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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:

4ejv

2.900 Å

X-ray

2012-04-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Transcriptional regulator TcaR
ID:Q5HLN6_STAEQ
AC:Q5HLN6
Organism:Staphylococcus epidermidis
Reign:Bacteria
TaxID:176279
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A70 %
B30 %


Ligand binding site composition:

B-Factor:51.944
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.6731836.000

% Hydrophobic% Polar
42.2857.72
According to VolSite

Ligand :
4ejv_1 Structure
HET Code: LCL
Formula: C11H11Cl2N2O5
Molecular weight: 322.121 g/mol
DrugBank ID: -
Buried Surface Area:53.17 %
Polar Surface area: 123.99 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 1
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-14.9396-39.3618-2.943


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
CL1CG2ILE- 164.460Hydrophobic
C4CBASN- 204.330Hydrophobic
O9BOALA- 382.62164.06H-Bond
(Ligand Donor)
C11CBALA- 383.820Hydrophobic
C9CBGLU- 394.070Hydrophobic
C9CBHIS- 423.710Hydrophobic
C5CGGLN- 614.470Hydrophobic
C5CG1VAL- 634.10Hydrophobic