scPDB - 4f5d entry

Protein Data Bank Entry:

PDB ID : 4f5d

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2012-05-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Stimulator of interferon genes protein
ID:	STING_HUMAN
AC:	Q86WV6
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	34.322
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.052	631.125

% Hydrophobic	% Polar
40.11	59.89
According to VolSite

Ligand :

HET Code:	C2E
Formula:	C20H22N10O14P2
Molecular weight:	688.395 g/mol
DrugBank ID:	-
Buried Surface Area:	73.88 %
Polar Surface area:	366.32 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	6
Rings:	7
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
35.9445	-19.9968	3.11037

Binding mode :

What is Poseview ?

2D View
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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
C4'	CD1	TYR- 163	4.39	0	Hydrophobic	false
C1'	CD1	TYR- 163	4.24	0	Hydrophobic	false
C4A	CD1	TYR- 163	4.41	0	Hydrophobic	false
C1A	CD1	TYR- 163	4.24	0	Hydrophobic	false
C1'	CB	TYR- 167	3.69	0	Hydrophobic	false
C1A	CB	TYR- 167	3.66	0	Hydrophobic	false
O2P	NH2	ARG- 238	3.13	145.67	H-Bond (Protein Donor)	false
O21	NH2	ARG- 238	3	148.17	H-Bond (Protein Donor)	false
O6	N	SER- 241	3.45	150.79	H-Bond (Protein Donor)	false
O61	N	SER- 241	3.41	150.5	H-Bond (Protein Donor)	false
N2	O	SER- 241	2.82	150.15	H-Bond (Ligand Donor)	false
N11	O	SER- 241	3.23	136.56	H-Bond (Ligand Donor)	false
N21	O	SER- 241	2.86	149.57	H-Bond (Ligand Donor)	false
C2'	CB	THR- 263	4.36	0	Hydrophobic	false
C2A	CB	THR- 263	4.38	0	Hydrophobic	false
O21	MG	MG- 401	2.67	0	Metal Acceptor	false