Ligand profile

PA5

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

Bound to: VK055_3061 — phosphoglucose isomerase family protein

Via homolog PDB 1g98 UniProt Q9N1E2 Formula C₅H₁₁O₉P
Mol. weight 246.11 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PA5
PDB
1g98
UniProt (similar protein)
Q9N1E2
Target protein
VK055_3061

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 246.11 Da
LogP (Crippen) -2.74
H-bond donors 6
H-bond acceptors 6
TPSA 164.75 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 15
Fraction sp³ C 0.80
Formula C₅H₁₁O₉P

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 164.8
  • −1 ≤ LogP ≤ 5 -2.74
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 246.1
  • LogP ≤ 5 -2.74
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 164.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]([C@H]([C@@H](C(=O)O)O)O)O)OP(=O)(O)O
InChI 
InChI=1S/C5H11O9P/c6-2(1-14-15(11,12)13)3(7)4(8)5(9)10/h2-4,6-8H,1H2,(H,9,10)(H2,11,12,13)/t2-,3-,4+/m1/s1
InChIKey 
HNECGPFIYSOYHF-JJYYJPOSSA-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
PF00342

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_3061.

PDB 8

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

Ligand PDB entry

ChEMBL 2

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)