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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:

4npt

1.660 Å

X-ray

2013-11-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Protease
ID:O38896_9HIV1
AC:O38896
Organism:Human immunodeficiency virus 1
Reign:Viruses
TaxID:11676
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:24.269
Number of residues:21
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.315303.750

% Hydrophobic% Polar
51.1148.89
According to VolSite

Ligand :
4npt_1 Structure
HET Code: 017
Formula: C27H37N3O7S
Molecular weight: 547.664 g/mol
DrugBank ID: DB01264
Buried Surface Area:37.71 %
Polar Surface area: 148.79 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 4
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 12

Mass center Coordinates

XYZ
11.7366-9.5026122.8336


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
C7CD2LEU- 234.260Hydrophobic
C15CD1ILE- 324.380Hydrophobic
C14CD1ILE- 473.770Hydrophobic
O22NILE- 502.84159.44H-Bond
(Protein Donor)
C35CG2ILE- 504.050Hydrophobic
C33CD1ILE- 503.780Hydrophobic
C15SDMET- 543.960Hydrophobic
C27CBMET- 544.240Hydrophobic
C29CBMET- 543.820Hydrophobic
C15CBTHR- 803.950Hydrophobic
C7CD1ILE- 823.880Hydrophobic
C6CG2VAL- 843.560Hydrophobic