Ligand profile

DLZ

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

Bound to: KP13_05136 — Riboflavin synthase alpha chain

Via homolog PDB 3a3g UniProt C4TPG1 Formula C₁₃H₁₈N₄O₆
Mol. weight 326.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DLZ
PDB
3a3g
UniProt (similar protein)
C4TPG1
Target protein
KP13_05136

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 326.31 Da
LogP (Crippen) -2.88
H-bond donors 5
H-bond acceptors 9
TPSA 161.56 Ų
Rotatable bonds 5
Aromatic rings 0 / 2
Heavy atoms 23
Fraction sp³ C 0.54
Formula C₁₃H₁₈N₄O₆

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 161.6
  • −1 ≤ LogP ≤ 5 -2.88
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 326.3
  • LogP ≤ 5 -2.88
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 161.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=C(N(C2=NC(=O)NC(=O)C2=N1)C[C@@H]([C@@H]([C@@H](CO)O)O)O)C
InChI 
InChI=1S/C13H18N4O6/c1-5-6(2)17(3-7(19)10(21)8(20)4-18)11-9(14-5)12(22)16-13(23)15-11/h7-8,10,18-21H,3-4H2,1-2H3,(H,16,22,23)/t7-,8+,10-/m0/s1
InChIKey 
SXDXRJZUAJBNFL-XKSSXDPKSA-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
PF00677

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_05136.

PDB 2

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)