scPDB - 3irx entry

Protein Data Bank Entry:

PDB ID : 3irx

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2009-08-24

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_HV1B1
AC:	P03366
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11678
EC Number:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	92 %
B	8 %

Ligand binding site composition:

B-Factor:	91.464
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.267	1464.750

% Hydrophobic	% Polar
58.76	41.24
According to VolSite

Ligand :

HET Code:	UDR
Formula:	C27H29N3O5S
Molecular weight:	507.601 g/mol
DrugBank ID:	-
Buried Surface Area:	57.33 %
Polar Surface area:	120.06 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-49.7959	-29.759	-39.1249

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
CAD	CD2	LEU- 100	3.59	0	Hydrophobic	false
CAN	CD1	LEU- 100	4.38	0	Hydrophobic	false
CAA	CB	LYS- 103	3.99	0	Hydrophobic	false
CAA	CB	VAL- 106	3.95	0	Hydrophobic	false
CAB	CG1	VAL- 106	4.27	0	Hydrophobic	false
CAF	CG1	VAL- 106	3.58	0	Hydrophobic	false
CAM	CG1	VAL- 106	4.28	0	Hydrophobic	false
CBF	CG2	VAL- 106	4.35	0	Hydrophobic	false
CBE	CG1	VAL- 106	4.26	0	Hydrophobic	false
CAF	CG2	VAL- 108	3.68	0	Hydrophobic	false
CBH	CG2	VAL- 108	3.47	0	Hydrophobic	false
CAD	CB	TYR- 181	3.9	0	Hydrophobic	false
CAP	CD2	TYR- 181	3.46	0	Hydrophobic	false
DuAr	DuAr	TYR- 181	3.72	0	Aromatic Face/Face	false
CAE	CE2	TYR- 188	4.28	0	Hydrophobic	false
CAP	CD1	TYR- 188	3.94	0	Hydrophobic	false
CAK	CE2	TYR- 188	3.41	0	Hydrophobic	false
CAC	CD1	PHE- 227	4.21	0	Hydrophobic	false
CAF	CE1	PHE- 227	3.51	0	Hydrophobic	false
CBA	CB	PHE- 227	4.39	0	Hydrophobic	false
CAE	CB	TRP- 229	4.38	0	Hydrophobic	false
CAK	CB	TRP- 229	4.09	0	Hydrophobic	false
CAN	CD2	TRP- 229	4.04	0	Hydrophobic	false
CAO	CE2	TRP- 229	3.36	0	Hydrophobic	false
CAP	CZ2	TRP- 229	4.2	0	Hydrophobic	false
CAN	CD1	LEU- 234	3.54	0	Hydrophobic	false
CAC	CB	LEU- 234	3.92	0	Hydrophobic	false
CAJ	CD1	LEU- 234	3.67	0	Hydrophobic	false
CBC	CD1	LEU- 234	4.2	0	Hydrophobic	false