Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4ahv

1.800 Å

X-ray

2012-02-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gag-Pol polyprotein
ID:POL_HV1N5
AC:P12497
Organism:Human immunodeficiency virus type 1 group M subtype B
Reign:Viruses
TaxID:11698
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A42 %
B58 %


Ligand binding site composition:

B-Factor:20.905
Number of residues:24
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.019246.375

% Hydrophobic% Polar
50.6849.32
According to VolSite

Ligand :
4ahv_2 Structure
HET Code: Z5P
Formula: C10H12N3
Molecular weight: 174.222 g/mol
DrugBank ID: -
Buried Surface Area:74.69 %
Polar Surface area: 45.46 Å2
Number of
H-Bond Acceptors: 1
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-7.4410823.397511.7014


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
C12CE3TRP- 1084.310Hydrophobic
C6CBPRO- 1094.120Hydrophobic
C9CBASN- 1843.640Hydrophobic
N13OGLY- 1972.59171.91H-Bond
(Ligand Donor)
C12CG2VAL- 2013.640Hydrophobic