1.700 Å
X-ray
2009-11-13
Name: | Hydroxymethylglutaryl-CoA synthase, mitochondrial |
---|---|
ID: | HMCS2_HUMAN |
AC: | P54868 |
Organism: | Homo sapiens |
Reign: | Eukaryota |
TaxID: | 9606 |
EC Number: | 2.3.3.10 |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 2 % |
C | 98 % |
B-Factor: | 16.413 |
---|---|
Number of residues: | 49 |
Including | |
Standard Amino Acids: | 47 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 2 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
1.305 | 405.000 |
% Hydrophobic | % Polar |
---|---|
56.67 | 43.33 |
According to VolSite |
HET Code: | HMG |
---|---|
Formula: | C27H39N7O20P3S |
Molecular weight: | 906.620 g/mol |
DrugBank ID: | DB03169 |
Buried Surface Area: | 57.28 % |
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 |
---|---|---|
21.3703 | 100.72 | -29.6403 |
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 |
N6A | O | ALA- 81 | 3.25 | 130.33 | H-Bond (Ligand Donor) |
O4A | NZ | LYS- 83 | 3.71 | 0 | Ionic (Protein Cationic) |
C5B | CD2 | LEU- 88 | 4.32 | 0 | Hydrophobic |
CCP | CD2 | LEU- 88 | 4.47 | 0 | Hydrophobic |
CDP | CD2 | LEU- 88 | 4.45 | 0 | Hydrophobic |
O4 | N | CYS- 166 | 3.16 | 145.22 | H-Bond (Protein Donor) |
C4 | SG | CYS- 166 | 3.71 | 0 | Hydrophobic |
O5A | ND2 | ASN- 204 | 2.83 | 164.74 | H-Bond (Protein Donor) |
OAP | O | ASN- 204 | 2.71 | 169.55 | H-Bond (Ligand Donor) |
CAP | CB | ALA- 205 | 4.45 | 0 | Hydrophobic |
N8P | OG1 | THR- 208 | 3.25 | 125.72 | H-Bond (Ligand Donor) |
C4 | CE1 | PHE- 241 | 3.57 | 0 | Hydrophobic |
C6 | CD1 | PHE- 241 | 4.12 | 0 | Hydrophobic |
C6P | CG2 | VAL- 253 | 3.82 | 0 | Hydrophobic |
N4P | OG | SER- 258 | 2.86 | 166.9 | H-Bond (Ligand Donor) |
S1P | CB | SER- 258 | 3.56 | 0 | Hydrophobic |
CDP | CD1 | ILE- 259 | 4.26 | 0 | Hydrophobic |
CEP | CD1 | ILE- 259 | 4.2 | 0 | Hydrophobic |
C2P | CG1 | ILE- 259 | 4.22 | 0 | Hydrophobic |
C2P | CB | TYR- 262 | 4.11 | 0 | Hydrophobic |
O7 | NE2 | HIS- 301 | 2.93 | 148.15 | H-Bond (Protein Donor) |
C2P | CG | PRO- 303 | 4.06 | 0 | Hydrophobic |
CDP | CE2 | PHE- 304 | 3.4 | 0 | Hydrophobic |
O9A | NZ | LYS- 306 | 3.91 | 0 | Ionic (Protein Cationic) |
C2P | SD | MET- 307 | 4.46 | 0 | Hydrophobic |
O7A | NZ | LYS- 310 | 2.92 | 123.56 | H-Bond (Protein Donor) |
O9A | NZ | LYS- 310 | 2.59 | 155.79 | H-Bond (Protein Donor) |
O7A | NZ | LYS- 310 | 2.92 | 0 | Ionic (Protein Cationic) |
O9A | NZ | LYS- 310 | 2.59 | 0 | Ionic (Protein Cationic) |
O7 | ND2 | ASN- 380 | 3.11 | 168.54 | H-Bond (Protein Donor) |
C4 | CE1 | TYR- 382 | 4.1 | 0 | Hydrophobic |
S1P | CE2 | TYR- 412 | 4.03 | 0 | Hydrophobic |
C2 | CD2 | TYR- 412 | 3.86 | 0 | Hydrophobic |
C4 | CB | SER- 414 | 4.44 | 0 | Hydrophobic |
O4 | N | SER- 414 | 2.84 | 174.14 | H-Bond (Protein Donor) |