Ligand profile

ZINC12506615

Virtual-screening candidate from ZINC.

Bound to: VK055_4699 — dihydrodipicolinate synthase

Via homolog UniProt D0CFC3 Formula C₆H₁₀F₃NO₃
Tanimoto 0.57
Mol. weight 201.14 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12506615
UniProt (similar protein)
D0CFC3
Tanimoto
0.571
Target protein
VK055_4699

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 201.14 Da
LogP (Crippen) 0.10
H-bond donors 3
H-bond acceptors 3
TPSA 83.55 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 0.83
Formula C₆H₁₀F₃NO₃

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 83.5
  • −1 ≤ LogP ≤ 5 0.10
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 201.1
  • LogP ≤ 5 0.10
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 83.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@@H](CC[C@H](O)C(F)(F)F)C(=O)O
InChI 
InChI=1S/C6H10F3NO3/c7-6(8,9)4(11)2-1-3(10)5(12)13/h3-4,11H,1-2,10H2,(H,12,13)/t3-,4-/m0/s1
InChIKey 
DYHJIJZBSHWATM-IMJSIDKUSA-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 VK055_4699.

PDB 7

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 49

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

Compound Similarity (Tanimoto)