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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:

2fxe

1.800 Å

X-ray

2006-02-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gag-Pol polyprotein
ID:POL_HV1RH
AC:P05959
Organism:Human immunodeficiency virus type 1 group M subtype B
Reign:Viruses
TaxID:11701
EC Number:3.4.23.16


Chains:

Chain Name:Percentage of Residues
within binding site
A50 %
B50 %


Ligand binding site composition:

B-Factor:11.186
Number of residues:43
Including
Standard Amino Acids: 42
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.090843.750

% Hydrophobic% Polar
46.4053.60
According to VolSite

Ligand :
2fxe_1 Structure
HET Code: DR7
Formula: C38H52N6O7
Molecular weight: 704.855 g/mol
DrugBank ID: DB01072
Buried Surface Area:63.29 %
Polar Surface area: 171.21 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 5
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 18

Mass center Coordinates

XYZ
5.6242-0.61580413.0574


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
CAUCD2LEU- 234.20Hydrophobic
CAXCD2LEU- 234.080Hydrophobic
OAMOD2ASP- 252.9134.22H-Bond
(Ligand Donor)
OAMOD1ASP- 252.64154.78H-Bond
(Ligand Donor)
NBGOGLY- 273.31127.19H-Bond
(Ligand Donor)
NBHOGLY- 273.14160.74H-Bond
(Ligand Donor)
CG1CBALA- 284.070Hydrophobic
CAFCBALA- 283.770Hydrophobic
CAACBASP- 294.240Hydrophobic
CABCBASP- 294.150Hydrophobic
OAINASP- 293172.45H-Bond
(Protein Donor)
OAJNASP- 292.82168.01H-Bond
(Protein Donor)
CAECBASP- 304.410Hydrophobic
CAGCBASP- 304.270Hydrophobic
CAECG2VAL- 324.030Hydrophobic
CG1CG2VAL- 324.460Hydrophobic
CAGCG2VAL- 324.480Hydrophobic
CAECD1ILE- 474.440Hydrophobic
CG2CD1ILE- 474.030Hydrophobic
CAHCD1ILE- 474.170Hydrophobic
NOGLY- 482.9168.41H-Bond
(Ligand Donor)
NBFOGLY- 482.99154.72H-Bond
(Ligand Donor)
CG2CG1ILE- 503.740Hydrophobic
CG1CG1ILE- 504.070Hydrophobic
CATCBILE- 504.490Hydrophobic
CAHCG2ILE- 5040Hydrophobic
CAWCG1ILE- 504.310Hydrophobic
CAPCGPRO- 813.70Hydrophobic
CANCBPRO- 813.780Hydrophobic
CAYCGPRO- 813.390Hydrophobic
CAVCBPRO- 813.560Hydrophobic
CBQCG1VAL- 823.840Hydrophobic
CAVCG1VAL- 824.270Hydrophobic
CAQCG2VAL- 823.710Hydrophobic
CAXCG2VAL- 823.730Hydrophobic
CG1CD1ILE- 843.440Hydrophobic
CAFCD1ILE- 843.890Hydrophobic
CATCD1ILE- 843.850Hydrophobic
CBBCD1ILE- 843.620Hydrophobic
OBIOHOH- 1113.35141.67H-Bond
(Protein Donor)