Ligand profile

1D0

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

Bound to: VK055_1196 — tryptophan synthase, beta subunit

Via homolog PDB 4hpj UniProt P0A2K1 Formula C₁₇H₂₀N₃O₈P
Mol. weight 425.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1D0
PDB
4hpj
UniProt (similar protein)
P0A2K1
Target protein
VK055_1196

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 425.33 Da
LogP (Crippen) 1.55
H-bond donors 6
H-bond acceptors 8
TPSA 181.80 Ų
Rotatable bonds 9
Aromatic rings 2 / 2
Heavy atoms 29
Fraction sp³ C 0.24
Formula C₁₇H₂₀N₃O₈P

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 181.8
  • −1 ≤ LogP ≤ 5 1.55
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 425.3
  • LogP ≤ 5 1.55
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 181.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C(\CNc2ccccc2O)/C(=O)O)O
InChI 
InChI=1S/C17H20N3O8P/c1-10-16(22)12(11(6-18-10)9-28-29(25,26)27)7-19-14(17(23)24)8-20-13-4-2-3-5-15(13)21/h2-6,20-22H,7-9H2,1H3,(H,23,24)(H2,25,26,27)/b19-14+
InChIKey 
MKNJFLJOSVXALN-XMHGGMMESA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF00291

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_1196.

PDB 40

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)