scPDB - 2pk6 entry

Protein Data Bank Entry:

PDB ID : 2pk6

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2007-04-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	V-1 protease
ID:	Q9Q2G8_9HIV1
AC:	Q9Q2G8
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	48 %
B	52 %

Ligand binding site composition:

B-Factor:	16.927
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.999	843.750

% Hydrophobic	% Polar
44.00	56.00
According to VolSite

Ligand :

HET Code:	O33
Formula:	C40H45N5O7S2
Molecular weight:	771.945 g/mol
DrugBank ID:	-
Buried Surface Area:	67.14 %
Polar Surface area:	220.79 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	5
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
13.7108	-21.2795	-16.2138

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
C9	CD2	LEU- 23	3.93	0	Hydrophobic	false
O2	OD1	ASP- 25	2.75	152.35	H-Bond (Protein Donor)	false
O1	OD1	ASP- 25	3.09	122.12	H-Bond (Protein Donor)	false
O1	OD2	ASP- 25	2.98	126.41	H-Bond (Ligand Donor)	false
O1	OD1	ASP- 25	2.62	157.13	H-Bond (Ligand Donor)	false
N2	O	GLY- 27	3.12	158.58	H-Bond (Ligand Donor)	false
N4	O	GLY- 27	3.4	146.04	H-Bond (Ligand Donor)	false
C5	CB	ALA- 28	4.46	0	Hydrophobic	false
C22	CB	ALA- 28	4.13	0	Hydrophobic	false
C38	CB	ALA- 28	3.68	0	Hydrophobic	false
O5	N	ASP- 29	2.88	157.19	H-Bond (Protein Donor)	false
O7	N	ASP- 29	3.02	172.18	H-Bond (Protein Donor)	false
C35	CB	ASP- 29	4.4	0	Hydrophobic	false
C22	CB	ASP- 30	4.03	0	Hydrophobic	false
C40	CB	ASP- 30	3.48	0	Hydrophobic	false
C22	CG2	VAL- 32	3.66	0	Hydrophobic	false
C39	CG1	VAL- 32	3.66	0	Hydrophobic	false
C20	CB	ILE- 47	4.26	0	Hydrophobic	false
S2	CD1	ILE- 47	3.8	0	Hydrophobic	false
C35	CB	ILE- 47	4.07	0	Hydrophobic	false
C39	CD1	ILE- 47	3.74	0	Hydrophobic	false
N1	O	GLY- 48	2.78	146	H-Bond (Ligand Donor)	false
S2	CD1	ILE- 50	3.56	0	Hydrophobic	false
C13	CD1	ILE- 50	4.38	0	Hydrophobic	false
S1	CG1	ILE- 50	4.21	0	Hydrophobic	false
C38	CD1	ILE- 50	3.9	0	Hydrophobic	false
C40	CD1	LEU- 76	4.4	0	Hydrophobic	false
C31	CG	PRO- 81	4.38	0	Hydrophobic	false
C27	CB	PRO- 81	4.12	0	Hydrophobic	false
C18	CG	PRO- 81	4.45	0	Hydrophobic	false
S1	CG	PRO- 81	4.29	0	Hydrophobic	false
C12	CG	PRO- 81	3.72	0	Hydrophobic	false
C9	CB	VAL- 82	4.47	0	Hydrophobic	false
C10	CG2	VAL- 82	3.51	0	Hydrophobic	false
C25	CG2	VAL- 82	3.75	0	Hydrophobic	false
C38	CG2	ILE- 84	4.03	0	Hydrophobic	false
C8	CD1	ILE- 84	3.87	0	Hydrophobic	false
S1	CD1	ILE- 84	3.37	0	Hydrophobic	false