Ligand profile

CHEMBL430409

Bioactivity hit from ChEMBL on a similar protein.

Bound to: HT085_RS00175 — 1-deoxy-D-xylulose-5-phosphate synthase

Via homolog UniProt P29401 Formula C₁₃H₂₁N₄O₆P₂S⁺
pchembl 6.77 ~169.8 nM
Mol. weight 423.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL430409
UniProt (similar protein)
P29401
pchembl
6.770 (~169.8 nM)
Target protein
HT085_RS00175

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 423.35 Da
LogP (Crippen) 1.56
H-bond donors 3
H-bond acceptors 8
TPSA 148.74 Ų
Rotatable bonds 8
Aromatic rings 2 / 2
Heavy atoms 26
Fraction sp³ C 0.46
Formula C₁₃H₂₁N₄O₆P₂S⁺

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 148.7
  • −1 ≤ LogP ≤ 5 1.56
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 423.3
  • LogP ≤ 5 1.56
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 148.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ncc(C[n+]2csc(CCOP(C)(=O)OP(=O)(O)O)c2C)c(N)n1
InChI 
InChI=1S/C13H20N4O6P2S/c1-9-12(4-5-22-24(3,18)23-25(19,20)21)26-8-17(9)7-11-6-15-10(2)16-13(11)14/h6,8H,4-5,7H2,1-3H3,(H3-,14,15,16,19,20,21)/p+1
InChIKey 
SCVOPPSBAGJFBD-UHFFFAOYSA-O

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00456' 'PF02779

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to HT085_RS00175.

PDB 10

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

Ligand PDB entry

ChEMBL 29

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)