scPDB - 2db3 entry

Protein Data Bank Entry:

PDB ID : 2db3

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2005-12-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ATP-dependent RNA helicase vasa, isoform A
ID:	VASA1_DROME
AC:	P09052
Organism:	Drosophila melanogaster
Reign:	Eukaryota
TaxID:	7227
EC Number:	3.6.4.13

Chains:

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

Ligand binding site composition:

B-Factor:	40.127
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.492	506.250

% Hydrophobic	% Polar
42.00	58.00
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	76.42 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
45.0993	78.4755	42.6198

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
O3'	N	ILE- 219	3.11	156.78	H-Bond (Protein Donor)	false
O2'	OH	TYR- 265	2.66	168.68	H-Bond (Ligand Donor)	false
DuAr	DuAr	TYR- 265	3.64	0	Aromatic Face/Face	false
C2'	CZ	TYR- 265	4.18	0	Hydrophobic	false
N6	O	ILE- 267	2.99	160.19	H-Bond (Ligand Donor)	false
N7	NE2	GLN- 272	2.99	153.9	H-Bond (Protein Donor)	false
N6	OE1	GLN- 272	3	143.11	H-Bond (Ligand Donor)	false
O2B	N	SER- 293	3.2	135.01	H-Bond (Protein Donor)	false
O3A	N	GLY- 294	3.3	137.55	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 295	2.85	164.14	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 295	2.95	143	H-Bond (Protein Donor)	false
O2B	N	LYS- 295	3	168.66	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 295	2.85	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 295	2.95	0	Ionic (Protein Cationic)	false
O1A	N	THR- 296	3.04	153.16	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 554	2.62	164.65	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 554	3.28	130.87	H-Bond (Ligand Donor)	false
O2G	CZ	ARG- 579	3.3	0	Ionic (Protein Cationic)	false
O2G	NH1	ARG- 579	3.21	127.28	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 579	2.54	165.42	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 582	3.88	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 582	3.78	0	Ionic (Protein Cationic)	false
C1'	CG2	VAL- 583	4.25	0	Hydrophobic	false
C4'	CG2	VAL- 583	3.7	0	Hydrophobic	false
O3G	MG	MG- 2801	2.2	0	Metal Acceptor	false
O1B	MG	MG- 2801	2.37	0	Metal Acceptor	false
N1	O	HOH- 2910	2.71	157.44	H-Bond (Protein Donor)	false
O1G	O	HOH- 2912	2.68	179.99	H-Bond (Protein Donor)	false