Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3lm4

1.800 Å

X-ray

2010-01-29

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Catechol 2,3-dioxygenase
ID:Q0S9X1_RHOJR
AC:Q0S9X1
Organism:Rhodococcus jostii
Reign:Bacteria
TaxID:101510
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:14.034
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: FE

Cavity properties

LigandabilityVolume (Å3)
1.461388.125

% Hydrophobic% Polar
79.1320.87
According to VolSite

Ligand :
3lm4_3 Structure
HET Code: HPX
Formula: C12H9O4
Molecular weight: 217.197 g/mol
DrugBank ID: DB07914
Buried Surface Area:66.26 %
Polar Surface area: 77.43 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 1
Rings: 1
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
12.090250.782750.6082


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
CB6CD1ILE- 1893.730Hydrophobic
CA3CZ2TRP- 1923.990Hydrophobic
OA1NE1TRP- 1923.08137.09H-Bond
(Protein Donor)
CB3CBMET- 2053.940Hydrophobic
CA3SDMET- 2053.850Hydrophobic
CB2SDMET- 2053.570Hydrophobic
CB4CGMET- 2083.860Hydrophobic
CB5SDMET- 2084.290Hydrophobic
CA3CZTYR- 3083.980Hydrophobic
CB3CBPHE- 3094.280Hydrophobic