Ligand profile

5YL

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

Bound to: VK055_2187 — 6,7-dimethyl-8-ribityllumazine synthase

Via homolog PDB 1nqw UniProt O66529 Formula C₁₄H₂₆N₃O₉P
Mol. weight 411.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5YL
PDB
1nqw
UniProt (similar protein)
O66529
Target protein
VK055_2187

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 411.35 Da
LogP (Crippen) -2.56
H-bond donors 9
H-bond acceptors 8
TPSA 216.20 Ų
Rotatable bonds 12
Aromatic rings 1 / 1
Heavy atoms 27
Fraction sp³ C 0.71
Formula C₁₄H₂₆N₃O₉P

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 216.2
  • −1 ≤ LogP ≤ 5 -2.56
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 411.3
  • LogP ≤ 5 -2.56
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 216.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCC1=C(NC(=O)NC1=O)NC[C@@H]([C@@H]([C@@H](CO)O)O)O)CCP(=O)(O)O
InChI 
InChI=1S/C14H26N3O9P/c18-7-10(20)11(21)9(19)6-15-12-8(13(22)17-14(23)16-12)4-2-1-3-5-27(24,25)26/h9-11,18-21H,1-7H2,(H2,24,25,26)(H3,15,16,17,22,23)/t9-,10+,11-/m0/s1
InChIKey 
BMATWAHJJFXMFA-AXFHLTTASA-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
PF00885

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_2187.

PDB 7

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)