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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:

1hwr

1.800 Å

X-ray

1998-03-20

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gag-Pol polyprotein
ID:POL_HV1H2
AC:P04585
Organism:Human immunodeficiency virus type 1 group M subtype B
Reign:Viruses
TaxID:11706
EC Number:3.4.23.16


Chains:

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


Ligand binding site composition:

B-Factor:18.898
Number of residues:36
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.902627.750

% Hydrophobic% Polar
48.3951.61
According to VolSite

Ligand :
1hwr_1 Structure
HET Code: 216
Formula: C25H30N2O3
Molecular weight: 406.517 g/mol
DrugBank ID: DB06910
Buried Surface Area:62.62 %
Polar Surface area: 64.01 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-9.2975316.129327.9111


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
C37CD2LEU- 234.280Hydrophobic
C63CD2LEU- 234.370Hydrophobic
O4OD1ASP- 252.82163.56H-Bond
(Ligand Donor)
O5OD1ASP- 252.91164.21H-Bond
(Ligand Donor)
C4CBALA- 284.430Hydrophobic
C5CBALA- 284.490Hydrophobic
O1NILE- 503.25158.57H-Bond
(Protein Donor)
O1NILE- 503.21164.91H-Bond
(Protein Donor)
C67CG1ILE- 504.130Hydrophobic
C33CG2ILE- 504.120Hydrophobic
C34CGPRO- 813.420Hydrophobic
C66CGPRO- 813.590Hydrophobic
C35CG1VAL- 823.690Hydrophobic
C65CG2VAL- 823.710Hydrophobic
C31CD1ILE- 843.960Hydrophobic
C61CD1ILE- 843.940Hydrophobic