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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:

4ced

1.750 Å

X-ray

2013-11-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Integrase
ID:Q76353_9HIV1
AC:Q76353
Organism:Human immunodeficiency virus 1
Reign:Viruses
TaxID:11676
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A61 %
B39 %


Ligand binding site composition:

B-Factor:15.992
Number of residues:28
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.646381.375

% Hydrophobic% Polar
47.7952.21
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4cedHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
4ced_2 Structure
HET Code: 9NS
Formula: C29H29N2O8
Molecular weight: 533.549 g/mol
DrugBank ID: -
Buried Surface Area:51.82 %
Polar Surface area: 145.4 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 2
Rings: 4
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 13

Mass center Coordinates

XYZ
33.6187-7.7216913.65
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4cedRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation8051015Highcharts.com


Binding mode :
What is Poseview ?
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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
C7CGGLN- 954.10Hydrophobic
C28CGGLU- 964.480Hydrophobic
C7CBALA- 984.430Hydrophobic
C22CD1TYR- 994.30Hydrophobic
C23CBTYR- 994.240Hydrophobic
C28CBTYR- 993.780Hydrophobic
C29CGTYR- 993.90Hydrophobic
C14CBTYR- 994.20Hydrophobic
C6CG2THR- 1254.250Hydrophobic
N30OGLN- 1682.74168.39H-Bond
(Ligand Donor)
O35NGLU- 1702.84161.88H-Bond
(Protein Donor)
C22CBHIS- 1714.160Hydrophobic
O32NHIS- 1712.92165.12H-Bond
(Protein Donor)
C22CGLYS- 1733.930Hydrophobic
C29CDLYS- 1734.250Hydrophobic
C15CBTHR- 1744.220Hydrophobic
C11CG2THR- 1744.070Hydrophobic
O32OG1THR- 1742.74163.66H-Bond
(Protein Donor)