scPDB - 2ynh entry

Protein Data Bank Entry:

PDB ID : 2ynh

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2012-10-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Gag-Pol polyprotein
ID:	POL_HV1H2
AC:	P04585
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11706
EC Number:	2.7.7.49

Chains:

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

Ligand binding site composition:

B-Factor:	20.237
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.532	405.000

% Hydrophobic	% Polar
66.67	33.33
According to VolSite

Ligand :

HET Code:	EUR
Formula:	C19H12Cl3FN4O3
Molecular weight:	469.681 g/mol
DrugBank ID:	-
Buried Surface Area:	73.83 %
Polar Surface area:	111.03 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-8.1639	66.3874	17.0066

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
CL3	CB	PRO- 95	4.32	0	Hydrophobic	false
C14	CB	LEU- 100	4.01	0	Hydrophobic	false
CL3	CD1	LEU- 100	4.09	0	Hydrophobic	false
C21	CD1	LEU- 100	4	0	Hydrophobic	false
C13	CD1	LEU- 100	3.87	0	Hydrophobic	false
O01	O	LYS- 103	3.05	154.95	H-Bond (Ligand Donor)	false
N08	O	LYS- 103	2.93	177.56	H-Bond (Ligand Donor)	false
O10	N	LYS- 103	2.93	153.59	H-Bond (Protein Donor)	false
C15	CG	LYS- 103	4.11	0	Hydrophobic	false
C18	CG1	VAL- 106	3.78	0	Hydrophobic	false
C20	CG1	VAL- 106	4.49	0	Hydrophobic	false
F30	CG1	VAL- 106	4.23	0	Hydrophobic	false
C16	CG2	VAL- 106	3.85	0	Hydrophobic	false
C28	CG2	VAL- 108	4.01	0	Hydrophobic	false
CL2	CG1	VAL- 179	3.99	0	Hydrophobic	false
CL2	CD1	TYR- 181	3.53	0	Hydrophobic	false
CL2	CB	TYR- 188	3.83	0	Hydrophobic	false
CL3	CD2	TYR- 188	4.01	0	Hydrophobic	false
C20	CB	TYR- 188	3.44	0	Hydrophobic	false
DuAr	DuAr	TYR- 188	3.78	0	Aromatic Face/Face	false
CL1	CD2	PHE- 227	3.87	0	Hydrophobic	false
CL3	CH2	TRP- 229	3.73	0	Hydrophobic	false
C24	CB	TRP- 229	4.47	0	Hydrophobic	false
CL1	CB	LEU- 234	4.32	0	Hydrophobic	false
F30	CD1	LEU- 234	3.65	0	Hydrophobic	false
C24	CD1	LEU- 234	3.62	0	Hydrophobic	false
C02	CB	PRO- 236	4.02	0	Hydrophobic	false