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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:

1fml

2.750 Å

X-ray

2000-08-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Retinol dehydratase
ID:Q26490_SPOFR
AC:Q26490
Organism:Spodoptera frugiperda
Reign:Eukaryota
TaxID:7108
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:29.846
Number of residues:27
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.4511248.750

% Hydrophobic% Polar
59.7340.27
According to VolSite

Ligand :
1fml_2 Structure
HET Code: RTL
Formula: C20H30O
Molecular weight: 286.452 g/mol
DrugBank ID: DB00162
Buried Surface Area:54.26 %
Polar Surface area: 20.23 Å2
Number of
H-Bond Acceptors: 1
H-Bond Donors: 1
Rings: 1
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 5

Mass center Coordinates

XYZ
44.3297.958625.82486


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
C16CZPHE- 314.060Hydrophobic
C15CZTYR- 1053.760Hydrophobic
C16CD1ILE- 1113.590Hydrophobic
C4CD1TYR- 1123.960Hydrophobic
C18CD1LEU- 1383.460Hydrophobic
C4CD2LEU- 1393.230Hydrophobic
C18CD2LEU- 1394.410Hydrophobic
O1NZLYS- 1622.91164.63H-Bond
(Protein Donor)
O1NE2HIS- 1643.08148.59H-Bond
(Protein Donor)
C17CBLEU- 2014.220Hydrophobic
C19CD2LEU- 2013.630Hydrophobic
C16CD2LEU- 2034.410Hydrophobic
C19CE2TYR- 2983.370Hydrophobic
C19CD1ILE- 3033.990Hydrophobic
C14CE1PHE- 3103.710Hydrophobic