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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:

2y1o

1.490 Å

X-ray

2010-12-09

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:19.525
Number of residues:42
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 1
Water Molecules: 4
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1011002.375

% Hydrophobic% Polar
49.8350.17
According to VolSite

Ligand :
2y1o_1 Structure
HET Code: T26
Formula: C23H18N3O6S2
Molecular weight: 496.536 g/mol
DrugBank ID: -
Buried Surface Area:53.41 %
Polar Surface area: 209.95 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 10

Mass center Coordinates

XYZ
-12.307231.717754.1384


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
NAXOG1THR- 362.59170.85H-Bond
(Ligand Donor)
CAOCBPRO- 724.350Hydrophobic
CAPCGPRO- 724.390Hydrophobic
CANCD1ILE- 1393.640Hydrophobic
CARCD1ILE- 1393.680Hydrophobic
OXTNZLYS- 3193.560Ionic
(Protein Cationic)
CBCG2THR- 3214.040Hydrophobic
CGCBALA- 4143.930Hydrophobic
OE1NSER- 4152.79160.14H-Bond
(Protein Donor)
OE1OGSER- 4152.85157.99H-Bond
(Protein Donor)
CGCGLEU- 4164.090Hydrophobic
OE2NPHE- 4222.89137.65H-Bond
(Protein Donor)
CBCD1PHE- 4224.50Hydrophobic