Ligand profile

PAI

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

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

Via homolog PDB 1g7v UniProt P0A715 Formula C₉H₂₃NO₁₃P₂
Mol. weight 415.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PAI
PDB
1g7v
UniProt (similar protein)
P0A715
Target protein
VK055_0220

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 415.23 Da
LogP (Crippen) -4.71
H-bond donors 10
H-bond acceptors 10
TPSA 248.91 Ų
Rotatable bonds 12
Aromatic rings 0 / 0
Heavy atoms 25
Fraction sp³ C 1.00
Formula C₉H₂₃NO₁₃P₂

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 248.9
  • −1 ≤ LogP ≤ 5 -4.71
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 415.2
  • LogP ≤ 5 -4.71
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 248.9
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)[N@](CC(O)O)CP(=O)(O)O
InChI 
InChI=1S/C9H23NO13P2/c11-5(1-10(2-7(13)14)4-24(17,18)19)8(15)9(16)6(12)3-23-25(20,21)22/h5-9,11-16H,1-4H2,(H2,17,18,19)(H2,20,21,22)/t5-,6-,8-,9-/m1/s1
InChIKey 
ATILYNKCRYHYEP-SQEXRHODSA-N

Provenance

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

Method
LigQ sequence
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)