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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:

3stv

2.200 Å

X-ray

2011-07-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Methylketone synthase I
ID:E0YCS2_SOLHA
AC:E0YCS2
Organism:Lycopersicon hirsutum f. glabratum
Reign:Eukaryota
TaxID:283673
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:20.280
Number of residues:23
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.6711076.625

% Hydrophobic% Polar
59.2540.75
According to VolSite

Ligand :
3stv_1 Structure
HET Code: 3HO
Formula: C8H15O3
Molecular weight: 159.203 g/mol
DrugBank ID: -
Buried Surface Area:54.78 %
Polar Surface area: 60.36 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 0
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
19.2665-5.418550.870364


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
O2OG1THR- 182.63167.18H-Bond
(Protein Donor)
C2CBALA- 874.240Hydrophobic
C3CBLEU- 8840Hydrophobic
C5CD1LEU- 883.920Hydrophobic
C5CBALA- 1284.290Hydrophobic
C2CG2VAL- 1324.430Hydrophobic
C4CG2VAL- 1323.730Hydrophobic
C6CG2VAL- 1324.490Hydrophobic
C7CD2LEU- 1834.250Hydrophobic
C8CD2LEU- 1854.020Hydrophobic
O2NE2HIS- 2432.78161.15H-Bond
(Protein Donor)