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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

1ec0

1.790 Å

X-ray

2000-01-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gag-Pol polyprotein
ID:POL_HV1B1
AC:P03366
Organism:Human immunodeficiency virus type 1 group M subtype B
Reign:Viruses
TaxID:11678
EC Number:3.4.23.16


Chains:

Chain Name:Percentage of Residues
within binding site
A50 %
B50 %


Ligand binding site composition:

B-Factor:13.700
Number of residues:47
Including
Standard Amino Acids: 46
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.725756.000

% Hydrophobic% Polar
41.5258.48
According to VolSite

Ligand :
1ec0_1 Structure
HET Code: BED
Formula: C38H38F2N2O8
Molecular weight: 688.714 g/mol
DrugBank ID: DB02629
Buried Surface Area:74.6 %
Polar Surface area: 157.57 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 6
Rings: 6
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
12.978722.87325.6249


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

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

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C02CD2LEU- 233.620Hydrophobic
O25OD2ASP- 252.65159.33H-Bond
(Ligand Donor)
N28OGLY- 273.13166.05H-Bond
(Ligand Donor)
O36OGLY- 273.31155.86H-Bond
(Ligand Donor)
C33CBALA- 283.540Hydrophobic
O36NASP- 293.06158.64H-Bond
(Protein Donor)
C38CBASP- 294.320Hydrophobic
C37CBASP- 303.780Hydrophobic
C33CG1VAL- 323.760Hydrophobic
C31CBILE- 474.430Hydrophobic
C37CG2ILE- 474.010Hydrophobic
C34CD1ILE- 473.920Hydrophobic
F50CG1ILE- 503.70Hydrophobic
C43CD1ILE- 503.360Hydrophobic
C34CD1LEU- 764.50Hydrophobic
F49CGPRO- 813.530Hydrophobic
C01CG1VAL- 823.580Hydrophobic
C01CG1VAL- 823.580Hydrophobic
C01CG1VAL- 823.580Hydrophobic
C33CG2ILE- 844.40Hydrophobic
C23CD1ILE- 843.360Hydrophobic
C07CD2LEU- 1234.420Hydrophobic
C12CD2LEU- 1233.490Hydrophobic
O24OD2ASP- 1252.69159.12H-Bond
(Ligand Donor)
O24OD1ASP- 1252.8129.09H-Bond
(Ligand Donor)
N21OGLY- 1272.98167.59H-Bond
(Ligand Donor)
O46OGLY- 1273.13153.96H-Bond
(Ligand Donor)
C43CBALA- 1283.50Hydrophobic
O46NASP- 1293.05150H-Bond
(Protein Donor)
C48CBASP- 1294.220Hydrophobic
C47CBASP- 1303.770Hydrophobic
C44CG2VAL- 1323.390Hydrophobic
C41CBILE- 1474.320Hydrophobic
C47CG2ILE- 1473.930Hydrophobic
C44CD1ILE- 1473.850Hydrophobic
F49CD1ILE- 1503.660Hydrophobic
F50CGPRO- 1813.710Hydrophobic
C09CBPRO- 1813.620Hydrophobic
C07CG2VAL- 1823.740Hydrophobic
C12CG2VAL- 1823.660Hydrophobic
C43CD1ILE- 1844.40Hydrophobic
F50CD1ILE- 1844.490Hydrophobic
C13CD1ILE- 1843.390Hydrophobic