scPDB - 2a1e entry

Protein Data Bank Entry:

PDB ID : 2a1e

Resolution :1.300 Å

Experimental Method : X-ray

Deposition Date : 2005-06-20

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	48 %
B	52 %

Ligand binding site composition:

B-Factor:	15.674
Number of residues:	49
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.889	837.000

% Hydrophobic	% Polar
41.53	58.47
According to VolSite

Ligand :

HET Code:	IPF
Formula:	C50H64N8O8
Molecular weight:	905.092 g/mol
DrugBank ID:	-
Buried Surface Area:	62.46 %
Polar Surface area:	237.84 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	9
Rings:	6
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
16.3998	21.9798	16.8173

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
C20	CD2	LEU- 23	4.45	0	Hydrophobic	false
C22	CD2	LEU- 23	3.96	0	Hydrophobic	false
C30	CD2	LEU- 23	3.63	0	Hydrophobic	false
O27	OD1	ASP- 25	2.63	145.38	H-Bond (Ligand Donor)	false
O27	OD2	ASP- 25	3.14	139.85	H-Bond (Ligand Donor)	false
O32	OD2	ASP- 25	3.21	128.94	H-Bond (Ligand Donor)	false
O32	OD1	ASP- 25	2.87	165.12	H-Bond (Ligand Donor)	false
N4	O	GLY- 27	3.18	157.68	H-Bond (Ligand Donor)	false
C35	CB	ALA- 28	4.09	0	Hydrophobic	false
C36	CB	ALA- 28	4.5	0	Hydrophobic	false
C16	CB	ALA- 28	3.88	0	Hydrophobic	false
N1	OD2	ASP- 29	2.94	167.87	H-Bond (Ligand Donor)	false
N7	OD2	ASP- 29	3.06	163.07	H-Bond (Ligand Donor)	false
O13	N	ASP- 29	2.82	176.51	H-Bond (Protein Donor)	false
O48	N	ASP- 29	2.87	167.34	H-Bond (Protein Donor)	false
C17	CB	ASP- 30	4.42	0	Hydrophobic	false
C36	CB	ASP- 30	4.45	0	Hydrophobic	false
C16	CG2	VAL- 32	4.27	0	Hydrophobic	false
C17	CG2	VAL- 32	4.05	0	Hydrophobic	false
C35	CG2	VAL- 32	4.24	0	Hydrophobic	false
C36	CG2	VAL- 32	3.79	0	Hydrophobic	false
C2	CG2	ILE- 47	4.18	0	Hydrophobic	false
C50	CG2	ILE- 47	4.22	0	Hydrophobic	false
C17	CD1	ILE- 47	4.06	0	Hydrophobic	false
C36	CD1	ILE- 47	3.96	0	Hydrophobic	false
O1	N	GLY- 48	2.7	165.18	H-Bond (Protein Donor)	false
O49	N	GLY- 48	2.87	168.95	H-Bond (Protein Donor)	false
N3	O	GLY- 48	2.76	162.42	H-Bond (Ligand Donor)	false
N6	O	GLY- 48	2.74	175.18	H-Bond (Ligand Donor)	false
C25	CD1	ILE- 50	4.35	0	Hydrophobic	false
C26	CB	ILE- 50	4.42	0	Hydrophobic	false
C34	CG1	ILE- 50	4.2	0	Hydrophobic	false
C35	CD1	ILE- 50	4.06	0	Hydrophobic	false
C16	CG1	ILE- 50	3.55	0	Hydrophobic	false
C10	CG	PRO- 81	3.92	0	Hydrophobic	false
C11	CB	PRO- 81	3.96	0	Hydrophobic	false
C24	CG	PRO- 81	3.87	0	Hydrophobic	false
C45	CB	PRO- 81	3.57	0	Hydrophobic	false
C30	CG1	VAL- 82	4.17	0	Hydrophobic	false
C23	CG2	VAL- 82	3.63	0	Hydrophobic	false
C16	CD1	ILE- 84	3.61	0	Hydrophobic	false
C29	CD1	ILE- 84	3.67	0	Hydrophobic	false
C35	CG2	ILE- 84	4.2	0	Hydrophobic	false
C21	CD1	ILE- 84	3.72	0	Hydrophobic	false