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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:

2xf3

1.550 Å

X-ray

2010-05-20

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:Q8KRB7_STRCL
AC:Q8KRB7
Organism:Streptomyces clavuligerus
Reign:Bacteria
TaxID:1901
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:11.978
Number of residues:22
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.002570.375

% Hydrophobic% Polar
52.0747.93
According to VolSite

Ligand :
2xf3_1 Structure
HET Code: J01
Formula: C8H8NO5
Molecular weight: 198.153 g/mol
DrugBank ID: DB00766
Buried Surface Area:49.04 %
Polar Surface area: 89.9 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 2
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
6.750335.6857574.9795


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
C4CE3TRP- 913.620Hydrophobic
C7CG2VAL- 934.30Hydrophobic
C7CD1ILE- 1033.990Hydrophobic
C4CD2LEU- 3624.480Hydrophobic
C4CD1LEU- 4153.980Hydrophobic
C7CD2LEU- 4154.460Hydrophobic
C4CDARG- 4184.020Hydrophobic
O5NZLYS- 4233.910Ionic
(Protein Cationic)