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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:

1ikx

2.800 Å

X-ray

2001-05-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gag-Pol polyprotein
ID:POL_HV1B1
AC:P03366
Organism:Human immunodeficiency virus type 1 group M subtype B
Reign:Viruses
TaxID:11678
EC Number:2.7.7.49


Chains:

Chain Name:Percentage of Residues
within binding site
A93 %
B7 %


Ligand binding site composition:

B-Factor:42.001
Number of residues:30
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.354462.375

% Hydrophobic% Polar
71.5328.47
According to VolSite

Ligand :
1ikx_1 Structure
HET Code: PNU
Formula: C13H11ClN4OS
Molecular weight: 306.771 g/mol
DrugBank ID: DB08414
Buried Surface Area:76.38 %
Polar Surface area: 103.13 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-10.3966141.925174.646


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
C4CD2LEU- 1004.390Hydrophobic
S17CGLEU- 1004.470Hydrophobic
C12CD2LEU- 1004.110Hydrophobic
N18OLYS- 1012.96149.86H-Bond
(Ligand Donor)
N2ND2ASN- 1033.28139.81H-Bond
(Protein Donor)
CL19CG2VAL- 1063.940Hydrophobic
S17CG1VAL- 1794.450Hydrophobic
C21CG1VAL- 1794.150Hydrophobic
C21CBTYR- 1813.940Hydrophobic
C11CBTYR- 1814.350Hydrophobic
C11CBTYR- 1883.740Hydrophobic
C21CBTYR- 1883.990Hydrophobic
CL19CD2PHE- 2273.560Hydrophobic
CL19CBLEU- 2343.420Hydrophobic
N18OPRO- 2363.43131.15H-Bond
(Ligand Donor)