scPDB - 2az9 entry

Protein Data Bank Entry:

PDB ID : 2az9

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2005-09-09

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_HV1BR
AC:	P03367
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11686
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	29.476
Number of residues:	18
Including
Standard Amino Acids:	18
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.402	347.625

% Hydrophobic	% Polar
45.63	54.37
According to VolSite

Ligand :

HET Code:	3TL
Formula:	C50H64N6O10
Molecular weight:	909.077 g/mol
DrugBank ID:	-
Buried Surface Area:	34.53 %
Polar Surface area:	233.51 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	8
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	4
Rotatable Bonds:	25

Mass center Coordinates

X	Y	Z
14.6627	58.2338	36.063

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
O1	OD2	ASP- 25	3.3	152.6	H-Bond (Ligand Donor)	false
N1	O	GLY- 27	3.41	156.98	H-Bond (Ligand Donor)	false
CG1	CB	ALA- 28	4.17	0	Hydrophobic	false
N4	OD2	ASP- 29	3.3	145.89	H-Bond (Ligand Donor)	false
O4	N	ASP- 29	2.92	168.66	H-Bond (Protein Donor)	false
CG1	CG1	VAL- 32	4.28	0	Hydrophobic	false
CG2	CD1	ILE- 47	4.37	0	Hydrophobic	false
N2	O	GLY- 48	3.01	166.44	H-Bond (Ligand Donor)	false
C9	CD1	ILE- 50	3.65	0	Hydrophobic	false
CG1	CG1	ILE- 84	4.48	0	Hydrophobic	false