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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:

1jum

2.980 Å

X-ray

2001-08-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:HTH-type transcriptional regulator QacR
ID:QACR_STAAU
AC:P0A0N4
Organism:Staphylococcus aureus
Reign:Bacteria
TaxID:1280
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:49.317
Number of residues:21
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.147955.125

% Hydrophobic% Polar
48.4151.59
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median1jumHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
1jum_1 Structure
HET Code: BER
Formula: C20H18NO4
Molecular weight: 336.361 g/mol
DrugBank ID: DB04115
Buried Surface Area:46.74 %
Polar Surface area: 40.79 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 0
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
109.82845.679493.0512
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median1jumRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


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
C10CBGLU- 583.590Hydrophobic
C19CBLYS- 604.370Hydrophobic
C12CBTRP- 614.010Hydrophobic
C20CBTHR- 894.040Hydrophobic
C16CBTHR- 893.620Hydrophobic
C19CE2TYR- 933.710Hydrophobic
C20CD2TYR- 934.490Hydrophobic
DuArDuArTYR- 933.970Aromatic Edge/Face
C17CE2TYR- 1233.440Hydrophobic
C9CBTYR- 12340Hydrophobic