Ligand profile

ZINC5113224

Virtual-screening candidate from ZINC.

Bound to: KP13_01654 — Dihydrodipicolinate synthase

Via homolog UniProt D0CFC3 Formula C₁₂H₂₅N₃O₅
Tanimoto 0.52
Mol. weight 291.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5113224
UniProt (similar protein)
D0CFC3
Tanimoto
0.515
Target protein
KP13_01654

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 291.35 Da
LogP (Crippen) -1.29
H-bond donors 6
H-bond acceptors 6
TPSA 158.90 Ų
Rotatable bonds 12
Aromatic rings 0 / 0
Heavy atoms 20
Fraction sp³ C 0.83
Formula C₁₂H₂₅N₃O₅

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 158.9
  • −1 ≤ LogP ≤ 5 -1.29
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 291.3
  • LogP ≤ 5 -1.29
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 158.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@@H](CC[C@H](O)CNCCCC[C@@H](N)C(=O)O)C(=O)O
InChI 
InChI=1S/C12H25N3O5/c13-9(11(17)18)3-1-2-6-15-7-8(16)4-5-10(14)12(19)20/h8-10,15-16H,1-7,13-14H2,(H,17,18)(H,19,20)/t8-,9+,10-/m0/s1
InChIKey 
SWTKBYSXMULFHZ-AEJSXWLSSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
LYZ
Homolog
D0CFC3

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_01654.

PDB 11

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)