Ligand profile

RDL

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

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

Via homolog PDB 1nqu UniProt O66529 Formula C₁₁H₁₄N₄O₈
Mol. weight 330.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RDL
PDB
1nqu
UniProt (similar protein)
O66529
Target protein
VK055_2187

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 330.25 Da
LogP (Crippen) -4.86
H-bond donors 7
H-bond acceptors 9
TPSA 201.50 Ų
Rotatable bonds 5
Aromatic rings 2 / 2
Heavy atoms 23
Fraction sp³ C 0.45
Formula C₁₁H₁₄N₄O₈

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 201.5
  • −1 ≤ LogP ≤ 5 -4.86
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 330.3
  • LogP ≤ 5 -4.86
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 201.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]([C@@H]([C@@H](CO)O)O)O)N1C2=C(C(=O)NC(=O)N2)NC(=O)C1=O
InChI 
InChI=1S/C11H14N4O8/c16-2-4(18)6(19)3(17)1-15-7-5(12-9(21)10(15)22)8(20)14-11(23)13-7/h3-4,6,16-19H,1-2H2,(H,12,21)(H2,13,14,20,23)/t3-,4+,6-/m0/s1
InChIKey 
MIBROOURCUHKMD-RPDRRWSUSA-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)