Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

2pu2

1.860 Å

X-ray

2007-05-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Beta-lactamase
ID:AMPC_ECOLI
AC:P00811
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:3.5.2.6


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:22.419
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.386570.375

% Hydrophobic% Polar
28.9971.01
According to VolSite

Ligand :
2pu2_1 Structure
HET Code: DK2
Formula: C18H11NO7
Molecular weight: 353.282 g/mol
DrugBank ID: DB07663
Buried Surface Area:49.35 %
Polar Surface area: 137.87 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
23.50696.6176514.585


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
C16CD1LEU- 1194.470Hydrophobic
C19CD2LEU- 1193.80Hydrophobic
O14OHTYR- 1502.98130.77H-Bond
(Protein Donor)
C16CE1TYR- 1504.110Hydrophobic
C6CGTYR- 2213.460Hydrophobic
C16CD2LEU- 2934.370Hydrophobic
C22CD1LEU- 2933.770Hydrophobic
O15NALA- 3182.73155.74H-Bond
(Protein Donor)
C2CBTHR- 3194.360Hydrophobic
O25NGLY- 3202.77144.88H-Bond
(Protein Donor)