Ligand profile

1NT

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

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

Via homolog PDB 2nxg UniProt O66496 Formula C₈H₁₈O₁₅P₂
Mol. weight 416.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1NT
PDB
2nxg
UniProt (similar protein)
O66496
Target protein
VK055_0220

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 416.17 Da
LogP (Crippen) -4.19
H-bond donors 10
H-bond acceptors 10
TPSA 271.97 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 25
Fraction sp³ C 0.88
Formula C₈H₁₈O₁₅P₂

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 272.0
  • −1 ≤ LogP ≤ 5 -4.19
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 416.2
  • LogP ≤ 5 -4.19
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 272.0
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@@](C(=O)O)(O)OP(=O)(O)O
InChI 
InChI=1S/C8H18O15P2/c9-3(1-8(15,7(13)14)23-25(19,20)21)5(11)6(12)4(10)2-22-24(16,17)18/h3-6,9-12,15H,1-2H2,(H,13,14)(H2,16,17,18)(H2,19,20,21)/t3-,4-,5-,6-,8-/m1/s1
InChIKey 
FGVVFQVXYXTAAW-HXUQBWEZSA-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)