scPDB - 3emd entry

Protein Data Bank Entry:

PDB ID : 3emd

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-09-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methyltransferase
ID:	D0VX01_9FLAV
AC:	D0VX01
Organism:	Wesselsbron virus
Reign:	Viruses
TaxID:	164416
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.318
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.470	337.500

% Hydrophobic	% Polar
52.00	48.00
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	64.37 %
Polar Surface area:	214.71 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-1.98759	5.29741	15.1614

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
OXT	OG	SER- 56	2.68	155.75	H-Bond (Protein Donor)	false
OXT	N	GLY- 86	3.19	143	H-Bond (Protein Donor)	false
O	N	TRP- 87	3.42	120.37	H-Bond (Protein Donor)	false
N3	N	LEU- 105	3.21	125.25	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 111	2.97	162.69	H-Bond (Ligand Donor)	false
C3'	CG	GLU- 111	3.94	0	Hydrophobic	false
N6	OD1	ASN- 131	2.87	154.97	H-Bond (Ligand Donor)	false
N1	N	VAL- 132	3.05	168.88	H-Bond (Protein Donor)	false
N	OD1	ASP- 146	2.88	170.7	H-Bond (Ligand Donor)	false
N	OD1	ASP- 146	2.88	0	Ionic (Ligand Cationic)	false
NE	OD1	ASP- 146	3.65	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 146	4.09	0	Hydrophobic	false
C1'	CG1	ILE- 147	4.46	0	Hydrophobic	false
N	O	HOH- 440	2.68	162.35	H-Bond (Ligand Donor)	false