Ligand profile

3NM

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

Bound to: VK055_3099 — thiamine-phosphate pyrophosphorylase

Via homolog PDB 3o15 UniProt P39594 Formula C₇H₁₀NO₆PS
Mol. weight 267.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3NM
PDB
3o15
UniProt (similar protein)
P39594
Target protein
VK055_3099

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 267.20 Da
LogP (Crippen) 0.80
H-bond donors 3
H-bond acceptors 5
TPSA 116.95 Ų
Rotatable bonds 5
Aromatic rings 1 / 1
Heavy atoms 16
Fraction sp³ C 0.43
Formula C₇H₁₀NO₆PS

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 117.0
  • −1 ≤ LogP ≤ 5 0.80
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 267.2
  • LogP ≤ 5 0.80
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 117.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc(n1)C(=O)O)CCOP(=O)(O)O
InChI 
InChI=1S/C7H10NO6PS/c1-4-5(2-3-14-15(11,12)13)16-6(8-4)7(9)10/h2-3H2,1H3,(H,9,10)(H2,11,12,13)
InChIKey 
XWECMAHAKFWYNV-UHFFFAOYSA-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
PF02581

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_3099.

PDB 9

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)