Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

2eg8

2.200 Å

X-ray

2007-02-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dihydroorotase
ID:PYRC_ECOLI
AC:P05020
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:3.5.2.3


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:45.247
Number of residues:24
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 3
Water Molecules: 0
Cofactors:
Metals: ZN ZN

Cavity properties

LigandabilityVolume (Å3)
0.005374.625

% Hydrophobic% Polar
43.2456.76
According to VolSite

Ligand :
2eg8_1 Structure
HET Code: FOT
Formula: C5H2FN2O4
Molecular weight: 173.079 g/mol
DrugBank ID: -
Buried Surface Area:72.76 %
Polar Surface area: 98.33 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 1
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
26.350440.927172.1402


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
O42CZARG- 203.780Ionic
(Protein Cationic)
O41CZARG- 203.780Ionic
(Protein Cationic)
O42NH1ARG- 202.98167.73H-Bond
(Protein Donor)
O41NH2ARG- 203.07154.12H-Bond
(Protein Donor)
O42ND2ASN- 442.79145.36H-Bond
(Protein Donor)
F5CE2TYR- 1043.970Hydrophobic
O2NLEU- 2222.84174.67H-Bond
(Protein Donor)
N1OLEU- 2222.89158.61H-Bond
(Ligand Donor)
O41NE2HIS- 2542.94138.06H-Bond
(Protein Donor)
N3OALA- 2662.97133.17H-Bond
(Ligand Donor)
O6ZN ZN- 4002.590Metal Acceptor