Ligand profile

APO

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

Bound to: VK055_0988 — fumarate hydratase, class II

Via homolog PDB 7lub UniProt P07954 Formula C₃H₈NO₅P
Mol. weight 169.07 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
APO
PDB
7lub
UniProt (similar protein)
P07954
Target protein
VK055_0988

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 169.07 Da
LogP (Crippen) -1.42
H-bond donors 4
H-bond acceptors 3
TPSA 120.85 Ų
Rotatable bonds 3
Aromatic rings 0 / 0
Heavy atoms 10
Fraction sp³ C 0.67
Formula C₃H₈NO₅P

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 120.8
  • −1 ≤ LogP ≤ 5 -1.42
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 169.1
  • LogP ≤ 5 -1.42
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 120.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H](C(=O)O)N)P(=O)(O)O
InChI 
InChI=1S/C3H8NO5P/c4-2(3(5)6)1-10(7,8)9/h2H,1,4H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1
InChIKey 
LBTABPSJONFLPO-UWTATZPHSA-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
PF00206

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_0988.

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)