scPDB - 1opb entry

Protein Data Bank Entry:

PDB ID : 1opb

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 1992-12-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Retinol-binding protein 2
ID:	RET2_RAT
AC:	P06768
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	16.553
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.480	523.125

% Hydrophobic	% Polar
62.58	37.42
According to VolSite

Ligand :

HET Code:	RET
Formula:	C20H28O
Molecular weight:	284.436 g/mol
DrugBank ID:	-
Buried Surface Area:	64.92 %
Polar Surface area:	17.07 Å2

Number of
H-Bond Acceptors:	1
H-Bond Donors:	0
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
-13.0538	56.8722	38.2495

Binding mode :

What is Poseview ?

2D View
3D View

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
C18	CZ	PHE- 16	4.07	0	Hydrophobic	false
C19	CE1	PHE- 16	4.3	0	Hydrophobic	false
C19	CE2	TYR- 19	4.02	0	Hydrophobic	false
C18	SD	MET- 20	4.18	0	Hydrophobic	false
C18	CD1	ILE- 25	3.91	0	Hydrophobic	false
C4	CB	ALA- 33	4.47	0	Hydrophobic	false
C16	CG	GLN- 38	4.36	0	Hydrophobic	false
C16	CB	SER- 55	4.45	0	Hydrophobic	false
C3	CD2	PHE- 57	4.43	0	Hydrophobic	false
C2	CB	ARG- 58	4.21	0	Hydrophobic	false
C3	CD	ARG- 58	3.93	0	Hydrophobic	false
C17	CB	TYR- 60	4.08	0	Hydrophobic	false
C4	CD2	LEU- 77	4.36	0	Hydrophobic	false
C17	CD2	LEU- 77	4.33	0	Hydrophobic	false
C18	CD2	LEU- 77	3.93	0	Hydrophobic	false
C15	CZ2	TRP- 106	3.86	0	Hydrophobic	false
C20	CE2	TRP- 106	3.68	0	Hydrophobic	false
O1	NE2	GLN- 108	3.05	131.01	H-Bond (Protein Donor)	false
O1	OE1	GLN- 108	2.65	159.73	H-Bond (Ligand Donor)	false
C20	CD2	LEU- 117	3.9	0	Hydrophobic	false
C19	CD1	LEU- 119	3.94	0	Hydrophobic	false
C20	CD2	LEU- 119	3.77	0	Hydrophobic	false