Complex 2fd0

Legend

Pocket colors by molecule type

RNA

Protein

DNA

These colors appear when a pocket is selected (the structure fades to show the pocket surface). Colors from the molecule-type palette (RNA / protein / DNA).

System information

Experimental technique	X-ray
Experimental resolution	1.80
System mass	16.65 kDa
Deposition year	2005
Molecule type	RNA
# RNA entities	1
Organism	N/A
RCSB PDB Entry	2fd0
Reference	Ennifar E.. 2006. Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell Nucleic Acids Research
Equivalence Class	NR_all_78706.4 BGSU version: 4.52

Pockets List

Legend

Cell colors for SiteScore and D Score:

Favourable

Intermediate

Unfavourable

Not available

Score	Threshold	Meaning
SiteScore	< 0.8	Non-drug binding site
SiteScore	0.8 – 1.0	Potential drug binding site
SiteScore	> 1.0	Promising binding site
D Score	< 0.83	Undruggable
D Score	0.83 – 0.98	Difficult
D Score	> 0.98	Druggable

Tick a pocket below to highlight it in the 3D structure above.

Pocket 1

Compound	LIV
Residue	. / 1001
Chain	C / A
Non-redundant	True
Interacting RNA chains	B/B, A/A
RNA environment detailled	other
RNA environment global	RNA/Other
RNA family chains	A/A: TAR_rna, B/B: TAR_rna
RNA family global	TAR_rna
Volume	466.82 Å³
Hydrophobicity	0.157
Hydrophilicity	1.010
Buriedness	0.651
Don/acc character	1.415
SiteScore	1.125
D Score	1.001
Kd	—

Pocket 2

Compound	LIV
Residue	. / 2001
Chain	F / B
Non-redundant	False
Interacting RNA chains	B/B, A/A
RNA environment detailled	other
RNA environment global	RNA/Other
RNA family chains	A/A: TAR_rna, B/B: TAR_rna
RNA family global	TAR_rna
Volume	499.41 Å³
Hydrophobicity	0.187
Hydrophilicity	1.202
Buriedness	0.682
Don/acc character	1.153
SiteScore	1.139
D Score	0.957
Kd	—