Ligand profile

ZINC2563982

Virtual-screening candidate from ZINC.

Bound to: VK055_3078 — isocitrate lyase

Via homolog UniProt P9WKK7 Formula C₈H₈O₉
Tanimoto 0.69
Mol. weight 248.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2563982
UniProt (similar protein)
P9WKK7
Tanimoto
0.688
Target protein
VK055_3078

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 248.14 Da
LogP (Crippen) -1.68
H-bond donors 4
H-bond acceptors 5
TPSA 158.43 Ų
Rotatable bonds 4
Aromatic rings 0 / 1
Heavy atoms 17
Fraction sp³ C 0.50
Formula C₈H₈O₉

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 158.4
  • −1 ≤ LogP ≤ 5 -1.68
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 248.1
  • LogP ≤ 5 -1.68
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 158.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)[C@H]1O[C@H](C(=O)O)[C@@H](C(=O)O)[C@@H]1C(=O)O
InChI 
InChI=1S/C8H8O9/c9-5(10)1-2(6(11)12)4(8(15)16)17-3(1)7(13)14/h1-4H,(H,9,10)(H,11,12)(H,13,14)(H,15,16)/t1-,2-,3-,4-/m0/s1
InChIKey 
UFOIOXZLTXNHQH-LDHWTSMMSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
U9S
Homolog
P9WKK7

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 9

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 49

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

Compound Similarity (Tanimoto)