Ligand profile

DDU

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

Bound to: KP13_02286 — Thymidylate synthase

Via homolog PDB 1aob UniProt P0A884 Formula C₉H₁₂N₂O₄
Mol. weight 212.20 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DDU
PDB
1aob
UniProt (similar protein)
P0A884
Target protein
KP13_02286

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 212.20 Da
LogP (Crippen) -0.80
H-bond donors 2
H-bond acceptors 5
TPSA 84.32 Ų
Rotatable bonds 1
Aromatic rings 1 / 2
Heavy atoms 15
Fraction sp³ C 0.56
Formula C₉H₁₂N₂O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 84.3
  • −1 ≤ LogP ≤ 5 -0.80
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 212.2
  • LogP ≤ 5 -0.80
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 84.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1[C@H](C[C@@H](O1)N2C=CC(=O)NC2=O)O
InChI 
InChI=1S/C9H12N2O4/c1-5-6(12)4-8(15-5)11-3-2-7(13)10-9(11)14/h2-3,5-6,8,12H,4H2,1H3,(H,10,13,14)/t5-,6+,8-/m1/s1
InChIKey 
FDCFKLBIAIKUKB-GKROBHDKSA-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
PF00303

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_02286.

PDB 32

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

Ligand PDB entry

ChEMBL 100

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)