2.250 Å
X-ray
2010-04-24
Name: | Hydroxymethylglutaryl-CoA lyase, mitochondrial |
---|---|
ID: | HMGCL_HUMAN |
AC: | P35914 |
Organism: | Homo sapiens |
Reign: | Eukaryota |
TaxID: | 9606 |
EC Number: | 4.1.3.4 |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 37.897 |
---|---|
Number of residues: | 51 |
Including | |
Standard Amino Acids: | 50 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 0 |
Cofactors: | |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.587 | 425.250 |
% Hydrophobic | % Polar |
---|---|
47.62 | 52.38 |
According to VolSite |
HET Code: | HMG |
---|---|
Formula: | C27H39N7O20P3S |
Molecular weight: | 906.620 g/mol |
DrugBank ID: | DB03169 |
Buried Surface Area: | 48.83 % |
Polar Surface area: | 490.04 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 25 |
H-Bond Donors: | 6 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 5 |
Cationic atoms: | 0 |
Rule of Five Violation: | 3 |
Rotatable Bonds: | 24 |
X | Y | Z |
---|---|---|
20.7884 | -13.5627 | -5.10443 |
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 |
O2 | NE2 | GLN- 45 | 3.32 | 171.25 | H-Bond (Protein Donor) |
C6P | CB | VAL- 77 | 4.19 | 0 | Hydrophobic |
O4B | OG | SER- 78 | 3.18 | 125.32 | H-Bond (Protein Donor) |
C1B | CB | SER- 78 | 3.97 | 0 | Hydrophobic |
O9A | NZ | LYS- 80 | 2.81 | 157.4 | H-Bond (Protein Donor) |
O9A | NZ | LYS- 80 | 2.81 | 0 | Ionic (Protein Cationic) |
O5A | NE1 | TRP- 81 | 3.38 | 121.87 | H-Bond (Protein Donor) |
C6P | CB | TRP- 81 | 4.31 | 0 | Hydrophobic |
C6P | CG1 | VAL- 82 | 3.83 | 0 | Hydrophobic |
C2P | CD2 | LEU- 106 | 4 | 0 | Hydrophobic |
CDP | CB | PRO- 108 | 4.1 | 0 | Hydrophobic |
C2P | CE2 | PHE- 127 | 3.88 | 0 | Hydrophobic |
S1P | CD2 | PHE- 127 | 3.66 | 0 | Hydrophobic |
CDP | CB | ILE- 139 | 4.34 | 0 | Hydrophobic |
O4A | ND2 | ASN- 140 | 2.72 | 161.73 | H-Bond (Protein Donor) |
C6 | CD2 | TYR- 167 | 3.41 | 0 | Hydrophobic |
C4 | CD1 | TYR- 167 | 3.46 | 0 | Hydrophobic |
O3 | OG | SER- 169 | 2.6 | 164.7 | H-Bond (Protein Donor) |
O3 | OG1 | THR- 205 | 3.36 | 141.51 | H-Bond (Protein Donor) |
O7 | MG | MG- 402 | 2.5 | 0 | Metal Acceptor |
O4 | MG | MG- 402 | 2.44 | 0 | Metal Acceptor |