Ligand profile

KD0

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_0220 — 3-deoxy-8-phosphooctulonate synthase

Via homolog PDB 3und UniProt Q3JP68 Formula C₈H₁₅O₁₁P
Mol. weight 318.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KD0
PDB
3und
UniProt (similar protein)
Q3JP68
Target protein
VK055_0220

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 318.17 Da
LogP (Crippen) -3.42
H-bond donors 7
H-bond acceptors 8
TPSA 202.05 Ų
Rotatable bonds 9
Aromatic rings 0 / 0
Heavy atoms 20
Fraction sp³ C 0.75
Formula C₈H₁₅O₁₁P

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 202.0
  • −1 ≤ LogP ≤ 5 -3.42
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 318.2
  • LogP ≤ 5 -3.42
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 202.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O)C(=O)C(=O)O
InChI 
InChI=1S/C8H15O11P/c9-3(1-4(10)8(14)15)6(12)7(13)5(11)2-19-20(16,17)18/h3,5-7,9,11-13H,1-2H2,(H,14,15)(H2,16,17,18)/t3-,5-,6-,7-/m1/s1
InChIKey 
RTNBXJBOAIDPME-SHUUEZRQSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00793

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_0220.

PDB 8

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)