scPDB - 3vaq entry

Protein Data Bank Entry:

PDB ID : 3vaq

Resolution :2.440 Å

Experimental Method : X-ray

Deposition Date : 2011-12-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative adenosine kinase
ID:	G4V7G8_SCHMA
AC:	G4V7G8
Organism:	Schistosoma mansoni
Reign:	Eukaryota
TaxID:	6183
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	41.455
Number of residues:	41
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
1.178	1110.375

% Hydrophobic	% Polar
43.47	56.53
According to VolSite

Ligand :

HET Code:	ADN
Formula:	C10H13N5O4
Molecular weight:	267.241 g/mol
DrugBank ID:	DB00640
Buried Surface Area:	75.83 %
Polar Surface area:	139.54 Å2

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

Mass center Coordinates

X	Y	Z
12.9996	-14.2077	8.08811

Binding mode :

What is Poseview ?

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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
N1	ND2	ASN- 14	3.06	166.62	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 18	3.41	134.26	H-Bond (Ligand Donor)	false
O2'	N	GLY- 64	3.05	168.16	H-Bond (Protein Donor)	false
C1'	CB	ALA- 65	4.47	0	Hydrophobic	false
N3	N	ALA- 65	3.21	170.23	H-Bond (Protein Donor)	false
O3'	ND2	ASN- 68	3.27	141.14	H-Bond (Protein Donor)	false
C2'	CG2	VAL- 123	3.91	0	Hydrophobic	false
C5'	SD	MET- 134	4.29	0	Hydrophobic	false
C3'	SD	MET- 134	4.11	0	Hydrophobic	false
N7	OG1	THR- 136	2.92	153.87	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 169	3.84	0	Aromatic Face/Face	false
O5'	OD2	ASP- 302	2.64	169.34	H-Bond (Ligand Donor)	false
N6	O	HOH- 510	2.91	148.87	H-Bond (Ligand Donor)	false