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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:

1fxv

2.250 Å

X-ray

2000-09-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Penicillin G acylase
ID:PAC_ECOLX
AC:P06875
Organism:Escherichia coli
Reign:Bacteria
TaxID:562
EC Number:3.5.1.11


Chains:

Chain Name:Percentage of Residues
within binding site
A23 %
B77 %


Ligand binding site composition:

B-Factor:13.326
Number of residues:30
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.023482.625

% Hydrophobic% Polar
49.6550.35
According to VolSite

Ligand :
1fxv_1 Structure
HET Code: PNN
Formula: C16H17N2O4S
Molecular weight: 333.382 g/mol
DrugBank ID: DB01053
Buried Surface Area:46.69 %
Polar Surface area: 114.84 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 3
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-0.00386957-0.132087-1.75704


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
O16NSER- 12.81141.12H-Bond
(Protein Donor)
C17CBSER- 13.30Hydrophobic
C22CBSER- 674.490Hydrophobic
S1CBALA- 693.870Hydrophobic
C19CBALA- 693.450Hydrophobic
S1CZPHE- 713.220Hydrophobic
C20SDMET- 1423.580Hydrophobic
C21CEMET- 1423.410Hydrophobic
C10CD1PHE- 1463.210Hydrophobic
C20CBPHE- 1463.740Hydrophobic
C21CD1ILE- 1774.410Hydrophobic