scPDB - 3hiv entry

Protein Data Bank Entry:

PDB ID : 3hiv

Resolution :2.140 Å

Experimental Method : X-ray

Deposition Date : 2009-05-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	rRNA N-glycosidase
ID:	Q2QEH4_SAPOF
AC:	Q2QEH4
Organism:	Saponaria officinalis
Reign:	Eukaryota
TaxID:	3572
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.306
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.113	307.125

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	TXN
Formula:	C37H52N15O20P3
Molecular weight:	1119.819 g/mol
DrugBank ID:	-
Buried Surface Area:	41.7 %
Polar Surface area:	526.54 Å2

Number of
H-Bond Acceptors:	28
H-Bond Donors:	10
Rings:	9
Aromatic rings:	3
Anionic atoms:	3
Cationic atoms:	3
Rule of Five Violation:	3
Rotatable Bonds:	23

Mass center Coordinates

X	Y	Z
26.5198	69.2153	44.8642

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
C1D	CB	ASN- 71	4.4	0	Hydrophobic	false
O2D	ND2	ASN- 71	3.38	157.47	H-Bond (Protein Donor)	false
C1D	CE2	TYR- 73	3.61	0	Hydrophobic	false
DuAr	DuAr	TYR- 73	3.85	0	Aromatic Face/Face	false
N1I	N	VAL- 74	2.87	170.26	H-Bond (Protein Donor)	false
N6I	O	VAL- 74	3.3	152.4	H-Bond (Ligand Donor)	false
N1N	OE1	GLU- 121	2.69	161.58	H-Bond (Ligand Donor)	false
N2N	OE1	GLU- 121	3.32	129.57	H-Bond (Ligand Donor)	false
N6I	O	GLU- 121	3.14	163.64	H-Bond (Ligand Donor)	false
N7I	O	GLU- 121	2.89	159.07	H-Bond (Ligand Donor)	false
O2V	N	TYR- 123	3.11	126.76	H-Bond (Protein Donor)	false
C4E	CG	PRO- 124	4.41	0	Hydrophobic	false
C5I	CG2	VAL- 169	4.12	0	Hydrophobic	false
N1C	OE2	GLU- 174	3.94	0	Ionic (Ligand Cationic)	false
N3I	NH2	ARG- 177	2.99	142.56	H-Bond (Protein Donor)	false
N3I	NH1	ARG- 177	2.97	143.59	H-Bond (Protein Donor)	false
O2Y	N	GLY- 210	2.7	168.49	H-Bond (Protein Donor)	false
O2Z	NH2	ARG- 214	3.32	145.52	H-Bond (Protein Donor)	false
O2V	OH	TYR- 233	3.05	146.36	H-Bond (Protein Donor)	false
C5E	CE1	TYR- 233	4.3	0	Hydrophobic	false
C4D	CD2	LEU- 254	4.17	0	Hydrophobic	false