scPDB - 4upj entry

Protein Data Bank Entry:

PDB ID : 4upj

Resolution :1.900 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_HV2RO
AC:	P04584
Organism:	Human immunodeficiency virus type 2 subtype A
Reign:	Viruses
TaxID:	11720
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	60 %
B	40 %

Ligand binding site composition:

B-Factor:	18.605
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.972	546.750

% Hydrophobic	% Polar
48.15	51.85
According to VolSite

Ligand :

HET Code:	U04
Formula:	C25H27N2O6
Molecular weight:	451.492 g/mol
DrugBank ID:	DB08664
Buried Surface Area:	66.37 %
Polar Surface area:	116.79 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-0.825182	21.0025	21.9739

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
OG3	NH2	ARG- 8	2.98	140.98	H-Bond (Protein Donor)	false
OG3	NH1	ARG- 8	3.25	131.42	H-Bond (Protein Donor)	false
CA6	CD2	LEU- 23	4.39	0	Hydrophobic	false
CB8	CD2	LEU- 23	4.37	0	Hydrophobic	false
OA9	OD1	ASP- 25	3.4	128.93	H-Bond (Ligand Donor)	false
CA7	CB	ALA- 28	4.13	0	Hydrophobic	false
CB3	CB	ALA- 28	3.44	0	Hydrophobic	false
OG1	N	ASP- 29	2.79	133.7	H-Bond (Protein Donor)	false
OG1	N	ASP- 30	3.03	150.7	H-Bond (Protein Donor)	false
CB3	CG2	ILE- 32	4.17	0	Hydrophobic	false
CB4	CG2	VAL- 47	3.76	0	Hydrophobic	false
NB5	O	GLY- 48	3.2	129.21	H-Bond (Ligand Donor)	false
OA2	N	ILE- 50	2.81	155.39	H-Bond (Protein Donor)	false
OA3	N	ILE- 50	3.16	158.03	H-Bond (Protein Donor)	false
CB2	CG1	ILE- 50	3.99	0	Hydrophobic	false
CG6	CZ	PHE- 53	4.04	0	Hydrophobic	false
CG5	CG	PRO- 81	4.39	0	Hydrophobic	false
CB8	CG2	ILE- 82	4.22	0	Hydrophobic	false
CG5	CG2	ILE- 82	4.13	0	Hydrophobic	false
CG7	CD1	ILE- 82	4.41	0	Hydrophobic	false
CA5	CD1	ILE- 82	3.46	0	Hydrophobic	false
CA8	CD1	ILE- 84	4.48	0	Hydrophobic	false
CB8	CD1	ILE- 84	3.27	0	Hydrophobic	false
CB2	CD1	ILE- 84	3.58	0	Hydrophobic	false