1.940 Å
X-ray
2012-07-10
Name: | NAD-dependent protein deacylase sirtuin-5, mitochondrial |
---|---|
ID: | SIR5_HUMAN |
AC: | Q9NXA8 |
Organism: | Homo sapiens |
Reign: | Eukaryota |
TaxID: | 9606 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 98 % |
B | 2 % |
B-Factor: | 33.697 |
---|---|
Number of residues: | 51 |
Including | |
Standard Amino Acids: | 45 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 6 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
1.157 | 1107.000 |
% Hydrophobic | % Polar |
---|---|
47.87 | 52.13 |
According to VolSite |
HET Code: | CNA |
---|---|
Formula: | C22H28N7O13P2 |
Molecular weight: | 660.444 g/mol |
DrugBank ID: | DB02498 |
Buried Surface Area: | 73.9 % |
Polar Surface area: | 334.31 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 17 |
H-Bond Donors: | 6 |
Rings: | 5 |
Aromatic rings: | 3 |
Anionic atoms: | 2 |
Cationic atoms: | 1 |
Rule of Five Violation: | 3 |
Rotatable Bonds: | 11 |
X | Y | Z |
---|---|---|
18.5855 | 5.60295 | 20.8205 |
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
Ligand | Protein | Interaction | |||
---|---|---|---|---|---|
Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
O1A | N | ALA- 59 | 2.72 | 159.75 | H-Bond (Protein Donor) |
C5B | CB | ALA- 59 | 4.16 | 0 | Hydrophobic |
C2D | CB | ALA- 59 | 4.14 | 0 | Hydrophobic |
C4N | CB | ALA- 59 | 3.91 | 0 | Hydrophobic |
N6A | OE1 | GLU- 64 | 3.04 | 150.64 | H-Bond (Ligand Donor) |
C4N | CG1 | VAL- 67 | 4.33 | 0 | Hydrophobic |
C5B | CG2 | THR- 69 | 4.19 | 0 | Hydrophobic |
O2N | N | PHE- 70 | 2.76 | 161.68 | H-Bond (Protein Donor) |
C4' | CE1 | PHE- 70 | 3.43 | 0 | Hydrophobic |
C5N | CE2 | PHE- 70 | 3.3 | 0 | Hydrophobic |
C5D | CD1 | PHE- 70 | 3.72 | 0 | Hydrophobic |
C5B | CG | ARG- 71 | 3.96 | 0 | Hydrophobic |
C3B | CG | ARG- 71 | 4.01 | 0 | Hydrophobic |
O2A | NE2 | GLN- 140 | 3.04 | 164.6 | H-Bond (Protein Donor) |
O2D | NE2 | GLN- 140 | 3.39 | 163.47 | H-Bond (Protein Donor) |
C3D | CB | GLN- 140 | 4.36 | 0 | Hydrophobic |
O2D | OD1 | ASN- 141 | 3.08 | 138.87 | H-Bond (Ligand Donor) |
O7N | N | ILE- 142 | 3.05 | 141.54 | H-Bond (Protein Donor) |
N7N | OD2 | ASP- 143 | 2.79 | 164.38 | H-Bond (Ligand Donor) |
O3D | ND1 | HIS- 158 | 3.48 | 120.12 | H-Bond (Protein Donor) |
C4D | CZ | PHE- 223 | 4.27 | 0 | Hydrophobic |
O2A | N | SER- 251 | 2.9 | 171.38 | H-Bond (Protein Donor) |
O2A | OG | SER- 251 | 2.72 | 174.21 | H-Bond (Protein Donor) |
C3B | CB | SER- 251 | 4.1 | 0 | Hydrophobic |
C3D | CG2 | VAL- 254 | 4.1 | 0 | Hydrophobic |
O3B | ND2 | ASN- 275 | 2.73 | 156.67 | H-Bond (Protein Donor) |
O2B | OD1 | ASN- 275 | 2.93 | 158.64 | H-Bond (Ligand Donor) |
O2B | OG1 | THR- 276 | 3.39 | 122.2 | H-Bond (Protein Donor) |
N1A | N | CYS- 293 | 2.84 | 155.44 | H-Bond (Protein Donor) |