Ligand profile

LYZ

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

Bound to: VK055_4699 — dihydrodipicolinate synthase

Via homolog PDB 3tce UniProt D0CFC3 Formula C₆H₁₄N₂O₃
Mol. weight 162.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LYZ
PDB
3tce
UniProt (similar protein)
D0CFC3
Target protein
VK055_4699

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 162.19 Da
LogP (Crippen) -1.50
H-bond donors 4
H-bond acceptors 4
TPSA 109.57 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 11
Fraction sp³ C 0.83
Formula C₆H₁₄N₂O₃

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 109.6
  • −1 ≤ LogP ≤ 5 -1.50
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 162.2
  • LogP ≤ 5 -1.50
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 109.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C[C@@H](C(=O)O)N)[C@H](CN)O
InChI 
InChI=1S/C6H14N2O3/c7-3-4(9)1-2-5(8)6(10)11/h4-5,9H,1-3,7-8H2,(H,10,11)/t4-,5+/m1/s1
InChIKey 
YSMODUONRAFBET-UHNVWZDZSA-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
PF00701

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_4699.

PDB 6

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

Ligand PDB entry

ChEMBL 1

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)