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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:

3ix4

1.800 Å

X-ray

2009-09-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Transcriptional activator protein LasR
ID:LASR_PSEAE
AC:P25084
Organism:Pseudomonas aeruginosa
Reign:Bacteria
TaxID:208964
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
G100 %


Ligand binding site composition:

B-Factor:15.262
Number of residues:42
Including
Standard Amino Acids: 42
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.340489.375

% Hydrophobic% Polar
63.4536.55
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3ix4HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3ix4_7 Structure
HET Code: TX1
Formula: C21H13Br2ClN2O5
Molecular weight: 568.599 g/mol
DrugBank ID: -
Buried Surface Area:79.22 %
Polar Surface area: 101.22 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 7

Mass center Coordinates

XYZ
35.662828.3217-45.7918
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3ix4RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.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
BR24CD1LEU- 363.850Hydrophobic
C4CD1LEU- 363.690Hydrophobic
C1CD2LEU- 364.140Hydrophobic
C29CD1LEU- 404.370Hydrophobic
CL31CGLEU- 404.120Hydrophobic
BR23CBTYR- 474.210Hydrophobic
CL31CD2TYR- 474.320Hydrophobic
CL31CBALA- 503.40Hydrophobic
BR23CD1ILE- 523.990Hydrophobic
O17OHTYR- 562.8154.41H-Bond
(Protein Donor)
BR24CD1TYR- 563.870Hydrophobic
O18NE1TRP- 603.05130.75H-Bond
(Protein Donor)
O19NE1TRP- 603.18156.9H-Bond
(Protein Donor)
BR24CGARG- 614.040Hydrophobic
C4CBTYR- 644.440Hydrophobic
BR23CE2TYR- 644.280Hydrophobic
BR24CD1TYR- 643.560Hydrophobic
DuArDuArTYR- 643.70Aromatic Face/Face
N8OD2ASP- 732.74162.84H-Bond
(Ligand Donor)
C11CG2THR- 753.560Hydrophobic
C26CG2VAL- 764.110Hydrophobic
C27CG1VAL- 764.430Hydrophobic
C27CBCYS- 793.910Hydrophobic
DuArDuArTRP- 883.890Aromatic Face/Face
C14CBALA- 1053.950Hydrophobic
C28CGLEU- 1253.920Hydrophobic
C26CBALA- 1273.550Hydrophobic
O17OGSER- 1293.2140.91H-Bond
(Protein Donor)