Ligand profile

8ML

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

Bound to: KP13_32378 — transketolase 2

Via homolog PDB 5xtx UniProt P34736 Formula C₁₈H₃₃N₄O₁₆P₃S
Mol. weight 686.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8ML
PDB
5xtx
UniProt (similar protein)
P34736
Target protein
KP13_32378

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 686.46 Da
LogP (Crippen) -2.34
H-bond donors 11
H-bond acceptors 16
TPSA 336.24 Ų
Rotatable bonds 16
Aromatic rings 1 / 2
Heavy atoms 42
Fraction sp³ C 0.67
Formula C₁₈H₃₃N₄O₁₆P₃S

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 336.2
  • −1 ≤ LogP ≤ 5 -2.34
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 686.5
  • LogP ≤ 5 -2.34
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 336.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ncc(c(n1)N)CN2C(SC(C2=C)CCOP(=O)(O)OP(=O)(O)O)[C@](CO)([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O
InChI 
InChI=1S/C18H33N4O16P3S/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/h5,12-15,17,23-27H,1,3-4,6-8H2,2H3,(H,34,35)(H2,19,20,21)(H2,28,29,30)(H2,31,32,33)/t12-,13?,14-,15+,17?,18+/m1/s1
InChIKey 
MJHVDDPQXKRRMA-SSHSPUMGSA-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
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)