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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:

5ej7

1.560 Å

X-ray

2015-11-01

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
ID:MEND_ECOLI
AC:P17109
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C69 %
D31 %


Ligand binding site composition:

B-Factor:11.221
Number of residues:54
Including
Standard Amino Acids: 50
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals: MN

Cavity properties

LigandabilityVolume (Å3)
1.2551326.375

% Hydrophobic% Polar
48.8551.15
According to VolSite

Ligand :
5ej7_3 Structure
HET Code: TD6
Formula: C16H21N4O10P2S
Molecular weight: 523.371 g/mol
DrugBank ID: -
Buried Surface Area:80.44 %
Polar Surface area: 285.67 Å2
Number of
H-Bond Acceptors: 13
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 12

Mass center Coordinates

XYZ
-48.365121.410510.7398


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
CM4CGPRO- 303.610Hydrophobic
N1'OE1GLU- 552.89158H-Bond
(Ligand Donor)
N1'OE2GLU- 553.02138.28H-Bond
(Ligand Donor)
C5'CG2THR- 784.040Hydrophobic
CM2CBALA- 824.370Hydrophobic
OL3ND2ASN- 1173.04153.03H-Bond
(Protein Donor)
S1CBSER- 3913.620Hydrophobic
C7CBSER- 3913.930Hydrophobic
O1BOGSER- 3912.54162.71H-Bond
(Protein Donor)
OL2NSER- 3912.89158.29H-Bond
(Protein Donor)
O2BNLEU- 3922.97150.35H-Bond
(Protein Donor)
OL2CZARG- 3953.70Ionic
(Protein Cationic)
OL3CZARG- 3953.510Ionic
(Protein Cationic)
OL2NH1ARG- 3952.86171.53H-Bond
(Protein Donor)
OL3NH2ARG- 3952.7173.68H-Bond
(Protein Donor)
OL3NH1ARG- 3953.44128.73H-Bond
(Protein Donor)
OL2CZARG- 4133.750Ionic
(Protein Cationic)
OL3CZARG- 4133.630Ionic
(Protein Cationic)
OL2NH2ARG- 4132.78166.03H-Bond
(Protein Donor)
OL3NH1ARG- 4133.1140.47H-Bond
(Protein Donor)
OL3NH2ARG- 4133.34132.72H-Bond
(Protein Donor)
C13CBSER- 4163.650Hydrophobic
N4'OSER- 4163.03162.29H-Bond
(Ligand Donor)
S1CG2ILE- 4184.410Hydrophobic
C5'CG1ILE- 4184.170Hydrophobic
CM2CG1ILE- 4184.140Hydrophobic
CM4CD1ILE- 4183.730Hydrophobic
C7CD1ILE- 4184.060Hydrophobic
N3'NILE- 4183.09159.07H-Bond
(Protein Donor)
CM2CBASP- 4193.650Hydrophobic
C6CD1LEU- 4434.320Hydrophobic
C7CBLEU- 4434.160Hydrophobic
O1ANLEU- 4433.03167.73H-Bond
(Protein Donor)
O2ANSER- 4442.94147.18H-Bond
(Protein Donor)
O2AOGSER- 4442.74163.6H-Bond
(Protein Donor)
CM2CE1TYR- 4473.760Hydrophobic
O3BND2ASN- 4693.01144.74H-Bond
(Protein Donor)
O3BNGLN- 4732.97158.31H-Bond
(Protein Donor)
S1CG2ILE- 4743.770Hydrophobic
C6CG2ILE- 4744.420Hydrophobic
CLBCD1ILE- 4744.370Hydrophobic
O1BNILE- 4743.05162.63H-Bond
(Protein Donor)
C6CE2PHE- 4754.210Hydrophobic
CM4CE2PHE- 4754.220Hydrophobic
O1AMN MN- 6022.080Metal Acceptor
O3BMN MN- 6022.170Metal Acceptor