Ligand profile

29P

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

Bound to: KP13_01706 — Porphobilinogen deaminase

Via homolog PDB 4mlq UniProt Q8GCA8 Formula C₂₀H₂₄N₂O₉
Mol. weight 436.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
29P
PDB
4mlq
UniProt (similar protein)
Q8GCA8
Target protein
KP13_01706

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 436.42 Da
LogP (Crippen) 0.64
H-bond donors 6
H-bond acceptors 5
TPSA 194.09 Ų
Rotatable bonds 12
Aromatic rings 1 / 2
Heavy atoms 31
Fraction sp³ C 0.45
Formula C₂₀H₂₄N₂O₉

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 194.1
  • −1 ≤ LogP ≤ 5 0.64
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 436.4
  • LogP ≤ 5 0.64
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 194.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c([nH]1)C[C@H]2C(=C(C(=O)N2)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
InChI 
InChI=1S/C20H24N2O9/c1-9-12(6-18(27)28)10(2-4-16(23)24)14(21-9)8-15-13(7-19(29)30)11(20(31)22-15)3-5-17(25)26/h15,21H,2-8H2,1H3,(H,22,31)(H,23,24)(H,25,26)(H,27,28)(H,29,30)/t15-/m0/s1
InChIKey 
DHEOBTWDCMSDOQ-HNNXBMFYSA-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
PF01379' 'PF03900

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_01706.

PDB 5

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 1

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)