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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:

1khr

2.800 Å

X-ray

2001-11-30

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Streptogramin A acetyltransferase
ID:VATD_ENTFC
AC:P50870
Organism:Enterococcus faecium
Reign:Bacteria
TaxID:1352
EC Number:2.3.1


Chains:

Chain Name:Percentage of Residues
within binding site
D41 %
E59 %


Ligand binding site composition:

B-Factor:22.571
Number of residues:30
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: COA
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.117654.750

% Hydrophobic% Polar
50.0050.00
According to VolSite

Ligand :
1khr_3 Structure
HET Code: VIR
Formula: C28H35N3O7
Molecular weight: 525.593 g/mol
DrugBank ID: DB01669
Buried Surface Area:47.2 %
Polar Surface area: 139.04 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 2
Rings: 3
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-7.49368-40.0861-27.633


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
C13CG2VAL- 174.030Hydrophobic
C16CG2VAL- 174.440Hydrophobic
O18OHTYR- 373.47171.18H-Bond
(Protein Donor)
C21CE2TYR- 524.330Hydrophobic
C3CE1TYR- 543.440Hydrophobic
C31CG2ILE- 564.340Hydrophobic
C35CD1ILE- 563.820Hydrophobic
C31CD2LEU- 5740Hydrophobic
O27ND2ASN- 923.15132.92H-Bond
(Protein Donor)
C16CD2LEU- 934.170Hydrophobic
C32CEMET- 1023.80Hydrophobic
C31CD1LEU- 1084.110Hydrophobic
C17S1PCOA- 3044.080Hydrophobic