scPDB - 2jlr entry

Protein Data Bank Entry:

PDB ID : 2jlr

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-09-15

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:	POLG_DEN4T
AC:	Q2YHF0
Organism:	Dengue virus type 4
Reign:	Viruses
TaxID:	408688
EC Number:	3.4.21.91

Chains:

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

Ligand binding site composition:

B-Factor:	31.023
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.102	583.875

% Hydrophobic	% Polar
36.99	63.01
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	54.83 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
12.6936	15.4787	26.9765

Binding mode :

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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
O2B	N	GLY- 198	3.14	160.17	H-Bond (Protein Donor)	false
O3A	N	GLY- 198	3.25	123.82	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 199	2.59	161.55	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 199	2.79	140.57	H-Bond (Protein Donor)	false
O2B	N	LYS- 199	3.11	154.42	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 199	2.59	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 199	2.79	0	Ionic (Protein Cationic)	false
O1B	N	THR- 200	3.15	158.56	H-Bond (Protein Donor)	false
O2A	N	LYS- 201	2.79	142.21	H-Bond (Protein Donor)	false
N7	NZ	LYS- 201	3.26	146.42	H-Bond (Protein Donor)	false
O3'	ND2	ASN- 329	3.39	120.66	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 460	2.92	151.77	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 460	3.71	0	Ionic (Protein Cationic)	false
O2G	NH2	ARG- 463	2.81	160.01	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 463	3.72	0	Ionic (Protein Cationic)	false
O3'	O	ARG- 463	2.72	135.31	H-Bond (Ligand Donor)	false
C3'	CB	ARG- 463	4.41	0	Hydrophobic	false
O3G	MN	MN- 1619	2.03	0	Metal Acceptor	false
O1B	MN	MN- 1619	2.17	0	Metal Acceptor	false