scPDB - 3sa9 entry

Protein Data Bank Entry:

PDB ID : 3sa9

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2011-06-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protease
ID:	O38732_9HIV1
AC:	O38732
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:	15.409
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.817	762.750

% Hydrophobic	% Polar
43.81	56.19
According to VolSite

Ligand :

HET Code:	A68
Formula:	C29H43N3O6S
Molecular weight:	561.733 g/mol
DrugBank ID:	-
Buried Surface Area:	72.1 %
Polar Surface area:	133.41 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
19.438	29.9257	13.8267

Binding mode :

What is Poseview ?

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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
C14	CD2	LEU- 23	4	0	Hydrophobic	false
C37	CD1	LEU- 23	3.96	0	Hydrophobic	false
O18	OD1	ASP- 25	2.61	165.58	H-Bond (Ligand Donor)	false
O18	OD2	ASP- 25	3.02	124.46	H-Bond (Ligand Donor)	false
O18	OD1	ASP- 25	2.68	163.45	H-Bond (Protein Donor)	false
N20	O	GLY- 27	3.11	147.55	H-Bond (Ligand Donor)	false
C24	CB	ALA- 28	3.85	0	Hydrophobic	false
C26	CB	ALA- 28	4.21	0	Hydrophobic	false
C16	CB	ALA- 28	4.36	0	Hydrophobic	false
C6	CB	ALA- 28	3.56	0	Hydrophobic	false
O27	N	ASP- 29	2.91	161.19	H-Bond (Protein Donor)	false
C1	CB	ASP- 29	3.88	0	Hydrophobic	false
C26	CB	ASP- 30	3.87	0	Hydrophobic	false
C1	CB	ASP- 30	3.97	0	Hydrophobic	false
O1	N	ASP- 30	3.37	139.71	H-Bond (Protein Donor)	false
C24	CG2	VAL- 32	4.44	0	Hydrophobic	false
C26	CG2	VAL- 32	4.26	0	Hydrophobic	false
C7	CG2	VAL- 32	3.72	0	Hydrophobic	false
C25	CD1	ILE- 47	3.91	0	Hydrophobic	false
C3	CB	ILE- 47	4.18	0	Hydrophobic	false
C2	CD1	ILE- 47	4.24	0	Hydrophobic	false
C1	CG2	ILE- 47	4.06	0	Hydrophobic	false
N27	O	GLY- 48	2.96	156.18	H-Bond (Ligand Donor)	false
C15	CG1	ILE- 50	4.28	0	Hydrophobic	false
C24	CG1	ILE- 50	3.65	0	Hydrophobic	false
C33	CB	ILE- 50	4.26	0	Hydrophobic	false
C5	CD1	ILE- 50	4.22	0	Hydrophobic	false
C14	CG	PRO- 81	4.43	0	Hydrophobic	false
C15	CG	PRO- 81	4.12	0	Hydrophobic	false
C35	CG	PRO- 81	3.61	0	Hydrophobic	false
C14	CG2	VAL- 82	3.76	0	Hydrophobic	false
C35	CG2	VAL- 82	3.77	0	Hydrophobic	false
C24	CD1	ILE- 84	3.81	0	Hydrophobic	false
C6	CD1	ILE- 84	4.47	0	Hydrophobic	false
C33	CD1	ILE- 84	3.84	0	Hydrophobic	false
C15	CD1	ILE- 84	3.85	0	Hydrophobic	false