisi, A.J.Woolford. Fragment-Based Discovery of A Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor. Acs Med.Chem.Lett. V. 13 1591 2022.
ISSN: ISSN 1948-5875
PubMed: 36262388
DOI: 10.1021/ACSMEDCHEMLETT.2C00272
Page generated: Fri Apr 7 17:44:48 2023

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