Ligand profile

ZINC8216134

Virtual-screening candidate from ZINC.

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

Via homolog UniProt P44490 Formula C₁₁H₂₀N₄O₁₁P₂
Tanimoto 0.57
Mol. weight 446.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC8216134
UniProt (similar protein)
P44490
Tanimoto
0.568
Target protein
VK055_1539

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 446.25 Da
LogP (Crippen) -2.35
H-bond donors 6
H-bond acceptors 13
TPSA 238.91 Ų
Rotatable bonds 9
Aromatic rings 1 / 2
Heavy atoms 28
Fraction sp³ C 0.64
Formula C₁₁H₂₀N₄O₁₁P₂

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 238.9
  • −1 ≤ LogP ≤ 5 -2.35
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 446.2
  • LogP ≤ 5 -2.35
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 238.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NCCO[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/C11H20N4O11P2/c12-2-4-23-27(19,20)26-28(21,22)24-5-6-8(16)9(17)10(25-6)15-3-1-7(13)14-11(15)18/h1,3,6,8-10,16-17H,2,4-5,12H2,(H,19,20)(H,21,22)(H2,13,14,18)/t6-,8-,9-,10-/m1/s1
InChIKey 
WVIMUEUQJFPNDK-PEBGCTIMSA-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)