scPDB - 1rti entry

Protein Data Bank Entry:

PDB ID : 1rti

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 1995-05-03

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_HV1H2
AC:	P04585
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11706
EC Number:	2.7.7.49

Chains:

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

Ligand binding site composition:

B-Factor:	53.674
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.837	465.750

% Hydrophobic	% Polar
78.99	21.01
According to VolSite

Ligand :

HET Code:	HEF
Formula:	C14H16N2O4S
Molecular weight:	308.353 g/mol
DrugBank ID:	DB07892
Buried Surface Area:	68.59 %
Polar Surface area:	104.17 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-2.22476	-34.6526	24.931

Binding mode :

What is Poseview ?

2D View
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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
CM	CD1	LEU- 100	4.01	0	Hydrophobic	false
C5'	CD2	LEU- 100	3.47	0	Hydrophobic	false
C6'	CD1	LEU- 100	3.33	0	Hydrophobic	false
N3	O	LYS- 101	3.09	157.82	H-Bond (Ligand Donor)	false
CM5	CG1	VAL- 106	4.12	0	Hydrophobic	false
CM	CG2	VAL- 106	4.24	0	Hydrophobic	false
CE1	CG2	VAL- 106	4.2	0	Hydrophobic	false
S'	CG1	VAL- 106	3.63	0	Hydrophobic	false
CM5	CD1	TYR- 181	4.35	0	Hydrophobic	false
CM5	CB	TYR- 188	3.48	0	Hydrophobic	false
S'	CD2	TYR- 188	3.77	0	Hydrophobic	false
C2'	CD2	TYR- 188	3.26	0	Hydrophobic	false
C2'	CB	TYR- 188	4.09	0	Hydrophobic	false
CE2	CB	PRO- 225	3.66	0	Hydrophobic	false
S'	CD2	PHE- 227	4.11	0	Hydrophobic	false
CE1	CD2	PHE- 227	3.51	0	Hydrophobic	false
CM	CB	LEU- 234	4.08	0	Hydrophobic	false
CE1	CB	LEU- 234	3.76	0	Hydrophobic	false
CM	CZ	TYR- 318	4.31	0	Hydrophobic	false