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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:

3hna

1.500 Å

X-ray

2009-05-30

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Histone-lysine N-methyltransferase EHMT1
ID:EHMT1_HUMAN
AC:Q9H9B1
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:15.199
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.8151090.125

% Hydrophobic% Polar
32.5167.49
According to VolSite

Ligand :
3hna_1 Structure
HET Code: SAH
Formula: C14H20N6O5S
Molecular weight: 384.411 g/mol
DrugBank ID: DB01752
Buried Surface Area:69.3 %
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

XYZ
43.41424.096124.80985


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
NOTRP- 11072.74171.29H-Bond
(Ligand Donor)
OXTNTRP- 11072.82161.69H-Bond
(Protein Donor)
SDCE1TYR- 11423.590Hydrophobic
OOHTYR- 11423.15142.98H-Bond
(Protein Donor)
CBCD1PHE- 11674.320Hydrophobic
NOD1ASN- 11692.77144.34H-Bond
(Ligand Donor)
N7NHIS- 11702.98161.35H-Bond
(Protein Donor)
N6OHIS- 11702.84147.78H-Bond
(Ligand Donor)
C5'CE2TYR- 12113.940Hydrophobic
C3'CZPHE- 12153.890Hydrophobic
C2'CZPHE- 12233.640Hydrophobic
N1NARG- 12262.96170.76H-Bond
(Protein Donor)