Ligand profile

ZINC255970296

Virtual-screening candidate from ZINC.

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

Via homolog UniProt P82610 Formula C₂₁H₂₂N₁₀O₄
Tanimoto 0.79
Mol. weight 478.47 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC255970296
UniProt (similar protein)
P82610
Tanimoto
0.794
Target protein
KP13_31808

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 478.47 Da
LogP (Crippen) 0.05
H-bond donors 4
H-bond acceptors 10
TPSA 226.71 Ų
Rotatable bonds 10
Aromatic rings 3 / 3
Heavy atoms 35
Fraction sp³ C 0.24
Formula C₂₁H₂₂N₁₀O₄

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 226.7
  • −1 ≤ LogP ≤ 5 0.05
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 478.5
  • LogP ≤ 5 0.05
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 226.7
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@@H](CCC(=O)C=[N+]=[N-])C(=O)O)cc1
InChI 
InChI=1S/C21H22N10O4/c1-31(10-12-8-25-18-16(27-12)17(22)29-21(23)30-18)13-4-2-11(3-5-13)19(33)28-15(20(34)35)7-6-14(32)9-26-24/h2-5,8-9,15H,6-7,10H2,1H3,(H,28,33)(H,34,35)(H4,22,23,25,29,30)/t15-/m0/s1
InChIKey 
DUYMESGXUXXYQB-HNNXBMFYSA-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)