Ligand profile

QSP

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

Bound to: KP13_03277 — 2-oxoglutarate dehydrogenase E1 component

Via homolog PDB 6r29 UniProt A0R2B1 Formula C₁₆H₂₇N₄O₁₃P₃S
Mol. weight 608.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
QSP
PDB
6r29
UniProt (similar protein)
A0R2B1
Target protein
KP13_03277

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 608.40 Da
LogP (Crippen) 0.82
H-bond donors 8
H-bond acceptors 12
TPSA 283.39 Ų
Rotatable bonds 13
Aromatic rings 1 / 2
Heavy atoms 37
Fraction sp³ C 0.56
Formula C₁₆H₂₇N₄O₁₃P₃S

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 283.4
  • −1 ≤ LogP ≤ 5 0.82
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 608.4
  • LogP ≤ 5 0.82
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 283.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ncc(c(n1)N)CN2[C@H](SC(=C2C)CCOP(=O)(O)OP(=O)(O)O)[C@@](CCC(=O)O)(O)P(=O)(O)O
InChI 
InChI=1S/C16H27N4O13P3S/c1-9-12(4-6-32-36(30,31)33-35(27,28)29)37-15(16(23,34(24,25)26)5-3-13(21)22)20(9)8-11-7-18-10(2)19-14(11)17/h7,15,23H,3-6,8H2,1-2H3,(H,21,22)(H,30,31)(H2,17,18,19)(H2,24,25,26)(H2,27,28,29)/t15-,16+/m1/s1
InChIKey 
XWZWGSGHSWWOAH-CVEARBPZSA-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
PF00676' '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_03277.

PDB 9

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)