Ligand profile

DI6

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

Bound to: KP13_03018 — Imidazolonepropionase

Via homolog PDB 2q09 UniProt A0KF84 Formula C₆H₈N₂O₄
Mol. weight 172.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DI6
PDB
2q09
UniProt (similar protein)
A0KF84
Target protein
KP13_03018

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 172.14 Da
LogP (Crippen) -0.94
H-bond donors 3
H-bond acceptors 3
TPSA 95.50 Ų
Rotatable bonds 3
Aromatic rings 0 / 1
Heavy atoms 12
Fraction sp³ C 0.50
Formula C₆H₈N₂O₄

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 95.5
  • −1 ≤ LogP ≤ 5 -0.94
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 172.1
  • LogP ≤ 5 -0.94
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 95.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CC(=O)O)[C@H]1C(=O)NC(=O)N1
InChI 
InChI=1S/C6H8N2O4/c9-4(10)2-1-3-5(11)8-6(12)7-3/h3H,1-2H2,(H,9,10)(H2,7,8,11,12)/t3-/m0/s1
InChIKey 
VWFWNXQAMGDPGG-VKHMYHEASA-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
PF01979

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_03018.

PDB 3

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

Ligand PDB entry

ChEMBL 3

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)