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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:

5i2h

1.550 Å

X-ray

2016-02-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:O-methyltransferase family 2
ID:D5STZ7_PLAL2
AC:D5STZ7
Organism:Planctopirus limnophila
Reign:Bacteria
TaxID:521674
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A12 %
B88 %


Ligand binding site composition:

B-Factor:16.486
Number of residues:17
Including
Standard Amino Acids: 16
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.195840.375

% Hydrophobic% Polar
58.2341.77
According to VolSite

Ligand :
5i2h_2 Structure
HET Code: AGI
Formula: C15H9O5
Molecular weight: 269.229 g/mol
DrugBank ID: DB07352
Buried Surface Area:52.07 %
Polar Surface area: 89.82 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
42.285842.678142.6779


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
CAGCD1LEU- 1583.880Hydrophobic
CAHCD2LEU- 1583.720Hydrophobic
CAKCD2LEU- 1623.920Hydrophobic
CATCD1LEU- 1623.980Hydrophobic
OACNH1ARG- 1652.85143.39H-Bond
(Protein Donor)
OACNH2ARG- 1653.46124.78H-Bond
(Protein Donor)
OADNE2HIS- 2702.57152.48H-Bond
(Protein Donor)
OAAOD2ASP- 2712.64126.34H-Bond
(Protein Donor)
CAICD2LEU- 3184.020Hydrophobic
CAHCBLEU- 3214.310Hydrophobic
CAGCD1LEU- 3213.830Hydrophobic
CAECD2LEU- 3213.940Hydrophobic