Ligand profile

T5X

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

Bound to: KP13_32378 — transketolase 2

Via homolog PDB 5xqk UniProt P34736 Formula C₁₇H₃₀N₄O₁₅P₃S⁺
Mol. weight 655.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
T5X
PDB
5xqk
UniProt (similar protein)
P34736
Target protein
KP13_32378

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 655.43 Da
LogP (Crippen) -2.15
H-bond donors 10
H-bond acceptors 14
TPSA 316.65 Ų
Rotatable bonds 15
Aromatic rings 2 / 2
Heavy atoms 40
Fraction sp³ C 0.59
Formula C₁₇H₃₀N₄O₁₅P₃S⁺

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 316.6
  • −1 ≤ LogP ≤ 5 -2.15
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 655.4
  • LogP ≤ 5 -2.15
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 316.6
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](COP(=O)(O)O)O)O)O)CCO[P@@](=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C17H29N4O15P3S/c1-9-13(3-4-34-39(32,33)36-38(29,30)31)40-16(21(9)6-11-5-19-10(2)20-15(11)18)17(25,8-22)14(24)12(23)7-35-37(26,27)28/h5,12,14,22-25H,3-4,6-8H2,1-2H3,(H6-,18,19,20,26,27,28,29,30,31,32,33)/p+1/t12-,14+,17+/m1/s1
InChIKey 
CRLXIEJPMQNLRP-IFIJOSMWSA-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 KP13_32378.

PDB 23

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)