scPDB - 3w3l entry

Protein Data Bank Entry:

PDB ID : 3w3l

Resolution :2.330 Å

Experimental Method : X-ray

Deposition Date : 2012-12-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Toll-like receptor 8
ID:	TLR8_HUMAN
AC:	Q9NR97
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	67 %
D	33 %

Ligand binding site composition:

B-Factor:	17.702
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.460	310.500

% Hydrophobic	% Polar
52.17	47.83
According to VolSite

Ligand :

HET Code:	RX8
Formula:	C17H22N4O2
Molecular weight:	314.382 g/mol
DrugBank ID:	DB06530
Buried Surface Area:	73.28 %
Polar Surface area:	86.19 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
20.404	20.1799	45.9055

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
C8	CE1	PHE- 346	3.68	0	Hydrophobic	false
C11	CD2	TYR- 348	3.6	0	Hydrophobic	false
C6	CZ	TYR- 348	3.84	0	Hydrophobic	false
C7	CE1	TYR- 348	4.12	0	Hydrophobic	false
C8	CD1	TYR- 348	3.75	0	Hydrophobic	false
C9	CG2	VAL- 378	3.51	0	Hydrophobic	false
C13	CG1	VAL- 378	4.44	0	Hydrophobic	false
C8	CG2	VAL- 378	3.7	0	Hydrophobic	false
C11	CG1	VAL- 378	3.96	0	Hydrophobic	false
C8	CG2	ILE- 403	4.37	0	Hydrophobic	false
C9	CE2	PHE- 405	4.3	0	Hydrophobic	false
C7	CE2	PHE- 405	4.11	0	Hydrophobic	false
C14	CB	PHE- 405	4.12	0	Hydrophobic	false
DuAr	DuAr	PHE- 405	3.6	0	Aromatic Face/Face	false
DuAr	DuAr	PHE- 405	3.78	0	Aromatic Face/Face	false
C16	CG2	VAL- 520	4.05	0	Hydrophobic	false
N	OD2	ASP- 543	3.29	121.93	H-Bond (Ligand Donor)	false
N	OD1	ASP- 543	2.74	174.31	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 543	2.51	160.06	H-Bond (Ligand Donor)	false
C7	CG1	VAL- 573	4.09	0	Hydrophobic	false
C6	CG2	THR- 574	4.1	0	Hydrophobic	false
N2	N	THR- 574	3.01	159.92	H-Bond (Protein Donor)	false
N	O	THR- 574	3.04	124.82	H-Bond (Ligand Donor)	false
O1	O	HOH- 1011	2.93	151.79	H-Bond (Ligand Donor)	false