Ligand profile

INI

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

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

Via homolog PDB 1rvv UniProt P11998 Formula C₉H₁₄N₄O₈
Mol. weight 306.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
INI
PDB
1rvv
UniProt (similar protein)
P11998
Target protein
VK055_2187

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 306.23 Da
LogP (Crippen) -3.54
H-bond donors 7
H-bond acceptors 9
TPSA 201.81 Ų
Rotatable bonds 7
Aromatic rings 1 / 1
Heavy atoms 21
Fraction sp³ C 0.56
Formula C₉H₁₄N₄O₈

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 201.8
  • −1 ≤ LogP ≤ 5 -3.54
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 306.2
  • LogP ≤ 5 -3.54
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 201.8
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)NC1=C(C(=O)NC(=O)N1)[N+](=O)[O-]
InChI 
InChI=1S/C9H14N4O8/c14-2-4(16)6(17)3(15)1-10-7-5(13(20)21)8(18)12-9(19)11-7/h3-4,6,14-17H,1-2H2,(H3,10,11,12,18,19)/t3-,4+,6-/m0/s1
InChIKey 
KSKGHNZSCSCHEQ-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)