scPDB - 2a4f entry

Protein Data Bank Entry:

PDB ID : 2a4f

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2005-06-28

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	52 %
B	48 %

Ligand binding site composition:

B-Factor:	14.708
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.820	837.000

% Hydrophobic	% Polar
42.34	57.66
According to VolSite

Ligand :

HET Code:	AAU
Formula:	C36H39N3O8
Molecular weight:	641.710 g/mol
DrugBank ID:	-
Buried Surface Area:	64.96 %
Polar Surface area:	143.24 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
11.7741	22.864	5.27134

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
C15	CD2	LEU- 23	4.35	0	Hydrophobic	false
C35	CD2	LEU- 23	3.96	0	Hydrophobic	false
O17	OD1	ASP- 25	2.85	143.69	H-Bond (Protein Donor)	false
O17	OD2	ASP- 25	2.53	157.77	H-Bond (Ligand Donor)	false
C46	CB	ALA- 28	3.49	0	Hydrophobic	false
C45	CB	ALA- 28	3.48	0	Hydrophobic	false
C25	CB	ALA- 28	3.41	0	Hydrophobic	false
C1	CB	ASP- 29	4.17	0	Hydrophobic	false
C29	CB	ASP- 29	3.96	0	Hydrophobic	false
O2	N	ASP- 29	3.14	163.59	H-Bond (Protein Donor)	false
O28	N	ASP- 29	3.09	165.59	H-Bond (Protein Donor)	false
O26	N	ASP- 30	2.81	153.99	H-Bond (Protein Donor)	false
O47	N	ASP- 30	2.77	155.45	H-Bond (Protein Donor)	false
O26	O	ASP- 30	2.91	144.67	H-Bond (Ligand Donor)	false
O47	O	ASP- 30	3.08	140.35	H-Bond (Ligand Donor)	false
C24	CG1	VAL- 32	4.42	0	Hydrophobic	false
C45	CG2	VAL- 32	4.09	0	Hydrophobic	false
C23	CB	ILE- 50	4.4	0	Hydrophobic	false
C44	CG1	ILE- 50	3.67	0	Hydrophobic	false
C11	CB	ILE- 50	4.27	0	Hydrophobic	false
O32	N	ILE- 50	3.43	133.34	H-Bond (Protein Donor)	false
O32	N	ILE- 50	2.96	174.49	H-Bond (Protein Donor)	false
C12	CG	PRO- 81	3.63	0	Hydrophobic	false
C38	CB	PRO- 81	3.77	0	Hydrophobic	false
C36	CG2	VAL- 82	3.47	0	Hydrophobic	false
C43	CG1	VAL- 82	3.73	0	Hydrophobic	false
C13	CG1	VAL- 82	3.48	0	Hydrophobic	false
C11	CD1	ILE- 84	3.98	0	Hydrophobic	false
C23	CD1	ILE- 84	4.02	0	Hydrophobic	false
C35	CD1	ILE- 84	4.16	0	Hydrophobic	false
C44	CD1	ILE- 84	3.99	0	Hydrophobic	false