Ligand profile

ZINC2539998

Virtual-screening candidate from ZINC.

Bound to: VK055_1442 — pyrimidine utilization protein D

Via homolog UniProt P96084 Formula C₁₂H₁₃NO₇
Tanimoto 0.65
Mol. weight 283.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2539998
UniProt (similar protein)
P96084
Tanimoto
0.645
Target protein
VK055_1442

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 283.24 Da
LogP (Crippen) -0.44
H-bond donors 4
H-bond acceptors 5
TPSA 147.15 Ų
Rotatable bonds 7
Aromatic rings 1 / 1
Heavy atoms 20
Fraction sp³ C 0.25
Formula C₁₂H₁₃NO₇

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 147.2
  • −1 ≤ LogP ≤ 5 -0.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 283.2
  • LogP ≤ 5 -0.44
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 147.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@H](Cc1ccc(OC(C(=O)O)C(=O)O)cc1)C(=O)O
InChI 
InChI=1S/C12H13NO7/c13-8(10(14)15)5-6-1-3-7(4-2-6)20-9(11(16)17)12(18)19/h1-4,8-9H,5,13H2,(H,14,15)(H,16,17)(H,18,19)/t8-/m1/s1
InChIKey 
SZIGXRNNKJDSAT-MRVPVSSYSA-N

Provenance

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

Method
LigQ nearest_k
Query
PHE
Homolog
P96084

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_1442.

PDB 5

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)