Ligand profile

ZINC33913782

Virtual-screening candidate from ZINC.

Bound to: VK055_1539 — 3-deoxy-D-manno-octulosonate cytidylyltransferase

Via homolog UniProt P44490 Formula C₉H₁₅N₃O₁₁P₂
Tanimoto 0.60
Mol. weight 403.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC33913782
UniProt (similar protein)
P44490
Tanimoto
0.600
Target protein
VK055_1539

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 403.18 Da
LogP (Crippen) -2.33
H-bond donors 6
H-bond acceptors 11
TPSA 223.89 Ų
Rotatable bonds 6
Aromatic rings 1 / 2
Heavy atoms 25
Fraction sp³ C 0.56
Formula C₉H₁₅N₃O₁₁P₂

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 223.9
  • −1 ≤ LogP ≤ 5 -2.33
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 403.2
  • LogP ≤ 5 -2.33
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 223.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[C@H](O)[C@@H]2O)c(=O)n1
InChI 
InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6+,7+,8-/m1/s1
InChIKey 
ZWIADYZPOWUWEW-YDKYIBAVSA-N

Provenance

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

Method
LigQ nearest_k
Query
CMK
Homolog
P44490

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_1539.

PDB 1

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)