Ligand profile

ZINC8551188

Virtual-screening candidate from ZINC.

Bound to: VK055_0213 — 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase

Via homolog UniProt P9WKG7 Formula C₁₂H₂₁N₃O₁₃P₂
Tanimoto 0.75
Mol. weight 477.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC8551188
UniProt (similar protein)
P9WKG7
Tanimoto
0.754
Target protein
VK055_0213

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 477.26 Da
LogP (Crippen) -2.95
H-bond donors 7
H-bond acceptors 14
TPSA 253.35 Ų
Rotatable bonds 10
Aromatic rings 1 / 2
Heavy atoms 30
Fraction sp³ C 0.67
Formula C₁₂H₂₁N₃O₁₃P₂

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 253.3
  • −1 ≤ LogP ≤ 5 -2.95
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 477.3
  • LogP ≤ 5 -2.95
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 253.3
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)O[P@](=O)(O)OC[C@@H](O)CO)[C@@H](O)[C@H]2O)c(=O)n1
InChI 
InChI=1S/C12H21N3O13P2/c13-8-1-2-15(12(20)14-8)11-10(19)9(18)7(27-11)5-26-30(23,24)28-29(21,22)25-4-6(17)3-16/h1-2,6-7,9-11,16-19H,3-5H2,(H,21,22)(H,23,24)(H2,13,14,20)/t6-,7+,9+,10+,11+/m0/s1
InChIKey 
HHPOUCCVONEPRK-CNYIRLTGSA-N

Provenance

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

Method
LigQ nearest_k
Query
CDM
Homolog
P9WKG7

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_0213.

PDB 2

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)