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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:

3kfp

1.770 Å

X-ray

2009-10-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gag-Pol polyprotein
ID:POL_HV1Z2
AC:P12499
Organism:Human immunodeficiency virus type 1 group M subtype D
Reign:Viruses
TaxID:11683
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:32.698
Number of residues:20
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.261310.500

% Hydrophobic% Polar
41.3058.70
According to VolSite

Ligand :
3kfp_1 Structure
HET Code: 3TL
Formula: C50H64N6O10
Molecular weight: 909.077 g/mol
DrugBank ID: -
Buried Surface Area:40.1 %
Polar Surface area: 233.51 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 8
Rings: 4
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 4
Rotatable Bonds: 25

Mass center Coordinates

XYZ
-11.3568-12.28258.89558


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
N1OGLY- 273145.66H-Bond
(Ligand Donor)
CG2CBALA- 284.40Hydrophobic
CG1CBALA- 283.850Hydrophobic
N4OD2ASP- 292.87162.86H-Bond
(Ligand Donor)
O4NASP- 293.01166.64H-Bond
(Protein Donor)
CG2CG1VAL- 324.30Hydrophobic
CG1CG1VAL- 324.360Hydrophobic
CACG2ILE- 474.40Hydrophobic
CG2CD1ILE- 473.90Hydrophobic
O8NGLY- 482.71156.26H-Bond
(Protein Donor)
N2OGLY- 482.88167.19H-Bond
(Ligand Donor)
C9CG1ILE- 503.580Hydrophobic
CG1CD1ILE- 843.560Hydrophobic