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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:

2uuo

2.500 Å

X-ray

2007-03-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UDP-N-acetylmuramoylalanine--D-glutamate ligase
ID:MURD_ECOLI
AC:P14900
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:6.3.2.9


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:12.316
Number of residues:36
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9761029.375

% Hydrophobic% Polar
41.3158.69
According to VolSite

Ligand :
2uuo_1 Structure
HET Code: LK3
Formula: C20H23NO7S
Molecular weight: 421.464 g/mol
DrugBank ID: DB08107
Buried Surface Area:52.08 %
Polar Surface area: 144.04 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 12

Mass center Coordinates

XYZ
-20.95462.0122119.7206


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
C30CG2ILE- 113.640Hydrophobic
C23CDARG- 374.210Hydrophobic
C26CBILE- 744.060Hydrophobic
CGCG2THR- 3214.190Hydrophobic
OXTNZLYS- 3483.910Ionic
(Protein Cationic)
ONZLYS- 3482.830Ionic
(Protein Cationic)
ONZLYS- 3482.83168.2H-Bond
(Protein Donor)
CGCBALA- 4143.580Hydrophobic
OE1OGSER- 4152.64170.41H-Bond
(Protein Donor)
OE1NSER- 4152.66161.45H-Bond
(Protein Donor)
CGCGLEU- 4163.950Hydrophobic
CACD1LEU- 4164.370Hydrophobic
C16CD1LEU- 4163.530Hydrophobic
OE2NPHE- 4222.86141.55H-Bond
(Protein Donor)