1.800 Å
X-ray
2011-09-13
Name: | Ras-related protein Rab-25 |
---|---|
ID: | RAB25_HUMAN |
AC: | P57735 |
Organism: | Homo sapiens |
Reign: | Eukaryota |
TaxID: | 9606 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 22.627 |
---|---|
Number of residues: | 39 |
Including | |
Standard Amino Acids: | 35 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 3 |
Cofactors: | |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.223 | 614.250 |
% Hydrophobic | % Polar |
---|---|
35.71 | 64.29 |
According to VolSite |
HET Code: | GNP |
---|---|
Formula: | C10H13N6O13P3 |
Molecular weight: | 518.164 g/mol |
DrugBank ID: | DB02082 |
Buried Surface Area: | 77.28 % |
Polar Surface area: | 338.36 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 16 |
H-Bond Donors: | 5 |
Rings: | 3 |
Aromatic rings: | 1 |
Anionic atoms: | 4 |
Cationic atoms: | 0 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 8 |
X | Y | Z |
---|---|---|
-0.49725 | 17.9917 | 14.9329 |
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 |
O1B | N | GLY- 24 | 3.06 | 149.36 | H-Bond (Protein Donor) |
O3A | N | GLY- 24 | 3.19 | 126.07 | H-Bond (Protein Donor) |
O3G | NZ | LYS- 25 | 2.71 | 145.4 | H-Bond (Protein Donor) |
O1B | N | LYS- 25 | 2.88 | 158.66 | H-Bond (Protein Donor) |
O1B | NZ | LYS- 25 | 2.94 | 153.63 | H-Bond (Protein Donor) |
O3G | NZ | LYS- 25 | 2.71 | 0 | Ionic (Protein Cationic) |
O1B | NZ | LYS- 25 | 2.94 | 0 | Ionic (Protein Cationic) |
O2B | N | THR- 26 | 3.04 | 152.89 | H-Bond (Protein Donor) |
O1A | ND2 | ASN- 27 | 2.93 | 123.84 | H-Bond (Protein Donor) |
O1A | N | ASN- 27 | 3.09 | 156.05 | H-Bond (Protein Donor) |
C2' | CZ | PHE- 37 | 4.24 | 0 | Hydrophobic |
O2' | O | SER- 38 | 2.62 | 150.4 | H-Bond (Ligand Donor) |
O3' | O | HIS- 39 | 2.85 | 149.55 | H-Bond (Ligand Donor) |
C3' | CB | SER- 41 | 4.37 | 0 | Hydrophobic |
O1G | OG1 | THR- 43 | 2.56 | 175.06 | H-Bond (Protein Donor) |
O2G | N | THR- 44 | 2.84 | 162.02 | H-Bond (Protein Donor) |
O3G | N | GLY- 70 | 2.94 | 157.31 | H-Bond (Protein Donor) |
N7 | ND2 | ASN- 125 | 3.26 | 137.89 | H-Bond (Protein Donor) |
O4' | NZ | LYS- 126 | 2.85 | 129.73 | H-Bond (Protein Donor) |
N1 | OD2 | ASP- 128 | 3.28 | 128.22 | H-Bond (Ligand Donor) |
N1 | OD1 | ASP- 128 | 2.72 | 170.97 | H-Bond (Ligand Donor) |
N2 | OD2 | ASP- 128 | 2.63 | 167.14 | H-Bond (Ligand Donor) |
O6 | N | LEU- 157 | 3.35 | 156.5 | H-Bond (Protein Donor) |
O2G | MG | MG- 200 | 1.99 | 0 | Metal Acceptor |
O2B | MG | MG- 200 | 2.01 | 0 | Metal Acceptor |