Ligand profile

M2A

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

Bound to: VK055_1726 — excinuclease ABC subunit B

Via homolog PDB 5elx UniProt P20449 Formula C₁₈H₂₂N₆O₁₁P₂
Mol. weight 560.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
M2A
PDB
5elx
UniProt (similar protein)
P20449
Target protein
VK055_1726

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 560.35 Da
LogP (Crippen) 0.16
H-bond donors 6
H-bond acceptors 14
TPSA 250.70 Ų
Rotatable bonds 9
Aromatic rings 3 / 4
Heavy atoms 37
Fraction sp³ C 0.33
Formula C₁₈H₂₂N₆O₁₁P₂

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 250.7
  • −1 ≤ LogP ≤ 5 0.16
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 560.4
  • LogP ≤ 5 0.16
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 250.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1ccccc1C(=O)O[C@@H]2[C@@H]([C@@H](O[C@H]2n3cnc4c3ncnc4N)COP(=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C18H22N6O11P2/c1-20-10-5-3-2-4-9(10)18(26)34-14-13(25)11(6-32-37(30,31)35-36(27,28)29)33-17(14)24-8-23-12-15(19)21-7-22-16(12)24/h2-5,7-8,11,13-14,17,20,25H,6H2,1H3,(H,30,31)(H2,19,21,22)(H2,27,28,29)/t11-,13+,14+,17+/m0/s1
InChIKey 
FYQOZQIQCITNBC-ZCTGUTNYSA-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
PF00270' 'PF00271

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_1726.

PDB 5

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)