scPDB - 2upj entry

Protein Data Bank Entry:

PDB ID : 2upj

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 1996-03-04

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	55 %
B	45 %

Ligand binding site composition:

B-Factor:	10.017
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.972	799.875

% Hydrophobic	% Polar
45.15	54.85
According to VolSite

Ligand :

HET Code:	U02
Formula:	C33H37N2O6
Molecular weight:	557.657 g/mol
DrugBank ID:	-
Buried Surface Area:	56.51 %
Polar Surface area:	116.79 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
11.1104	24.0083	5.00737

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
OA6	OD1	ASP- 25	3.23	138.64	H-Bond (Ligand Donor)	false
CB3	CB	ALA- 28	3.55	0	Hydrophobic	false
CE2	CB	ALA- 28	3.84	0	Hydrophobic	false
CZ2	CB	ASP- 29	4.28	0	Hydrophobic	false
CE4	CB	ASP- 29	3.57	0	Hydrophobic	false
OZ1	N	ASP- 29	2.91	140.72	H-Bond (Protein Donor)	false
OZ1	N	ASP- 30	3.38	141.87	H-Bond (Protein Donor)	false
CE3	CB	ASP- 30	4.24	0	Hydrophobic	false
CB4	CG2	VAL- 32	4.27	0	Hydrophobic	false
CZ2	CB	ILE- 47	4.41	0	Hydrophobic	false
CB4	CD1	ILE- 47	4.41	0	Hydrophobic	false
NZ1	O	GLY- 48	2.93	128.49	H-Bond (Ligand Donor)	false
CB3	CG1	ILE- 50	4.49	0	Hydrophobic	false
CE	CD1	ILE- 50	4.19	0	Hydrophobic	false
CG3	CG1	ILE- 50	4.11	0	Hydrophobic	false
OA2	N	ILE- 50	2.74	157.02	H-Bond (Protein Donor)	false
CG3	CG	PRO- 81	4.5	0	Hydrophobic	false
CZ7	CB	PRO- 81	3.25	0	Hydrophobic	false
CZ6	CG1	VAL- 82	3.35	0	Hydrophobic	false
CD2	CG1	VAL- 82	4.15	0	Hydrophobic	false
CG3	CG2	VAL- 82	3.84	0	Hydrophobic	false
CB3	CD1	ILE- 84	4.36	0	Hydrophobic	false
CG3	CD1	ILE- 84	4.16	0	Hydrophobic	false
CD2	CD1	ILE- 84	4.19	0	Hydrophobic	false