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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:

4zo3

1.670 Å

X-ray

2015-05-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Acylhomoserine lactonase
ID:I7HB71_9FLAO
AC:I7HB71
Organism:Chryseobacterium sp. StRB126
Reign:Bacteria
TaxID:878220
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:18.474
Number of residues:29
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors:
Metals: ZN ZN

Cavity properties

LigandabilityVolume (Å3)
0.105590.625

% Hydrophobic% Polar
47.4352.57
According to VolSite

Ligand :
4zo3_1 Structure
HET Code: C6L
Formula: C10H18NO4
Molecular weight: 216.254 g/mol
DrugBank ID: DB07532
Buried Surface Area:62.51 %
Polar Surface area: 89.46 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 0
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
7.95713-0.926267-55.2351


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
C1CD1ILE- 604.250Hydrophobic
C6CBHIS- 1474.460Hydrophobic
N1OD1ASP- 1493.18127.54H-Bond
(Ligand Donor)
C10CH2TRP- 1783.690Hydrophobic
C9CD1LEU- 1913.960Hydrophobic
C10CD2LEU- 1983.640Hydrophobic
C10CG2ILE- 2013.60Hydrophobic
O2NE2HIS- 2613.5137.49H-Bond
(Protein Donor)
O1NE2HIS- 2612.8133.89H-Bond
(Protein Donor)
C2CZPHE- 2743.50Hydrophobic
O2ZN ZN- 4012.520Metal Acceptor
O1ZN ZN- 4022.420Metal Acceptor