scPDB - 4onq entry

Protein Data Bank Entry:

PDB ID : 4onq

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2014-01-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA methyltransferase
ID:	Q76KU6_TOBAC
AC:	Q76KU6
Organism:	Nicotiana tabacum
Reign:	Eukaryota
TaxID:	4097
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	52.376
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.010	469.125

% Hydrophobic	% Polar
33.81	66.19
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	67.67 %
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
-18.7447	28.9266	-7.71572

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
NE	O	ASN- 460	3.43	163.78	H-Bond (Ligand Donor)	false
O	N	PHE- 462	3	155.06	H-Bond (Protein Donor)	false
N	O	PHE- 488	3.28	158.24	H-Bond (Ligand Donor)	false
C1'	CB	PHE- 488	4.3	0	Hydrophobic	false
C5'	CB	PHE- 488	3.47	0	Hydrophobic	false
OXT	N	ILE- 491	3.03	153.71	H-Bond (Protein Donor)	false
O	N	GLY- 493	3.47	136.43	H-Bond (Protein Donor)	false
N7	NZ	LYS- 513	3.42	123.45	H-Bond (Protein Donor)	false
N3	N	LYS- 513	3.46	139.98	H-Bond (Protein Donor)	false
O3'	OD1	ASN- 517	3.31	148.55	H-Bond (Ligand Donor)	false
NE	O	SER- 565	2.87	134.06	H-Bond (Ligand Donor)	false
N	O	HOH- 838	3.41	162.61	H-Bond (Ligand Donor)	false