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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4onj

2.810 Å

X-ray

2014-01-28

Interactomes:
Molecular Function:
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
B100 %


Ligand binding site composition:

B-Factor:74.636
Number of residues:34
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.578772.875

% Hydrophobic% Polar
40.1759.83
According to VolSite

Ligand :
4onj_2 Structure
HET Code: SFG
Formula: C15H24N7O5
Molecular weight: 382.395 g/mol
DrugBank ID: DB01910
Buried Surface Area:66.78 %
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

XYZ
-37.5157-58.181-29.8555


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
ONPHE- 4623.45120.13H-Bond
(Protein Donor)
OXTNPHE- 4622.7158H-Bond
(Protein Donor)
NOPHE- 4883.3157.03H-Bond
(Ligand Donor)
CGCBPHE- 4884.390Hydrophobic
C1'CBPHE- 4884.430Hydrophobic
C5'CBPHE- 4884.020Hydrophobic
O3'OE1GLU- 5123.47156.68H-Bond
(Ligand Donor)
O2'OE1GLU- 5122.75154.16H-Bond
(Ligand Donor)
N3NLYS- 5133.12132.42H-Bond
(Protein Donor)
O2'ND2ASN- 5173.13127.86H-Bond
(Protein Donor)
C5'CBPRO- 5663.980Hydrophobic