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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:

2oem

1.700 Å

X-ray

2006-12-30

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:2,3-diketo-5-methylthiopentyl-1-phosphate enolase
ID:MTNW_GEOKA
AC:Q5L1E2
Organism:Geobacillus kaustophilus
Reign:Bacteria
TaxID:235909
EC Number:5.3.2.5


Chains:

Chain Name:Percentage of Residues
within binding site
A6 %
B94 %


Ligand binding site composition:

B-Factor:17.990
Number of residues:17
Including
Standard Amino Acids: 14
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.128715.500

% Hydrophobic% Polar
41.9858.02
According to VolSite

Ligand :
2oem_2 Structure
HET Code: 1AE
Formula: C6H9O6P
Molecular weight: 208.106 g/mol
DrugBank ID: DB06881
Buried Surface Area:40.3 %
Polar Surface area: 119.53 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 1
Rings: 0
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
28.065-23.4017-19.8118


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
C6CD1ILE- 1454.430Hydrophobic
O10NGLY- 3373.39173.14H-Bond
(Protein Donor)
O7NGLY- 3603.32174.82H-Bond
(Protein Donor)
O9OHOH- 12273170.6H-Bond
(Protein Donor)