Ligand profile

ZINC8627939

Virtual-screening candidate from ZINC.

Bound to: VK055_3151 — 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase

Via homolog UniProt P82610 Formula C₂₁H₂₇N₉O₃
Tanimoto 0.81
Mol. weight 453.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC8627939
UniProt (similar protein)
P82610
Tanimoto
0.812
Target protein
VK055_3151

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 453.51 Da
LogP (Crippen) 0.53
H-bond donors 5
H-bond acceptors 10
TPSA 199.26 Ų
Rotatable bonds 10
Aromatic rings 3 / 3
Heavy atoms 33
Fraction sp³ C 0.33
Formula C₂₁H₂₇N₉O₃

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 0.53
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 453.5
  • LogP ≤ 5 0.53
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • 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](CCCCN)C(=O)O)cc1
InChI 
InChI=1S/C21H27N9O3/c1-30(11-13-10-25-18-16(26-13)17(23)28-21(24)29-18)14-7-5-12(6-8-14)19(31)27-15(20(32)33)4-2-3-9-22/h5-8,10,15H,2-4,9,11,22H2,1H3,(H,27,31)(H,32,33)(H4,23,24,25,28,29)/t15-/m1/s1
InChIKey 
XERJQLWAFDLUGV-OAHLLOKOSA-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 VK055_3151.

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)