Ligand profile

U9S

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

Bound to: VK055_3078 — isocitrate lyase

Via homolog PDB 6wsi UniProt P9WKK7 Formula C₄H₄O₅
Mol. weight 132.07 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
U9S
PDB
6wsi
UniProt (similar protein)
P9WKK7
Target protein
VK055_3078

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 132.07 Da
LogP (Crippen) -1.08
H-bond donors 2
H-bond acceptors 3
TPSA 87.13 Ų
Rotatable bonds 2
Aromatic rings 0 / 1
Heavy atoms 9
Fraction sp³ C 0.50
Formula C₄H₄O₅

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 87.1
  • −1 ≤ LogP ≤ 5 -1.08
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 132.1
  • LogP ≤ 5 -1.08
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 87.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[C@@H]1([C@H](O1)C(=O)O)C(=O)O
InChI 
InChI=1S/C4H4O5/c5-3(6)1-2(9-1)4(7)8/h1-2H,(H,5,6)(H,7,8)/t1-,2+
InChIKey 
DCEMCPAKSGRHCN-XIXRPRMCSA-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
PF00463

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_3078.

PDB 8

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

Ligand PDB entry

ChEMBL 7

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)