Ligand profile

HMH

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

Bound to: KP13_03172 — Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase bifunctional protein

Via homolog PDB 1jxi UniProt P55882 Formula C₆H₉N₃O
Mol. weight 139.16 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HMH
PDB
1jxi
UniProt (similar protein)
P55882
Target protein
KP13_03172

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 139.16 Da
LogP (Crippen) -0.14
H-bond donors 2
H-bond acceptors 4
TPSA 72.03 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 10
Fraction sp³ C 0.33
Formula C₆H₉N₃O

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 72.0
  • −1 ≤ LogP ≤ 5 -0.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 139.2
  • LogP ≤ 5 -0.14
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 72.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ncc(c(n1)N)CO
InChI 
InChI=1S/C6H9N3O/c1-4-8-2-5(3-10)6(7)9-4/h2,10H,3H2,1H3,(H2,7,8,9)
InChIKey 
VUTBELPREDJDDH-UHFFFAOYSA-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
PF08543

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_03172.

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)