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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:

4dko

1.980 Å

X-ray

2012-02-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Envelope glycoprotein gp160
ID:Q0ED31_9HIV1
AC:Q0ED31
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:32.644
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.008273.375

% Hydrophobic% Polar
61.7338.27
According to VolSite

Ligand :
4dko_1 Structure
HET Code: 0LM
Formula: C18H26ClFN3O2
Molecular weight: 370.869 g/mol
DrugBank ID: -
Buried Surface Area:54.35 %
Polar Surface area: 62.64 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 3
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
27.8264-14.328137.8429


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
F25CG1VAL- 2553.670Hydrophobic
F25CG2THR- 2573.60Hydrophobic
C04CGGLU- 3704.090Hydrophobic
C06CGGLU- 3703.790Hydrophobic
F25CBSER- 3754.140Hydrophobic
CLCBASN- 3774.460Hydrophobic
CLCD2PHE- 3823.680Hydrophobic
C06CG2ILE- 4243.740Hydrophobic
N07OASN- 4253.29126.68H-Bond
(Ligand Donor)
C04CBTRP- 42740Hydrophobic
C06CBTRP- 4273.850Hydrophobic
N11OGLY- 4733.41162.72H-Bond
(Ligand Donor)
C21CBASN- 4744.330Hydrophobic
C04CD1ILE- 4754.470Hydrophobic
F25CD1ILE- 4754.490Hydrophobic