scPDB - 5dst entry

Protein Data Bank Entry:

PDB ID : 5dst

Resolution :2.960 Å

Experimental Method : X-ray

Deposition Date : 2015-09-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein arginine N-methyltransferase 8
ID:	ANM8_HUMAN
AC:	Q9NR22
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	35.527
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.274	745.875

% Hydrophobic	% Polar
41.63	58.37
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	73.07 %
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
43.9912	-42.7179	22.4031

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
C3'	CD1	TYR- 80	3.53	0	Hydrophobic	false
C2'	CD2	TYR- 80	3.54	0	Hydrophobic	false
SD	CE1	TYR- 80	4.15	0	Hydrophobic	false
SD	SD	MET- 89	3.51	0	Hydrophobic	false
O	NH2	ARG- 95	2.77	137.04	H-Bond (Protein Donor)	false
O	NH1	ARG- 95	2.65	144.34	H-Bond (Protein Donor)	false
O	CZ	ARG- 95	3.12	0	Ionic (Protein Cationic)	false
O3'	OE1	GLU- 141	2.77	174.07	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 141	2.66	160.41	H-Bond (Ligand Donor)	false
N3	N	CYS- 142	3.31	155.97	H-Bond (Protein Donor)	false
N1	N	VAL- 169	3.18	145.68	H-Bond (Protein Donor)	false
N6	OE2	GLU- 170	2.8	145.28	H-Bond (Ligand Donor)	false
CG	CG	GLU- 185	3.75	0	Hydrophobic	false
C5'	SD	MET- 196	3.94	0	Hydrophobic	false
C4'	CE	MET- 196	4.38	0	Hydrophobic	false
C1'	CE	MET- 196	4.45	0	Hydrophobic	false
N6	OG1	THR- 199	3.29	122.18	H-Bond (Ligand Donor)	false