scPDB - 2i4v entry

Protein Data Bank Entry:

PDB ID : 2i4v

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2006-08-22

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	51 %
B	49 %

Ligand binding site composition:

B-Factor:	14.975
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.849	725.625

% Hydrophobic	% Polar
41.40	58.60
According to VolSite

Ligand :

HET Code:	DJR
Formula:	C28H38N2O8S
Molecular weight:	562.675 g/mol
DrugBank ID:	-
Buried Surface Area:	68.47 %
Polar Surface area:	132.01 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
15.2677	22.8859	16.7142

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
C10	CD2	LEU- 23	4.41	0	Hydrophobic	false
O6	OD2	ASP- 25	2.75	145.65	H-Bond (Protein Donor)	false
C15	CB	ALA- 28	4.4	0	Hydrophobic	false
C19	CB	ALA- 28	3.55	0	Hydrophobic	false
C26	CB	ASP- 29	3.97	0	Hydrophobic	false
O1	N	ASP- 30	3.37	149.54	H-Bond (Protein Donor)	false
C26	CB	ASP- 30	4.32	0	Hydrophobic	false
C20	CG2	VAL- 32	3.47	0	Hydrophobic	false
C22	CB	ILE- 47	4.01	0	Hydrophobic	false
C21	CD1	ILE- 47	4.21	0	Hydrophobic	false
C26	CG2	ILE- 47	3.61	0	Hydrophobic	false
C24	CG1	ILE- 50	4.34	0	Hydrophobic	false
C5	CD1	ILE- 50	3.83	0	Hydrophobic	false
C26	CD1	LEU- 76	4.16	0	Hydrophobic	false
C13	CG	PRO- 81	3.43	0	Hydrophobic	false
C14	CG1	VAL- 82	3.27	0	Hydrophobic	false
C8	CG1	VAL- 84	4.19	0	Hydrophobic	false
C19	CG2	VAL- 84	4.46	0	Hydrophobic	false
C25	CD2	LEU- 223	3.9	0	Hydrophobic	false
O6	OD1	ASP- 225	2.54	125.89	H-Bond (Ligand Donor)	false
O6	OD2	ASP- 225	2.92	153.16	H-Bond (Ligand Donor)	false
N1	O	GLY- 227	3.18	158.49	H-Bond (Ligand Donor)	false
C3	CB	ALA- 228	3.76	0	Hydrophobic	false
C27	CB	ASP- 229	3.99	0	Hydrophobic	false
O9	N	ASP- 229	2.96	166.57	H-Bond (Protein Donor)	false
O	N	ASP- 230	3.06	165.26	H-Bond (Protein Donor)	false
C3	CG2	VAL- 232	3.98	0	Hydrophobic	false
C11	CB	ILE- 250	4.25	0	Hydrophobic	false
C18	CD1	ILE- 250	4.05	0	Hydrophobic	false
C25	CG	PRO- 281	4.25	0	Hydrophobic	false
C25	CG1	VAL- 282	4.11	0	Hydrophobic	false
C25	CG2	VAL- 284	4.06	0	Hydrophobic	false