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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:

4u0o

1.600 Å

X-ray

2014-07-13

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Lipoyl synthase 2
ID:LIPA2_THEEB
AC:Q8DLC2
Organism:Thermosynechococcus elongatus
Reign:Bacteria
TaxID:197221
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:32.942
Number of residues:30
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.893907.875

% Hydrophobic% Polar
39.0360.97
According to VolSite

Ligand :
4u0o_1 Structure
HET Code: MTA
Formula: C11H15N5O3S
Molecular weight: 297.333 g/mol
DrugBank ID: DB02282
Buried Surface Area:60.25 %
Polar Surface area: 144.61 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
10.579261.903621.6517


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
S5'CG2ILE- 364.090Hydrophobic
N6OPHE- 693.14136.99H-Bond
(Ligand Donor)
C2'CE1PHE- 694.10Hydrophobic
C5'CD2LEU- 1383.970Hydrophobic
CSCD2LEU- 1384.350Hydrophobic
O3'ND2ASN- 1693.01162.47H-Bond
(Protein Donor)
O2'OE1GLU- 1713.42133.43H-Bond
(Ligand Donor)
O2'OE2GLU- 1712.51169.48H-Bond
(Ligand Donor)
O3'OE1GLU- 1712.62162.22H-Bond
(Ligand Donor)
C2'SDMET- 2103.910Hydrophobic
N6OLEU- 2412.77170.68H-Bond
(Ligand Donor)
N1NLEU- 2413.09170.75H-Bond
(Protein Donor)
CSCBARG- 2813.710Hydrophobic
C1'CDARG- 2814.240Hydrophobic
CSCBSER- 2833.960Hydrophobic