scPDB - 1x8l entry

Protein Data Bank Entry:

PDB ID : 1x8l

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-08-18

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
B	100 %

Ligand binding site composition:

B-Factor:	24.976
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.485	999.000

% Hydrophobic	% Polar
63.18	36.82
According to VolSite

Ligand :

HET Code:	OXR
Formula:	C20H28O2
Molecular weight:	300.435 g/mol
DrugBank ID:	DB02699
Buried Surface Area:	52.68 %
Polar Surface area:	37.29 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	1
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
44.296	7.68395	5.39445

Binding mode :

What is Poseview ?

2D View
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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
C20	CE1	TYR- 105	3.54	0	Hydrophobic	false
O1	OH	TYR- 105	3.46	146.42	H-Bond (Ligand Donor)	false
C16	CB	TYR- 112	4.08	0	Hydrophobic	false
C3	CB	TYR- 120	3.68	0	Hydrophobic	false
C2	CE1	TYR- 135	4.27	0	Hydrophobic	false
C17	CE1	TYR- 135	4.49	0	Hydrophobic	false
C17	CG	LEU- 138	3.69	0	Hydrophobic	false
C2	CD2	LEU- 139	3.28	0	Hydrophobic	false
C1	CD2	LEU- 139	3.95	0	Hydrophobic	false
C16	CB	SER- 142	3.98	0	Hydrophobic	false
O1	NZ	LYS- 162	2.57	150.34	H-Bond (Protein Donor)	false
O1	NE2	HIS- 164	2.98	165.2	H-Bond (Protein Donor)	false
C18	CB	LEU- 201	4.04	0	Hydrophobic	false
C18	CD2	LEU- 203	4.39	0	Hydrophobic	false
C19	CE2	TYR- 298	4.14	0	Hydrophobic	false
C17	CD1	ILE- 303	4.43	0	Hydrophobic	false
C20	CE1	PHE- 310	4.34	0	Hydrophobic	false
C15	CE1	PHE- 310	4.04	0	Hydrophobic	false