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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:

4dku

2.490 Å

X-ray

2012-02-04

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
B100 %


Ligand binding site composition:

B-Factor:66.387
Number of residues:26
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.084280.125

% Hydrophobic% Polar
61.4538.55
According to VolSite

Ligand :
4dku_2 Structure
HET Code: 0KU
Formula: C19H24ClN4O3S
Molecular weight: 423.937 g/mol
DrugBank ID: -
Buried Surface Area:44.1 %
Polar Surface area: 136.16 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-10.1755-33.1024-1.56529


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
C02CG1VAL- 2554.120Hydrophobic
C03CG2THR- 2573.640Hydrophobic
C03CBGLU- 3704.060Hydrophobic
C05CGGLU- 3703.730Hydrophobic
C17CG1ILE- 3713.810Hydrophobic
C01CBSER- 3754.180Hydrophobic
CL1CD1PHE- 3824.340Hydrophobic
C05CG2ILE- 4244.350Hydrophobic
N08OASN- 4253.16154.52H-Bond
(Ligand Donor)
C03CBTRP- 4274.010Hydrophobic
C05CBTRP- 4273.910Hydrophobic
C03CD1ILE- 4754.10Hydrophobic