Sodium in PDB 7zzp: Structure of HDAC2 Complexed with An Inhibitory Ligand

Enzymatic activity of Structure of HDAC2 Complexed with An Inhibitory Ligand

All present enzymatic activity of Structure of HDAC2 Complexed with An Inhibitory Ligand:
3.5.1.98;

Protein crystallography data

The structure of Structure of HDAC2 Complexed with An Inhibitory Ligand, PDB code: 7zzp 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) 80.90 / 1.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.247, 98.847, 140.77, 90, 90, 90
R / Rfree (%) 15.3 / 17.4

Other elements in 7zzp:

The structure of Structure of HDAC2 Complexed with An Inhibitory Ligand 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 Structure of HDAC2 Complexed with An Inhibitory Ligand (pdb code 7zzp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of HDAC2 Complexed with An Inhibitory Ligand, PDB code: 7zzp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7zzp

Go back to Sodium Binding Sites List in 7zzp
Sodium binding site 1 out of 3 in the Structure of HDAC2 Complexed with An Inhibitory Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of HDAC2 Complexed with An Inhibitory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:18.3
occ:1.00
 O A:PHE192 2.4 15.2 1.0
O A:HOH791 2.4 16.5 1.0
O A:VAL198 2.4 16.5 1.0
O A:THR195 2.6 17.3 1.0
O A:HOH842 2.8 21.2 1.0
C A:PHE192 3.5 15.7 1.0
O A:TYR227 3.6 16.9 1.0
C A:VAL198 3.7 14.7 1.0
C A:THR195 3.8 18.1 1.0
CB A:TYR227 3.9 16.8 1.0
CB A:PHE192 4.0 14.7 1.0
C A:TYR227 4.2 15.4 1.0
N A:THR195 4.3 18.6 1.0
CA A:PHE192 4.3 15.1 1.0
CG2 A:THR195 4.4 18.1 1.0
N A:TYR193 4.4 15.7 1.0
C A:TYR193 4.4 17.5 1.0
CA A:TYR193 4.4 16.7 1.0
O A:TYR193 4.5 17.7 1.0
CA A:THR195 4.5 18.9 1.0
N A:MET199 4.6 14.8 1.0
CA A:MET199 4.6 15.2 1.0
CA A:VAL198 4.6 14.9 1.0
CA A:TYR227 4.6 16.2 1.0
N A:VAL198 4.7 15.9 1.0
CA A:GLY224 4.7 20.2 1.0
CB A:VAL198 4.7 14.1 1.0
O A:GLY224 4.7 18.3 1.0
N A:ASP196 4.8 18.9 1.0
N A:THR200 4.9 12.9 1.0
N A:THR194 4.9 18.1 1.0
N A:ALA228 4.9 15.4 1.0
CA A:ASP196 5.0 19.4 1.0

Sodium binding site 2 out of 3 in 7zzp

Go back to Sodium Binding Sites List in 7zzp
Sodium binding site 2 out of 3 in the Structure of HDAC2 Complexed with An Inhibitory Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of HDAC2 Complexed with An Inhibitory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:16.7
occ:1.00
 O B:VAL198 2.3 14.6 1.0
O B:HOH861 2.4 14.6 1.0
O B:PHE192 2.4 14.8 1.0
O B:THR195 2.5 16.7 1.0
O B:HOH872 2.7 22.0 1.0
C B:PHE192 3.5 14.6 1.0
O B:TYR227 3.5 15.7 1.0
C B:VAL198 3.6 14.2 1.0
C B:THR195 3.7 17.3 1.0
CB B:TYR227 3.8 16.4 1.0
CB B:PHE192 4.1 13.7 1.0
C B:TYR227 4.1 15.5 1.0
N B:THR195 4.3 17.7 1.0
CG2 B:THR195 4.3 16.5 1.0
N B:TYR193 4.4 15.4 1.0
CA B:PHE192 4.4 13.9 1.0
C B:TYR193 4.4 16.6 1.0
CA B:TYR193 4.4 16.2 1.0
O B:TYR193 4.4 17.4 1.0
N B:MET199 4.5 13.6 1.0
CA B:THR195 4.5 17.9 1.0
CA B:MET199 4.5 14.4 1.0
CA B:VAL198 4.5 13.8 1.0
CA B:TYR227 4.6 16.2 1.0
N B:VAL198 4.6 14.5 1.0
CB B:VAL198 4.7 13.6 1.0
CA B:GLY224 4.8 18.8 1.0
N B:ASP196 4.8 17.8 1.0
O B:GLY224 4.8 17.2 1.0
N B:THR200 4.9 12.4 1.0
N B:THR194 4.9 17.3 1.0
N B:ALA228 4.9 15.2 1.0
CA B:ASP196 5.0 18.2 1.0

Sodium binding site 3 out of 3 in 7zzp

Go back to Sodium Binding Sites List in 7zzp
Sodium binding site 3 out of 3 in the Structure of HDAC2 Complexed with An Inhibitory Ligand


Mono view


Stereo pair view

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

b:15.6
occ:1.00
 O C:VAL198 2.3 15.5 1.0
O C:PHE192 2.4 13.3 1.0
O C:HOH790 2.4 14.7 1.0
O C:THR195 2.4 15.5 1.0
O C:HOH774 2.8 24.1 1.0
C C:PHE192 3.5 13.3 1.0
C C:VAL198 3.6 15.6 1.0
C C:THR195 3.6 15.8 1.0
O C:TYR227 3.7 17.7 1.0
CB C:TYR227 3.9 16.9 1.0
CB C:PHE192 4.0 13.5 1.0
N C:THR195 4.1 15.0 1.0
CG2 C:THR195 4.2 15.1 1.0
C C:TYR227 4.2 16.8 1.0
CA C:PHE192 4.4 13.3 1.0
CA C:THR195 4.4 15.7 1.0
N C:TYR193 4.4 14.1 1.0
C C:TYR193 4.4 15.0 1.0
N C:MET199 4.5 16.1 1.0
CA C:MET199 4.5 17.0 1.0
O C:TYR193 4.5 15.2 1.0
CA C:VAL198 4.5 14.9 1.0
CA C:TYR193 4.5 14.8 1.0
N C:VAL198 4.6 15.1 1.0
CA C:TYR227 4.7 17.2 1.0
CA C:GLY224 4.7 17.1 1.0
N C:ASP196 4.7 16.5 1.0
CB C:VAL198 4.7 14.5 1.0
O C:GLY224 4.8 16.4 1.0
CB C:THR195 4.9 15.4 1.0
N C:THR194 4.9 14.2 1.0
CA C:ASP196 4.9 17.6 1.0
N C:THR200 5.0 15.3 1.0
N C:ALA228 5.0 16.4 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: Wed Oct 9 10:21:41 2024

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