Ligand profile

PHY

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

Bound to: VK055_2233 — D-alanine-D-alanine ligase A

Via homolog PDB 1e4e UniProt P25051 Formula C₆H₁₅NO₇P₂
Mol. weight 275.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PHY
PDB
1e4e
UniProt (similar protein)
P25051
Target protein
VK055_2233

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 275.13 Da
LogP (Crippen) 0.40
H-bond donors 4
H-bond acceptors 5
TPSA 147.15 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.83
Formula C₆H₁₅NO₇P₂

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 147.2
  • −1 ≤ LogP ≤ 5 0.40
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 275.1
  • LogP ≤ 5 0.40
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 147.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](C[P@](=O)([C@@H](C)N)OP(=O)(O)O)C(=O)O
InChI 
InChI=1S/C6H15NO7P2/c1-4(6(8)9)3-15(10,5(2)7)14-16(11,12)13/h4-5H,3,7H2,1-2H3,(H,8,9)(H2,11,12,13)/t4-,5-,15+/m0/s1
InChIKey 
BAIYWTZQRMCJBV-DKDXWZAISA-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
PF01820' 'PF07478

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_2233.

PDB 3

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)