scPDB - 5cfl entry

Protein Data Bank Entry:

PDB ID : 5cfl

Resolution :1.840 Å

Experimental Method : X-ray

Deposition Date : 2015-07-08

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_NEMVE
AC:	A7SLZ2
Organism:	Nematostella vectensis
Reign:	Eukaryota
TaxID:	45351
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.000
Number of residues:	60
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.970	1042.875

% Hydrophobic	% Polar
37.22	62.78
According to VolSite

Ligand :

HET Code:	C2E
Formula:	C20H22N10O14P2
Molecular weight:	688.395 g/mol
DrugBank ID:	-
Buried Surface Area:	71.3 %
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
17.9203	31.0303	-6.78543

Binding mode :

What is Poseview ?

2D View
3D View

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'	CB	SER- 201	4.19	0	Hydrophobic	false
C5A	CB	SER- 201	4.22	0	Hydrophobic	false
C1'	CD1	TYR- 202	3.98	0	Hydrophobic	false
C1A	CD1	TYR- 202	4.03	0	Hydrophobic	false
C1'	CB	TYR- 206	4.46	0	Hydrophobic	false
C1A	CB	TYR- 206	4.31	0	Hydrophobic	false
O2P	NH1	ARG- 272	3.16	168.9	H-Bond (Protein Donor)	false
O11	NH1	ARG- 272	3.28	169.46	H-Bond (Protein Donor)	false
C2'	CZ	PHE- 276	4.22	0	Hydrophobic	false
C2A	CZ	PHE- 276	4.17	0	Hydrophobic	false
N7	NH1	ARG- 278	2.97	176.13	H-Bond (Protein Donor)	false
O6	NH2	ARG- 278	2.81	153.37	H-Bond (Protein Donor)	false
N71	NH2	ARG- 278	2.96	176.44	H-Bond (Protein Donor)	false
O61	NH1	ARG- 278	2.8	153.78	H-Bond (Protein Donor)	false
O2'	OG1	THR- 303	2.83	149.78	H-Bond (Protein Donor)	false
N31	OG1	THR- 303	2.89	159.9	H-Bond (Protein Donor)	false
N3	OG1	THR- 303	2.91	157.19	H-Bond (Ligand Donor)	false
O2A	OG1	THR- 303	2.94	152.64	H-Bond (Ligand Donor)	false
C2A	CB	THR- 303	4.14	0	Hydrophobic	false
C2'	CB	THR- 303	4.07	0	Hydrophobic	false
O2P	O	HOH- 507	2.58	155.26	H-Bond (Protein Donor)	false
N21	O	HOH- 518	2.87	129.35	H-Bond (Ligand Donor)	false
N2	O	HOH- 526	2.9	129.56	H-Bond (Ligand Donor)	false