scPDB - 4n6h entry

Protein Data Bank Entry:

PDB ID : 4n6h

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2013-10-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Delta-type opioid receptor
ID:	OPRD_HUMAN
AC:	P41143
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:	27.993
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.079	759.375

% Hydrophobic	% Polar
51.56	48.44
According to VolSite

Ligand :

HET Code:	EJ4
Formula:	C26H27N2O3
Molecular weight:	415.504 g/mol
DrugBank ID:	-
Buried Surface Area:	58.13 %
Polar Surface area:	69.92 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	4
Rings:	8
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-5.91094	-69.3666	70.8058

Binding mode :

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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
NAS	OD2	ASP- 128	2.87	136.63	H-Bond (Ligand Donor)	false
NAS	OD2	ASP- 128	2.87	0	Ionic (Ligand Cationic)	false
NAS	OD1	ASP- 128	3.97	0	Ionic (Ligand Cationic)	false
CAE	CZ	TYR- 129	4.05	0	Hydrophobic	false
CAU	CE1	TYR- 129	3.94	0	Hydrophobic	false
CAU	CE	MET- 132	3.96	0	Hydrophobic	false
CBD	CZ3	TRP- 274	4.12	0	Hydrophobic	false
CBE	CH2	TRP- 274	3.61	0	Hydrophobic	false
CAO	CG1	ILE- 277	4.44	0	Hydrophobic	false
CBD	CG2	ILE- 277	4.19	0	Hydrophobic	false
CAO	CG2	VAL- 281	3.77	0	Hydrophobic	false
CAH	CG2	VAL- 281	3.64	0	Hydrophobic	false
CAI	CD1	LEU- 300	4.36	0	Hydrophobic	false
CAJ	CD2	LEU- 300	4.01	0	Hydrophobic	false
CBD	CG2	ILE- 304	4.33	0	Hydrophobic	false
CBC	CZ	TYR- 308	3.64	0	Hydrophobic	false
CBE	CE1	TYR- 308	3.8	0	Hydrophobic	false