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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:

1upj

2.220 Å

X-ray

1996-03-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gag-Pol polyprotein
ID:POL_HV1BR
AC:P03367
Organism:Human immunodeficiency virus type 1 group M subtype B
Reign:Viruses
TaxID:11686
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:31.099
Number of residues:19
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.586394.875

% Hydrophobic% Polar
46.1553.85
According to VolSite

Ligand :
1upj_1 Structure
HET Code: U01
Formula: C19H16BrO3
Molecular weight: 372.233 g/mol
DrugBank ID: DB08662
Buried Surface Area:31.6 %
Polar Surface area: 49.36 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 0
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
9.2406516.76313.257


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
CD3CD1LEU- 234.130Hydrophobic
CB3CBALA- 283.750Hydrophobic
BRCG2VAL- 324.060Hydrophobic
BRCD1ILE- 474.230Hydrophobic
OA2NILE- 503.37160.5H-Bond
(Protein Donor)
CG4CD1ILE- 503.330Hydrophobic
CD1CGPRO- 814.250Hydrophobic
CD1CG2VAL- 823.780Hydrophobic
CD2CG2VAL- 823.890Hydrophobic
CB3CG2ILE- 844.330Hydrophobic