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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:

2clh

1.700 Å

X-ray

2006-04-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Tryptophan synthase alpha chain
ID:TRPA_SALTY
AC:P00929
Organism:Salmonella typhimurium
Reign:Bacteria
TaxID:99287
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A92 %
B8 %


Ligand binding site composition:

B-Factor:20.855
Number of residues:41
Including
Standard Amino Acids: 38
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.358344.250

% Hydrophobic% Polar
70.5929.41
According to VolSite

Ligand :
2clh_1 Structure
HET Code: F19
Formula: C12H12NO6PS
Molecular weight: 329.266 g/mol
DrugBank ID: DB07732
Buried Surface Area:76.02 %
Polar Surface area: 136.78 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
49.053526.004613.713


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
C3CD2LEU- 1003.490Hydrophobic
C9CD2LEU- 1274.140Hydrophobic
C10CD1LEU- 1273.690Hydrophobic
C6CBALA- 1294.220Hydrophobic
C9CG1ILE- 1533.430Hydrophobic
C10CZTYR- 1754.410Hydrophobic
O12OHTYR- 1752.61141.09H-Bond
(Protein Donor)
C18CG2THR- 1833.380Hydrophobic
C1CG2THR- 1833.660Hydrophobic
O22NGLY- 1843.19168.02H-Bond
(Protein Donor)
C10CE1PHE- 2124.080Hydrophobic
C18CE1PHE- 2124.360Hydrophobic
O22NGLY- 2132.66169.81H-Bond
(Protein Donor)
O20NGLY- 2342.91163.13H-Bond
(Protein Donor)
O20NSER- 2353.29137.06H-Bond
(Protein Donor)
O21NSER- 2352.73153.29H-Bond
(Protein Donor)
O20OHOH- 21562.9163.57H-Bond
(Protein Donor)
O20OHOH- 21882.54162.87H-Bond
(Protein Donor)