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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:

3ckt

1.650 Å

X-ray

2008-03-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gag-Pol polyprotein
ID:POL_HV1BR
AC:P03367
Organism:Human immunodeficiency virus type 1 group M subtype B
Reign:Viruses
TaxID:11686
EC Number:3.4.23.16


Chains:

Chain Name:Percentage of Residues
within binding site
A53 %
B47 %


Ligand binding site composition:

B-Factor:18.419
Number of residues:46
Including
Standard Amino Acids: 45
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.181951.750

% Hydrophobic% Polar
45.0454.96
According to VolSite

Ligand :
3ckt_1 Structure
HET Code: YDP
Formula: C28H38N5O6S2
Molecular weight: 604.761 g/mol
DrugBank ID: -
Buried Surface Area:65.1 %
Polar Surface area: 194.3 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 12

Mass center Coordinates

XYZ
5.890372.27812-14.0873


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
C11CD2LEU- 233.560Hydrophobic
C12CD2LEU- 233.680Hydrophobic
N22OD1ASP- 252.83135.65H-Bond
(Ligand Donor)
N22OD2ASP- 252.94144.22H-Bond
(Ligand Donor)
N22OD2ASP- 252.75145.93H-Bond
(Ligand Donor)
N22OD1ASP- 252.830Ionic
(Ligand Cationic)
N22OD2ASP- 252.940Ionic
(Ligand Cationic)
N22OD1ASP- 252.840Ionic
(Ligand Cationic)
N22OD2ASP- 252.750Ionic
(Ligand Cationic)
C18CBALA- 283.50Hydrophobic
C7CBALA- 283.530Hydrophobic
O2NASP- 302.57134.33H-Bond
(Protein Donor)
O3NASP- 302.68152.58H-Bond
(Protein Donor)
N2OD1ASP- 302.82160.99H-Bond
(Ligand Donor)
C18CG2VAL- 323.870Hydrophobic
C5CBILE- 473.890Hydrophobic
C18CD1ILE- 474.130Hydrophobic
C3CD1ILE- 504.440Hydrophobic
C19CG1ILE- 504.060Hydrophobic
C28CG2ILE- 504.130Hydrophobic
O12NILE- 502.61165.97H-Bond
(Protein Donor)
C13CGPRO- 814.040Hydrophobic
C10CG1VAL- 824.420Hydrophobic
C12CG1VAL- 824.110Hydrophobic
C10CD1ILE- 844.440Hydrophobic
C33CD1ILE- 843.650Hydrophobic
C11CG1ILE- 844.450Hydrophobic
C12CD1ILE- 844.040Hydrophobic
C21CD1ILE- 844.180Hydrophobic
C37CD1ILE- 843.630Hydrophobic