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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:

1k8z

1.700 Å

X-ray

2001-10-26

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
A96 %
B4 %


Ligand binding site composition:

B-Factor:27.603
Number of residues:25
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.469543.375

% Hydrophobic% Polar
62.1137.89
According to VolSite

Ligand :
1k8z_1 Structure
HET Code: IAG
Formula: C12H11N2O3
Molecular weight: 231.227 g/mol
DrugBank ID: DB07952
Buried Surface Area:69.34 %
Polar Surface area: 85.02 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
50.443927.010614.1644


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
C9CD2PHE- 223.240Hydrophobic
O1OE1GLU- 492.69159.35H-Bond
(Protein Donor)
C6CBALA- 594.120Hydrophobic
N1OD2ASP- 603.43158.96H-Bond
(Ligand Donor)
C9CGLEU- 1004.320Hydrophobic
C3CD2LEU- 1003.620Hydrophobic
C5CBALA- 1294.040Hydrophobic
C4CD1ILE- 1533.840Hydrophobic
O1OHTYR- 1752.53156.75H-Bond
(Protein Donor)
C3CE1PHE- 2123.470Hydrophobic
O2NGLY- 2343.17135.35H-Bond
(Protein Donor)
O3NSER- 2353.31122.96H-Bond
(Protein Donor)
O2NSER- 2353.07174.15H-Bond
(Protein Donor)
O2OHOH- 5452.7145.05H-Bond
(Protein Donor)