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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:

2ej2

2.000 Å

X-ray

2007-03-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Branched-chain amino acid aminotransferase (IlvE)
ID:Q5SM19_THET8
AC:Q5SM19
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:300852
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C90 %
F10 %


Ligand binding site composition:

B-Factor:20.138
Number of residues:45
Including
Standard Amino Acids: 41
Non Standard Amino Acids: 0
Water Molecules: 4
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.498482.625

% Hydrophobic% Polar
46.8553.15
According to VolSite

Ligand :
2ej2_3 Structure
HET Code: PPE
Formula: C13H16N2O9P
Molecular weight: 375.248 g/mol
DrugBank ID: DB01813
Buried Surface Area:70.06 %
Polar Surface area: 212.22 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 2
Rings: 1
Aromatic rings: 1
Anionic atoms: 4
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 10

Mass center Coordinates

XYZ
34.46265.910232.1688


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
OP3NH1ARG- 592.89149.36H-Bond
(Protein Donor)
OP3NH2ARG- 593.06139.99H-Bond
(Protein Donor)
OP3CZARG- 593.40Ionic
(Protein Cationic)
OAOHTYR- 952.58170.54H-Bond
(Protein Donor)
OANZLYS- 1593.960Ionic
(Protein Cationic)
C2ACE2TYR- 1644.250Hydrophobic
O3OHTYR- 1642.69159.14H-Bond
(Protein Donor)
C2ACBLEU- 2164.490Hydrophobic
C5CD2LEU- 2163.640Hydrophobic
OP3NILE- 2192.79169.02H-Bond
(Protein Donor)
OP1OG1THR- 2202.78146.91H-Bond
(Protein Donor)
OP1NTHR- 2202.79158.1H-Bond
(Protein Donor)
OP2NTHR- 2562.97149.85H-Bond
(Protein Donor)
OP2OG1THR- 2562.68154.84H-Bond
(Protein Donor)
OXTNALA- 2572.74146.09H-Bond
(Protein Donor)
OP1OHOH- 14222.81150.39H-Bond
(Protein Donor)
OXTOHOH- 14242.93179.96H-Bond
(Protein Donor)
OP2OHOH- 14252.86145.05H-Bond
(Protein Donor)