scPDB - 1s6q entry

Protein Data Bank Entry:

PDB ID : 1s6q

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2004-01-26

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_HV1B1
AC:	P03366
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11678
EC Number:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	90 %
B	10 %

Ligand binding site composition:

B-Factor:	87.240
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.719	475.875

% Hydrophobic	% Polar
70.21	29.79
According to VolSite

Ligand :

HET Code:	TPB
Formula:	C20H19N5
Molecular weight:	329.398 g/mol
DrugBank ID:	DB08639
Buried Surface Area:	74.46 %
Polar Surface area:	73.63 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
145.709	-24.5596	73.8757

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
C21	CG	PRO- 95	3.73	0	Hydrophobic	false
C3	CD1	LEU- 100	4.38	0	Hydrophobic	false
C7	CD2	LEU- 100	3.97	0	Hydrophobic	false
C21	CD2	LEU- 100	3.36	0	Hydrophobic	false
C16	CD1	LEU- 100	3.84	0	Hydrophobic	false
N5	O	LYS- 101	2.67	157.11	H-Bond (Ligand Donor)	false
N3	N	LYS- 101	3.46	130.37	H-Bond (Protein Donor)	false
C12	CG	LYS- 103	4.07	0	Hydrophobic	false
C14	CG2	VAL- 106	3.66	0	Hydrophobic	false
C21	CB	GLU- 138	4.33	0	Hydrophobic	false
C61	CG2	VAL- 179	3.53	0	Hydrophobic	false
C7	CB	VAL- 179	3.95	0	Hydrophobic	false
C21	CD1	TYR- 181	3.78	0	Hydrophobic	false
C61	CB	TYR- 181	3.91	0	Hydrophobic	false
C41	CD2	TYR- 181	4.12	0	Hydrophobic	false
C1	CB	TYR- 181	3.38	0	Hydrophobic	false
C41	CD2	TYR- 188	3.33	0	Hydrophobic	false
C5	CB	TYR- 188	3.32	0	Hydrophobic	false
C41	CD2	TRP- 229	4.28	0	Hydrophobic	false
C14	CB	LEU- 234	4.43	0	Hydrophobic	false
C15	CD1	LEU- 234	4.41	0	Hydrophobic	false
C41	CD1	LEU- 234	3.97	0	Hydrophobic	false