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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:

4dkp

1.800 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
C100 %


Ligand binding site composition:

B-Factor:35.498
Number of residues:25
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.569286.875

% Hydrophobic% Polar
49.4150.59
According to VolSite

Ligand :
4dkp_2 Structure
HET Code: 0LL
Formula: C17H16ClFN3O2
Molecular weight: 348.779 g/mol
DrugBank ID: -
Buried Surface Area:51.77 %
Polar Surface area: 85.84 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-9.52175-33.01270.197542


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
CLCH2TRP- 1124.080Hydrophobic
F24CG1VAL- 2553.670Hydrophobic
C22CG2THR- 2574.160Hydrophobic
F24CG2THR- 2574.060Hydrophobic
C22CGGLU- 3704.160Hydrophobic
C18CGGLU- 3703.950Hydrophobic
C02CD1ILE- 3713.860Hydrophobic
F24CBSER- 3754.190Hydrophobic
CLCBASN- 3774.150Hydrophobic
CLCD2PHE- 3823.970Hydrophobic
N14OASN- 4253.21139.62H-Bond
(Ligand Donor)
C22CBTRP- 4273.930Hydrophobic
C18CBTRP- 4273.950Hydrophobic
C06CBASN- 4744.240Hydrophobic