scPDB - 5eku entry

Protein Data Bank Entry:

PDB ID : 5eku

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2015-11-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Arginine N-methyltransferase, putative
ID:	D6XJ80_TRYB2
AC:	D6XJ80
Organism:	Trypanosoma brucei brucei
Reign:	Eukaryota
TaxID:	185431
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	80.233
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.440	644.625

% Hydrophobic	% Polar
46.60	53.40
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	67.25 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
11.4749	110.624	54.0925

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
SD	SD	MET- 75	3.72	0	Hydrophobic	false
CG	CE	MET- 75	3.9	0	Hydrophobic	false
O	CZ	ARG- 81	3.46	0	Ionic (Protein Cationic)	false
OXT	NH2	ARG- 81	3.38	139.37	H-Bond (Protein Donor)	false
N	OE2	GLU- 101	2.57	0	Ionic (Ligand Cationic)	false
N	O	GLY- 103	3.12	157.62	H-Bond (Ligand Donor)	false
OXT	OG	SER- 106	3.28	129.73	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 125	3.46	124.9	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 125	3.25	174.13	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 125	2.68	149.86	H-Bond (Ligand Donor)	false
N3	N	GLY- 126	3.41	127.06	H-Bond (Protein Donor)	false
C3'	CD1	LEU- 130	4.4	0	Hydrophobic	false
N6	OG	SER- 154	3.38	136.15	H-Bond (Ligand Donor)	false
N1	N	SER- 154	3.2	155.96	H-Bond (Protein Donor)	false
CB	CB	GLU- 172	4.45	0	Hydrophobic	false
C5'	CG2	ILE- 173	4.36	0	Hydrophobic	false