2.000 Å
X-ray
2008-07-05
Name: | 3-oxo-5-beta-steroid 4-dehydrogenase |
---|---|
ID: | AK1D1_HUMAN |
AC: | P51857 |
Organism: | Homo sapiens |
Reign: | Eukaryota |
TaxID: | 9606 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 19.559 |
---|---|
Number of residues: | 45 |
Including | |
Standard Amino Acids: | 44 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 1 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
1.312 | 1113.750 |
% Hydrophobic | % Polar |
---|---|
51.52 | 48.48 |
According to VolSite |
HET Code: | NAP |
---|---|
Formula: | C21H25N7O17P3 |
Molecular weight: | 740.381 g/mol |
DrugBank ID: | DB03461 |
Buried Surface Area: | 67.11 % |
Polar Surface area: | 405.54 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 21 |
H-Bond Donors: | 5 |
Rings: | 5 |
Aromatic rings: | 3 |
Anionic atoms: | 4 |
Cationic atoms: | 1 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 13 |
X | Y | Z |
---|---|---|
5.42431 | -16.3283 | 2.09556 |
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 |
O2D | N | THR- 25 | 3.23 | 144.43 | H-Bond (Protein Donor) |
O3D | N | TYR- 26 | 2.96 | 150.13 | H-Bond (Protein Donor) |
C3D | CB | TYR- 26 | 3.87 | 0 | Hydrophobic |
O2D | OD2 | ASP- 53 | 2.59 | 179.01 | H-Bond (Ligand Donor) |
C2D | CE2 | TYR- 58 | 3.79 | 0 | Hydrophobic |
N7N | OG | SER- 169 | 2.97 | 126.36 | H-Bond (Ligand Donor) |
O7N | ND2 | ASN- 170 | 2.76 | 154.71 | H-Bond (Protein Donor) |
N7N | OE1 | GLN- 193 | 3.24 | 145.62 | H-Bond (Ligand Donor) |
DuAr | DuAr | TYR- 219 | 3.78 | 0 | Aromatic Face/Face |
C3N | CB | TYR- 219 | 4.13 | 0 | Hydrophobic |
O1N | OG | SER- 220 | 2.92 | 155.38 | H-Bond (Protein Donor) |
O5D | N | SER- 220 | 3.1 | 128.12 | H-Bond (Protein Donor) |
O1A | N | LEU- 222 | 2.93 | 141.34 | H-Bond (Protein Donor) |
O1A | N | THR- 224 | 3.06 | 154.53 | H-Bond (Protein Donor) |
C3B | CB | SER- 225 | 3.84 | 0 | Hydrophobic |
C4D | CG1 | ILE- 271 | 4.18 | 0 | Hydrophobic |
O2A | N | LYS- 273 | 2.93 | 172.88 | H-Bond (Protein Donor) |
O1X | NZ | LYS- 273 | 2.75 | 175.68 | H-Bond (Protein Donor) |
C3D | CB | LYS- 273 | 4.25 | 0 | Hydrophobic |
C3B | CD | LYS- 273 | 4.37 | 0 | Hydrophobic |
C5D | CB | LYS- 273 | 4.01 | 0 | Hydrophobic |
O1X | NZ | LYS- 273 | 2.75 | 0 | Ionic (Protein Cationic) |
O3X | OG | SER- 274 | 2.7 | 170.57 | H-Bond (Protein Donor) |
O1X | N | PHE- 275 | 2.92 | 156.8 | H-Bond (Protein Donor) |
O2X | NH2 | ARG- 279 | 3.03 | 165.77 | H-Bond (Protein Donor) |
O3X | NE | ARG- 279 | 2.79 | 172.71 | H-Bond (Protein Donor) |
O2X | CZ | ARG- 279 | 3.9 | 0 | Ionic (Protein Cationic) |
O3X | CZ | ARG- 279 | 3.65 | 0 | Ionic (Protein Cationic) |
N6A | OE1 | GLU- 282 | 2.97 | 157.12 | H-Bond (Ligand Donor) |
N7A | ND2 | ASN- 283 | 3.01 | 173.08 | H-Bond (Protein Donor) |
N6A | OD1 | ASN- 283 | 2.83 | 147.75 | H-Bond (Ligand Donor) |