Ligand profile

DN9

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

Bound to: VK055_4273 — diaminopimelate decarboxylase

Via homolog PDB 6knk UniProt A0A0H3JPF2 Formula C₁₆H₂₄N₃O₁₁P
Mol. weight 465.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DN9
PDB
6knk
UniProt (similar protein)
A0A0H3JPF2
Target protein
VK055_4273

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 465.35 Da
LogP (Crippen) -1.41
H-bond donors 8
H-bond acceptors 9
TPSA 235.84 Ų
Rotatable bonds 13
Aromatic rings 1 / 1
Heavy atoms 31
Fraction sp³ C 0.50
Formula C₁₆H₂₄N₃O₁₁P

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 235.8
  • −1 ≤ LogP ≤ 5 -1.41
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 465.4
  • LogP ≤ 5 -1.41
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 235.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CNCCNC(=O)C[C@](CC(=O)O)(C(=O)O)O)O
InChI 
InChI=1S/C16H24N3O11P/c1-9-14(23)11(10(6-19-9)8-30-31(27,28)29)7-17-2-3-18-12(20)4-16(26,15(24)25)5-13(21)22/h6,17,23,26H,2-5,7-8H2,1H3,(H,18,20)(H,21,22)(H,24,25)(H2,27,28,29)/t16-/m0/s1
InChIKey 
LHKUXYWSSPZJHQ-INIZCTEOSA-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
PF00278' 'PF02784

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4273.

PDB 5

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)