Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T15739 Target Info
Target Name Cellular tumor antigen p53 (TP53)
Synonyms Tumor suppressor p53; Phosphoprotein p53; P53; Antigen NY-CO-13
Target Type Clinical trial Target
Gene Name TP53
UniProt ID
P53_HUMAN
Ligand General Information  Top
Ligand Name N6-Acetyl-L-lysine Ligand Info
Canonical SMILES CC(=O)NCCCCC(C(=O)O)N
InChI 1S/C8H16N2O3/c1-6(11)10-5-3-2-4-7(9)8(12)13/h7H,2-5,9H2,1H3,(H,10,11)(H,12,13)/t7-/m0/s1
InChIKey DTERQYGMUDWYAZ-ZETCQYMHSA-N
PubChem Compound ID 92832
Drug Binding Sites of Target  Top
PDB ID: 1YC5      Sir2-p53 peptide-nicotinamide
Method X-ray diffraction Resolution 1.40 Å Mutation Yes [1]
PDB Sequence
KGQSTSRHKL
383
MF
Residue
Distance (Å)
HIS380
4.048
LYS381
1.327
Residue
Distance (Å)
LEU383
1.335
MET384
4.508
PDB ID: 2H4H      Sir2 H116Y mutant-p53 peptide-NAD
Method X-ray diffraction Resolution 1.99 Å Mutation Yes [2]
PDB Sequence
SRHKLMF
Residue
Distance (Å)
HIS9
4.014
LYS10
1.533
Residue
Distance (Å)
LEU12
1.399
MET13
4.236
PDB ID: 2H4F      Sir2-p53 peptide-NAD+
Method X-ray diffraction Resolution 2.00 Å Mutation Yes [2]
PDB Sequence
SRHKLMF
Residue
Distance (Å)
HIS9
3.991
LYS10
1.515
Residue
Distance (Å)
LEU12
1.606
MET13
4.616
PDB ID: 4BUZ      SIR2 COMPLEX STRUCTURE MIXTURE OF EX-527 INHIBITOR AND REACTION PRODUCTS OR OF REACTION SUBSTRATES P53 PEPTIDE AND NAD
Method X-ray diffraction Resolution 1.90 Å Mutation No [3]
PDB Sequence
RHKLMF
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ALY or .ALY2 or .ALY3 or :3ALY;style chemicals stick;color identity;select .P:380 or .P:381 or .P:383 or .P:384; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
HIS380
3.919
LYS381
1.323
Residue
Distance (Å)
LEU383
1.322
MET384
4.585
PDB ID: 4ZZJ      SIRT1/Activator/Substrate Complex
Method X-ray diffraction Resolution 2.74 Å Mutation No [4]
PDB Sequence
RHKLF
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ALY or .ALY2 or .ALY3 or :3ALY;style chemicals stick;color identity;select .B:2 or .B:3 or .B:5; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
HIS2
4.175
LYS3
1.330
Residue
Distance (Å)
LEU5
1.331
References  Top
REF 1 Mechanism of sirtuin inhibition by nicotinamide: altering the NAD(+) cosubstrate specificity of a Sir2 enzyme. Mol Cell. 2005 Mar 18;17(6):855-68.
REF 2 Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide. Structure. 2006 Aug;14(8):1231-40.
REF 3 Ex-527 inhibits Sirtuins by exploiting their unique NAD+-dependent deacetylation mechanism. Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):E2772-81.
REF 4 Crystallographic structure of a small molecule SIRT1 activator-enzyme complex. Nat Commun. 2015 Jul 2;6:7645.

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