Ligand profile

T6F

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

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

Via homolog PDB 6ha3 UniProt P29401 Formula C₁₈H₃₂N₄O₁₆P₃S⁺
Mol. weight 685.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
T6F
PDB
6ha3
UniProt (similar protein)
P29401
Target protein
HT085_RS00175

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 685.46 Da
LogP (Crippen) -2.79
H-bond donors 11
H-bond acceptors 15
TPSA 336.88 Ų
Rotatable bonds 16
Aromatic rings 2 / 2
Heavy atoms 42
Fraction sp³ C 0.61
Formula C₁₈H₃₂N₄O₁₆P₃S⁺

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 336.9
  • −1 ≤ LogP ≤ 5 -2.79
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 685.5
  • LogP ≤ 5 -2.79
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 336.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](CO)([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O)CCO[P@@](=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C18H31N4O16P3S/c1-9-13(3-4-36-41(34,35)38-40(31,32)33)42-17(22(9)6-11-5-20-10(2)21-16(11)19)18(27,8-23)15(26)14(25)12(24)7-37-39(28,29)30/h5,12,14-15,23-27H,3-4,6-8H2,1-2H3,(H6-,19,20,21,28,29,30,31,32,33,34,35)/p+1/t12-,14-,15+,18+/m1/s1
InChIKey 
AJFWOWNNZFXSES-TXPWEPMLSA-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
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 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)