Ligand profile

HPD

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

Bound to: VK055_2594 — deoxyribose-phosphate aldolase

Via homolog PDB 1jcj UniProt P0A6L0 Formula C₅H₁₃O₇P
Mol. weight 216.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HPD
PDB
1jcj
UniProt (similar protein)
P0A6L0
Target protein
VK055_2594

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 216.13 Da
LogP (Crippen) -1.80
H-bond donors 5
H-bond acceptors 5
TPSA 127.45 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 1.00
Formula C₅H₁₃O₇P

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 127.5
  • −1 ≤ LogP ≤ 5 -1.80
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 216.1
  • LogP ≤ 5 -1.80
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 127.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CO)[C@@H]([C@@H](COP(=O)(O)O)O)O
InChI 
InChI=1S/C5H13O7P/c6-2-1-4(7)5(8)3-12-13(9,10)11/h4-8H,1-3H2,(H2,9,10,11)/t4-,5+/m0/s1
InChIKey 
YCHBTVQJICBXEI-CRCLSJGQSA-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
PF01791

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_2594.

PDB 2

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

Ligand PDB entry

ChEMBL 1

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)