Ligand profile

ZINC13604299

Virtual-screening candidate from ZINC.

Bound to: KP13_31808 — 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase

Via homolog UniProt P82610 Formula C₂₀H₂₅N₉O₃
Tanimoto 0.83
Mol. weight 439.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13604299
UniProt (similar protein)
P82610
Tanimoto
0.825
Target protein
KP13_31808

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 439.48 Da
LogP (Crippen) 0.14
H-bond donors 5
H-bond acceptors 10
TPSA 199.26 Ų
Rotatable bonds 9
Aromatic rings 3 / 3
Heavy atoms 32
Fraction sp³ C 0.30
Formula C₂₀H₂₅N₉O₃

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 199.3
  • −1 ≤ LogP ≤ 5 0.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 439.5
  • LogP ≤ 5 0.14
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 199.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@@H](CCCN)C(=O)O)cc1
InChI 
InChI=1S/C20H25N9O3/c1-29(10-12-9-24-17-15(25-12)16(22)27-20(23)28-17)13-6-4-11(5-7-13)18(30)26-14(19(31)32)3-2-8-21/h4-7,9,14H,2-3,8,10,21H2,1H3,(H,26,30)(H,31,32)(H4,22,23,24,27,28)/t14-/m0/s1
InChIKey 
XZMFYMLGNMSYOG-AWEZNQCLSA-N

Provenance

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

Method
LigQ nearest_k
Query
MTX
Homolog
P82610

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_31808.

PDB 6

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)