scPDB - 4c04 entry

Protein Data Bank Entry:

PDB ID : 4c04

Resolution :1.580 Å

Experimental Method : X-ray

Deposition Date : 2013-07-31

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 6
ID:	ANM6_MOUSE
AC:	Q6NZB1
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.708
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.520	634.500

% Hydrophobic	% Polar
38.30	61.70
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	68.13 %
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
20.4796	-10.6912	1.65715

Binding mode :

What is Poseview ?

2D View
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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
CG	SD	MET- 63	3.99	0	Hydrophobic	false
O	CZ	ARG- 69	3.57	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 69	3.8	0	Ionic (Protein Cationic)	false
O	NH1	ARG- 69	2.69	169.09	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 69	3.33	137.76	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 69	3.45	133.5	H-Bond (Protein Donor)	false
N	O	GLY- 93	2.92	164.29	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 115	2.78	170.16	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 115	3.14	129.25	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 115	2.52	161.66	H-Bond (Ligand Donor)	false
N3	N	ALA- 116	3.15	145.67	H-Bond (Protein Donor)	false
N1	N	VAL- 143	3.09	156.22	H-Bond (Protein Donor)	false
N6	OE1	GLU- 144	3.08	159.3	H-Bond (Ligand Donor)	false
CG	CB	GLU- 158	4.13	0	Hydrophobic	false
NE	OE2	GLU- 158	3.16	133.73	H-Bond (Ligand Donor)	false
NE	O	GLU- 158	2.97	168.97	H-Bond (Ligand Donor)	false
NE	OE2	GLU- 158	3.16	0	Ionic (Ligand Cationic)	false
NE	OE1	GLU- 158	3.79	0	Ionic (Ligand Cationic)	false
C1'	CE	MET- 169	4.16	0	Hydrophobic	false
C5'	SD	MET- 169	3.44	0	Hydrophobic	false
OXT	O	HOH- 2009	2.53	179.95	H-Bond (Protein Donor)	false
N	O	HOH- 2036	2.98	167.46	H-Bond (Ligand Donor)	false