scPDB - 3qn8 entry

Protein Data Bank Entry:

PDB ID : 3qn8

Resolution :1.380 Å

Experimental Method : X-ray

Deposition Date : 2011-02-08

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_HV1BR
AC:	P03367
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11686
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	51 %
B	49 %

Ligand binding site composition:

B-Factor:	14.847
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.889	840.375

% Hydrophobic	% Polar
44.18	55.82
According to VolSite

Ligand :

HET Code:	NI7
Formula:	C20H22N3O4
Molecular weight:	368.406 g/mol
DrugBank ID:	-
Buried Surface Area:	68.16 %
Polar Surface area:	97.69 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
16.9011	20.4004	5.57733

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
N27	OD1	ASP- 25	3.05	0	Ionic (Ligand Cationic)	false
N27	OD2	ASP- 25	2.75	0	Ionic (Ligand Cationic)	false
N27	OD1	ASP- 25	2.96	0	Ionic (Ligand Cationic)	false
N27	OD2	ASP- 25	3.08	0	Ionic (Ligand Cationic)	false
N27	OD2	ASP- 25	2.75	159.43	H-Bond (Ligand Donor)	false
N27	OD1	ASP- 25	2.96	149.8	H-Bond (Ligand Donor)	false
N27	OD2	ASP- 25	3.08	147.97	H-Bond (Ligand Donor)	false
C8	CB	ALA- 28	3.65	0	Hydrophobic	false
C21	CB	ALA- 28	3.61	0	Hydrophobic	false
C8	CB	ASP- 30	4.47	0	Hydrophobic	false
O9	N	ASP- 30	3.05	147	H-Bond (Protein Donor)	false
O22	N	ASP- 30	3.34	153.68	H-Bond (Protein Donor)	false
C10	CG2	VAL- 32	3.44	0	Hydrophobic	false
C23	CG2	VAL- 32	3.65	0	Hydrophobic	false
C10	CD1	ILE- 47	4.3	0	Hydrophobic	false
C23	CD1	ILE- 47	4.04	0	Hydrophobic	false
C21	CG2	ILE- 47	3.84	0	Hydrophobic	false
O16	N	ILE- 50	3.32	144.84	H-Bond (Protein Donor)	false
C25	CG2	ILE- 50	4.36	0	Hydrophobic	false
C11	CD1	ILE- 50	3.69	0	Hydrophobic	false
C11	CG2	ILE- 84	4.04	0	Hydrophobic	false
C24	CD1	ILE- 84	3.81	0	Hydrophobic	false
O14	O	HOH- 140	2.86	149.53	H-Bond (Protein Donor)	false