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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:

2am2

2.800 Å

X-ray

2005-08-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
ID:Q8DNV6_STRR6
AC:Q8DNV6
Organism:Streptococcus pneumoniae
Reign:Bacteria
TaxID:171101
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:44.698
Number of residues:34
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.0682716.875

% Hydrophobic% Polar
41.9958.01
According to VolSite

Ligand :
2am2_1 Structure
HET Code: 2LG
Formula: C19H20ClN3O3S2
Molecular weight: 437.963 g/mol
DrugBank ID: DB06970
Buried Surface Area:64.53 %
Polar Surface area: 126.89 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 1
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
17.842943.783853.6601


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
CL19CD2PHE- 313.850Hydrophobic
C28CZPHE- 314.260Hydrophobic
C18CD1LEU- 454.270Hydrophobic
CL19CBLEU- 454.120Hydrophobic
N11NARG- 493.1169.83H-Bond
(Protein Donor)
C4CE2PHE- 544.190Hydrophobic
C26CE1TYR- 1354.140Hydrophobic
C28CZTYR- 1353.340Hydrophobic
C27CBASN- 1374.20Hydrophobic
C21CG2ILE- 1394.370Hydrophobic
C26CG2ILE- 1394.140Hydrophobic
S5CBASN- 3283.840Hydrophobic
C4CGPRO- 3294.190Hydrophobic
N10OG1THR- 3303.34154.87H-Bond
(Ligand Donor)
C15CBTHR- 3303.730Hydrophobic
C17CG2THR- 3303.690Hydrophobic
C18CG2THR- 3304.020Hydrophobic
C6CD2LEU- 3604.270Hydrophobic
C9CD1LEU- 3673.490Hydrophobic