scPDB - 5jjs entry

Protein Data Bank Entry:

PDB ID : 5jjs

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2016-04-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Genome polyprotein
ID:	Q6DLV0_9FLAV
AC:	Q6DLV0
Organism:	Dengue virus 3
Reign:	Viruses
TaxID:	11069
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	23.382
Number of residues:	38
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.588	644.625

% Hydrophobic	% Polar
38.74	61.26
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	67.12 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
27.2572	128.749	18.315

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
O	OG	SER- 56	2.75	169.14	H-Bond (Protein Donor)	false
O	N	GLY- 86	3.08	143.64	H-Bond (Protein Donor)	false
N3	OG1	THR- 104	3.43	171.69	H-Bond (Protein Donor)	false
N3	N	LYS- 105	3.12	145.61	H-Bond (Protein Donor)	false
O2'	ND1	HIS- 110	3.15	163.23	H-Bond (Ligand Donor)	false
C3'	CG	GLU- 111	4.35	0	Hydrophobic	false
O2'	N	GLU- 111	3.43	137.06	H-Bond (Protein Donor)	false
N6	OD1	ASP- 131	2.63	160.44	H-Bond (Ligand Donor)	false
N1	N	VAL- 132	3.11	155.28	H-Bond (Protein Donor)	false
N	OD2	ASP- 146	3.39	161.99	H-Bond (Ligand Donor)	false
N	OD2	ASP- 146	3.39	0	Ionic (Ligand Cationic)	false
N	O	HOH- 1174	2.78	154.14	H-Bond (Ligand Donor)	false
O2'	O	HOH- 1220	2.72	163.82	H-Bond (Protein Donor)	false