Ligand profile

ZINC6585366

Virtual-screening candidate from ZINC.

Bound to: KP13_02046 — Riboflavin biosynthesis bifunctional protein ribD

Via homolog UniProt D0CB74 Formula C₁₀H₁₂FN₅O₄
Tanimoto 0.63
Mol. weight 285.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC6585366
UniProt (similar protein)
D0CB74
Tanimoto
0.627
Target protein
KP13_02046

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 285.23 Da
LogP (Crippen) -1.71
H-bond donors 4
H-bond acceptors 8
TPSA 139.28 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.50
Formula C₁₀H₁₂FN₅O₄

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 139.3
  • −1 ≤ LogP ≤ 5 -1.71
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 285.2
  • LogP ≤ 5 -1.71
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 139.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](F)[C@@H]2O)c(=O)[nH]1
InChI 
InChI=1S/C10H12FN5O4/c11-4-3(1-17)20-9(6(4)18)16-2-13-5-7(16)14-10(12)15-8(5)19/h2-4,6,9,17-18H,1H2,(H3,12,14,15,19)/t3-,4-,6+,9-/m1/s1
InChIKey 
VDOWHLFGBWKXJC-AOTGGKNNSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
5GP
Homolog
D0CB74

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02046.

PDB 7

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)