Ligand profile

DPM

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

Bound to: KP13_01706 — Porphobilinogen deaminase

Via homolog PDB 1ah5 UniProt P06983 Formula C₂₀H₂₄N₂O₈
Mol. weight 420.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DPM
PDB
1ah5
UniProt (similar protein)
P06983
Target protein
KP13_01706

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 420.42 Da
LogP (Crippen) 1.53
H-bond donors 6
H-bond acceptors 4
TPSA 180.78 Ų
Rotatable bonds 12
Aromatic rings 2 / 2
Heavy atoms 30
Fraction sp³ C 0.40
Formula C₂₀H₂₄N₂O₈

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 180.8
  • −1 ≤ LogP ≤ 5 1.53
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 420.4
  • LogP ≤ 5 1.53
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 180.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c([nH]1)Cc2c(c(c[nH]2)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
InChI 
InChI=1S/C20H24N2O8/c1-10-13(6-19(27)28)12(3-5-18(25)26)16(22-10)8-15-14(7-20(29)30)11(9-21-15)2-4-17(23)24/h9,21-22H,2-8H2,1H3,(H,23,24)(H,25,26)(H,27,28)(H,29,30)
InChIKey 
LCAXMKQKEYTFDM-UHFFFAOYSA-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)