Ligand profile

PRX

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

Bound to: KP13_00433 — Acetyl-coenzyme A synthetase

Via homolog PDB 1pg3 UniProt Q8ZKF6 Formula C₁₃H₂₀N₅O₇P
Mol. weight 389.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PRX
PDB
1pg3
UniProt (similar protein)
Q8ZKF6
Target protein
KP13_00433

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 389.31 Da
LogP (Crippen) -0.43
H-bond donors 4
H-bond acceptors 11
TPSA 175.07 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.62
Formula C₁₃H₂₀N₅O₇P

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 175.1
  • −1 ≤ LogP ≤ 5 -0.43
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 389.3
  • LogP ≤ 5 -0.43
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 175.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCO[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
InChI 
InChI=1S/C13H20N5O7P/c1-2-3-23-26(21,22)24-4-7-9(19)10(20)13(25-7)18-6-17-8-11(14)15-5-16-12(8)18/h5-7,9-10,13,19-20H,2-4H2,1H3,(H,21,22)(H2,14,15,16)/t7-,9-,10-,13-/m1/s1
InChIKey 
XAMXMSZRQHPMRX-QYVSTXNMSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00501

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_00433.

PDB 4

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)