scPDB - 4r09 entry

Protein Data Bank Entry:

PDB ID : 4r09

Resolution :2.620 Å

Experimental Method : X-ray

Deposition Date : 2014-07-30

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	57 %
B	43 %

Ligand binding site composition:

B-Factor:	40.998
Number of residues:	23
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.066	391.500

% Hydrophobic	% Polar
60.34	39.66
According to VolSite

Ligand :

HET Code:	URI
Formula:	C9H12N2O6
Molecular weight:	244.201 g/mol
DrugBank ID:	DB02745
Buried Surface Area:	70.14 %
Polar Surface area:	119.33 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
22.1455	-21.4119	38.0464

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
C5'	CZ	TYR- 348	3.5	0	Hydrophobic	false
C4'	CE2	TYR- 348	3.75	0	Hydrophobic	false
O3'	N	GLY- 351	3.19	168.63	H-Bond (Protein Donor)	false
C1'	CG1	VAL- 378	3.89	0	Hydrophobic	false
C4'	CG2	VAL- 378	4.33	0	Hydrophobic	false
C1'	CE2	PHE- 405	4.43	0	Hydrophobic	false
O4	NE	ARG- 429	2.82	150.03	H-Bond (Protein Donor)	false
O4	NH2	ARG- 429	2.96	139.85	H-Bond (Protein Donor)	false
N3	OD2	ASP- 543	2.82	163.33	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 545	3.21	149.34	H-Bond (Ligand Donor)	false
C3'	CG2	THR- 574	4.05	0	Hydrophobic	false
C5'	CG2	THR- 574	4.08	0	Hydrophobic	false
O5'	N	THR- 574	3.19	155.27	H-Bond (Protein Donor)	false