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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:

4ddy

1.360 Å

X-ray

2012-01-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Beta-lactamase
ID:Q9L5C8_ECOLX
AC:Q9L5C8
Organism:Escherichia coli
Reign:Bacteria
TaxID:562
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:10.502
Number of residues:32
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 1
Water Molecules: 4
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.255347.625

% Hydrophobic% Polar
32.0467.96
According to VolSite

Ligand :
4ddy_1 Structure
HET Code: DN6
Formula: C15H9F3N5O
Molecular weight: 332.260 g/mol
DrugBank ID: -
Buried Surface Area:59.78 %
Polar Surface area: 81.87 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-7.8100455.96112.1218


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
O21ND2ASN- 1042.92163.04H-Bond
(Protein Donor)
C14CBTYR- 1053.760Hydrophobic
C13CBSER- 1303.950Hydrophobic
O21ND2ASN- 1323.16136.17H-Bond
(Protein Donor)
F23CBPRO- 1673.580Hydrophobic
C5CBPRO- 1674.150Hydrophobic
F24CBASN- 1703.920Hydrophobic
C5CBASN- 1703.640Hydrophobic
F24CG2THR- 1713.350Hydrophobic
N18OG1THR- 2352.71175.83H-Bond
(Protein Donor)
N20OGSER- 2372.8171.08H-Bond
(Protein Donor)
C1CBASP- 2404.440Hydrophobic