Ligand profile

CRM

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

Bound to: KP13_05136 — Riboflavin synthase alpha chain

Via homolog PDB 1kzl UniProt Q9Y7P0 Formula C₁₄H₁₈N₄O₉
Mol. weight 386.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CRM
PDB
1kzl
UniProt (similar protein)
Q9Y7P0
Target protein
KP13_05136

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 386.32 Da
LogP (Crippen) -4.13
H-bond donors 7
H-bond acceptors 10
TPSA 218.83 Ų
Rotatable bonds 8
Aromatic rings 2 / 2
Heavy atoms 27
Fraction sp³ C 0.50
Formula C₁₄H₁₈N₄O₉

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 218.8
  • −1 ≤ LogP ≤ 5 -4.13
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 386.3
  • LogP ≤ 5 -4.13
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 218.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CC(=O)O)C1=NC2=C(NC(=O)NC2=O)N(C1=O)C[C@@H]([C@@H]([C@@H](CO)O)O)O
InChI 
InChI=1S/C14H18N4O9/c19-4-7(21)10(24)6(20)3-18-11-9(12(25)17-14(27)16-11)15-5(13(18)26)1-2-8(22)23/h6-7,10,19-21,24H,1-4H2,(H,22,23)(H2,16,17,25,27)/t6-,7+,10-/m0/s1
InChIKey 
PTYCEIBBGGLADD-PJKMHFRUSA-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)