Ligand profile

CDM

Ligand co-crystallized with a similar protein (Protein Data Bank).

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

Via homolog PDB 3pye UniProt P9WKG7 Formula C₁₄H₂₅N₃O₁₄P₂
Mol. weight 521.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CDM
PDB
3pye
UniProt (similar protein)
P9WKG7
Target protein
VK055_0213

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 521.31 Da
LogP (Crippen) -3.20
H-bond donors 8
H-bond acceptors 15
TPSA 273.58 Ų
Rotatable bonds 11
Aromatic rings 1 / 2
Heavy atoms 33
Fraction sp³ C 0.71
Formula C₁₄H₂₅N₃O₁₄P₂

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 273.6
  • −1 ≤ LogP ≤ 5 -3.20
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 521.3
  • LogP ≤ 5 -3.20
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 273.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O)O)O
InChI 
InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1
InChIKey 
YFAUKWZNPVBCFF-XHIBXCGHSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00288

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 1

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)