Ligand profile

C

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

Bound to: VK055_3750 — translation elongation factor Tu

Via homolog PDB 4v5p UniProt Q5SHN6 Formula C₉H₁₄N₃O₈P
Mol. weight 323.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C
PDB
4v5p
UniProt (similar protein)
Q5SHN6
Target protein
VK055_3750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 323.20 Da
LogP (Crippen) -2.45
H-bond donors 5
H-bond acceptors 9
TPSA 177.36 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 21
Fraction sp³ C 0.56
Formula C₉H₁₄N₃O₈P

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 177.4
  • −1 ≤ LogP ≤ 5 -2.45
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 323.2
  • LogP ≤ 5 -2.45
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 177.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
InChI 
InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKey 
IERHLVCPSMICTF-XVFCMESISA-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
PF00276

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_3750.

PDB 19

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)