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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:

1u3q

2.400 Å

X-ray

2004-07-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Estrogen receptor beta
ID:ESR2_HUMAN
AC:Q92731
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:38.234
Number of residues:30
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.784273.375

% Hydrophobic% Polar
85.1914.81
According to VolSite

Ligand :
1u3q_1 Structure
HET Code: 272
Formula: C13H9NO4
Molecular weight: 243.215 g/mol
DrugBank ID: DB06937
Buried Surface Area:78.25 %
Polar Surface area: 86.72 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 3
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
17.0815-3.7723914.3501


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
O24OHOH- 823.45142.59H-Bond
(Protein Donor)
C16SDMET- 2954.490Hydrophobic
C18CBLEU- 2983.720Hydrophobic
C6CD2LEU- 3013.970Hydrophobic
C6CBALA- 3024.010Hydrophobic
O24OE1GLU- 3053.21122.07H-Bond
(Ligand Donor)
C13CEMET- 3364.20Hydrophobic
C6CD1LEU- 3394.080Hydrophobic
C2CBLEU- 3393.960Hydrophobic
C2CD2LEU- 3434.060Hydrophobic
C15CD1ILE- 3733.770Hydrophobic
C15CD1ILE- 3764.240Hydrophobic
O22ND1HIS- 4753.22153.69H-Bond
(Ligand Donor)
C17CD1LEU- 4764.020Hydrophobic