Ligand profile

ZINC106404522

Virtual-screening candidate from ZINC.

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

Via homolog UniProt P44490 Formula C₁₄H₂₇N₄O₁₁P₂⁺
Tanimoto 0.54
Mol. weight 489.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC106404522
UniProt (similar protein)
P44490
Tanimoto
0.538
Target protein
VK055_1539

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 489.34 Da
LogP (Crippen) -1.60
H-bond donors 5
H-bond acceptors 12
TPSA 212.89 Ų
Rotatable bonds 10
Aromatic rings 1 / 2
Heavy atoms 31
Fraction sp³ C 0.71
Formula C₁₄H₂₇N₄O₁₁P₂⁺

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 212.9
  • −1 ≤ LogP ≤ 5 -1.60
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 489.3
  • LogP ≤ 5 -1.60
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 212.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1O[C@H](n2ccc(N)nc2=O)[C@H](O)[C@H]1O
InChI 
InChI=1S/C14H26N4O11P2/c1-18(2,3)6-7-26-30(22,23)29-31(24,25)27-8-9-11(19)12(20)13(28-9)17-5-4-10(15)16-14(17)21/h4-5,9,11-13,19-20H,6-8H2,1-3H3,(H3-,15,16,21,22,23,24,25)/p+1/t9-,11-,12+,13-/m0/s1
InChIKey 
RZZPDXZPRHQOCG-SYEHKZFSSA-O

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)