Ligand profile

1N5

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

Bound to: VK055_4863 — L-rhamnonate dehydratase

Via homolog PDB 3cxo UniProt Q8ZNF9 Formula C₇H₁₄O₅
Mol. weight 178.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1N5
PDB
3cxo
UniProt (similar protein)
Q8ZNF9
Target protein
VK055_4863

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 178.18 Da
LogP (Crippen) -1.04
H-bond donors 4
H-bond acceptors 4
TPSA 97.99 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.86
Formula C₇H₁₄O₅

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 98.0
  • −1 ≤ LogP ≤ 5 -1.04
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 178.2
  • LogP ≤ 5 -1.04
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 98.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C[C@@H](C[C@H](C(=O)O)O)O)CO
InChI 
InChI=1S/C7H14O5/c8-3-1-2-5(9)4-6(10)7(11)12/h5-6,8-10H,1-4H2,(H,11,12)/t5-,6+/m0/s1
InChIKey 
UZWBQTOHZVUOKI-NTSWFWBYSA-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
PF13378

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_4863.

PDB 9

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)