Ligand profile

TDK

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

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

Via homolog PDB 6ouv UniProt Q9RUB5 Formula C₁₅H₂₆N₄O₁₁P₃S⁺
Mol. weight 563.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TDK
PDB
6ouv
UniProt (similar protein)
Q9RUB5
Target protein
HT085_RS00175

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 563.38 Da
LogP (Crippen) 0.84
H-bond donors 6
H-bond acceptors 11
TPSA 235.73 Ų
Rotatable bonds 11
Aromatic rings 2 / 2
Heavy atoms 34
Fraction sp³ C 0.53
Formula C₁₅H₂₆N₄O₁₁P₃S⁺

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 235.7
  • −1 ≤ LogP ≤ 5 0.84
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 563.4
  • LogP ≤ 5 0.84
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 235.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)[P@@](=O)(O)OC)CCO[P@@](=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C15H25N4O11P3S/c1-9-12(5-6-29-33(26,27)30-32(23,24)25)34-14(15(3,20)31(21,22)28-4)19(9)8-11-7-17-10(2)18-13(11)16/h7,20H,5-6,8H2,1-4H3,(H5-,16,17,18,21,22,23,24,25,26,27)/p+1/t15-/m0/s1
InChIKey 
ILGXNMPRCMTAOK-HNNXBMFYSA-O

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
PF02779' 'PF13292

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 9

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

Ligand PDB entry

ChEMBL 30

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)