Ligand profile

2TL

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

Bound to: VK055_2645 — putative D-serine deaminase (D-serine dehydratase) protein

Via homolog PDB 3wqe UniProt B2DFG5 Formula C₄H₉NO₃
Mol. weight 119.12 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2TL
PDB
3wqe
UniProt (similar protein)
B2DFG5
Target protein
VK055_2645

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 119.12 Da
LogP (Crippen) -1.22
H-bond donors 3
H-bond acceptors 3
TPSA 83.55 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 8
Fraction sp³ C 0.75
Formula C₄H₉NO₃

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 83.5
  • −1 ≤ LogP ≤ 5 -1.22
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 119.1
  • LogP ≤ 5 -1.22
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 83.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]([C@H](C(=O)O)N)O
InChI 
InChI=1S/C4H9NO3/c1-2(6)3(5)4(7)8/h2-3,6H,5H2,1H3,(H,7,8)/t2-,3-/m1/s1
InChIKey 
AYFVYJQAPQTCCC-PWNYCUMCSA-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
PF01168' 'PF14031

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_2645.

PDB 1

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

Ligand PDB entry

ZINC 14

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

Compound Similarity (Tanimoto)