Ligand profile

1VU

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

Bound to: KP13_01043 — 3-ketoacyl-CoA thiolase

Via homolog PDB 6bjb UniProt F1KYX0 Formula C₂₄H₄₀N₇O₁₇P₃S
Mol. weight 823.61 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1VU
PDB
6bjb
UniProt (similar protein)
F1KYX0
Target protein
KP13_01043

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 823.61 Da
LogP (Crippen) -0.93
H-bond donors 9
H-bond acceptors 19
TPSA 363.63 Ų
Rotatable bonds 20
Aromatic rings 2 / 3
Heavy atoms 52
Fraction sp³ C 0.67
Formula C₂₄H₄₀N₇O₁₇P₃S

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 363.6
  • −1 ≤ LogP ≤ 5 -0.93
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 823.6
  • LogP ≤ 5 -0.93
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 363.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
InChI 
InChI=1S/C24H40N7O17P3S/c1-4-15(33)52-8-7-26-14(32)5-6-27-22(36)19(35)24(2,3)10-45-51(42,43)48-50(40,41)44-9-13-18(47-49(37,38)39)17(34)23(46-13)31-12-30-16-20(25)28-11-29-21(16)31/h11-13,17-19,23,34-35H,4-10H2,1-3H3,(H,26,32)(H,27,36)(H,40,41)(H,42,43)(H2,25,28,29)(H2,37,38,39)/t13-,17-,18-,19+,23-/m1/s1
InChIKey 
QAQREVBBADEHPA-IEXPHMLFSA-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
PF00108' 'PF02803

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_01043.

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)