scPDB - 1fmj entry

Protein Data Bank Entry:

PDB ID : 1fmj

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2000-08-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
A	100 %

Ligand binding site composition:

B-Factor:	22.529
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.730	867.375

% Hydrophobic	% Polar
66.93	33.07
According to VolSite

Ligand :

HET Code:	RTL
Formula:	C20H30O
Molecular weight:	286.452 g/mol
DrugBank ID:	DB00162
Buried Surface Area:	55.62 %
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

X	Y	Z
20.4626	-6.39229	41.622

Binding mode :

What is Poseview ?

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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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C16	CZ	PHE- 31	4.01	0	Hydrophobic	false
C15	CZ	TYR- 105	3.82	0	Hydrophobic	false
C16	CD1	ILE- 111	4.1	0	Hydrophobic	false
C4	CD1	TYR- 112	3.61	0	Hydrophobic	false
C18	CG	LEU- 138	4.42	0	Hydrophobic	false
C4	CD2	LEU- 139	3.44	0	Hydrophobic	false
C18	CD2	LEU- 139	4.17	0	Hydrophobic	false
C18	CB	SER- 142	4	0	Hydrophobic	false
O1	NZ	LYS- 162	2.9	152.59	H-Bond (Protein Donor)	false
O1	NE2	HIS- 164	2.88	160.66	H-Bond (Ligand Donor)	false
C16	CB	LEU- 201	4.21	0	Hydrophobic	false
C19	CD2	LEU- 201	4.19	0	Hydrophobic	false
C16	CD2	LEU- 203	4.02	0	Hydrophobic	false
C19	CD2	TYR- 298	4.47	0	Hydrophobic	false
C17	CB	ILE- 303	4.2	0	Hydrophobic	false
C19	CD1	ILE- 303	3.93	0	Hydrophobic	false
C14	CE1	PHE- 310	3.88	0	Hydrophobic	false