scPDB - 5h8t entry

Protein Data Bank Entry:

PDB ID : 5h8t

Resolution :1.210 Å

Experimental Method : X-ray

Deposition Date : 2015-12-23

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 1
ID:	RET1_HUMAN
AC:	P09455
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	8.197
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.474	445.500

% Hydrophobic	% Polar
66.67	33.33
According to VolSite

Ligand :

HET Code:	RTL
Formula:	C20H30O
Molecular weight:	286.452 g/mol
DrugBank ID:	DB00162
Buried Surface Area:	68.25 %
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
15.3041	-2.93943	-13.0798

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
C19	CE1	PHE- 16	4.16	0	Hydrophobic	false
C19	CE2	TYR- 19	4.23	0	Hydrophobic	false
C18	CD2	LEU- 20	3.71	0	Hydrophobic	false
C4	CD1	LEU- 29	3.94	0	Hydrophobic	false
C4	CB	ALA- 33	4.14	0	Hydrophobic	false
C18	CB	ALA- 33	4.11	0	Hydrophobic	false
C2	CD1	LEU- 36	3.91	0	Hydrophobic	false
C17	CD1	LEU- 36	4.4	0	Hydrophobic	false
O1	NZ	LYS- 40	2.95	170.4	H-Bond (Protein Donor)	false
C15	CG2	ILE- 51	4.02	0	Hydrophobic	false
C3	CD2	PHE- 57	3.89	0	Hydrophobic	false
C3	CD	ARG- 58	4.38	0	Hydrophobic	false
C16	CB	TYR- 60	3.88	0	Hydrophobic	false
C15	SD	MET- 62	4.18	0	Hydrophobic	false
C16	CG1	ILE- 77	4.33	0	Hydrophobic	false
C18	CG2	ILE- 77	4.09	0	Hydrophobic	false
C19	CD1	ILE- 77	4.14	0	Hydrophobic	false
C15	CZ2	TRP- 106	3.65	0	Hydrophobic	false
C20	CE2	TRP- 106	4.01	0	Hydrophobic	false
O1	OE1	GLN- 108	2.81	170.81	H-Bond (Ligand Donor)	false
C15	CD1	LEU- 117	4.24	0	Hydrophobic	false
C20	CD2	LEU- 117	4.02	0	Hydrophobic	false
C19	SD	MET- 119	4.03	0	Hydrophobic	false
C20	SD	MET- 119	3.67	0	Hydrophobic	false