Ligand profile

RBZ

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

Bound to: KP13_02342 — Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase

Via homolog PDB 1d0v UniProt Q05603 Formula C₁₄H₁₉N₂O₇P
Mol. weight 358.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RBZ
PDB
1d0v
UniProt (similar protein)
Q05603
Target protein
KP13_02342

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 358.29 Da
LogP (Crippen) 0.38
H-bond donors 4
H-bond acceptors 7
TPSA 134.27 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.50
Formula C₁₄H₁₉N₂O₇P

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 134.3
  • −1 ≤ LogP ≤ 5 0.38
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 358.3
  • LogP ≤ 5 0.38
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 134.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c(cc1C)n(cn2)[C@@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O
InChI 
InChI=1S/C14H19N2O7P/c1-7-3-9-10(4-8(7)2)16(6-15-9)14-13(18)12(17)11(23-14)5-22-24(19,20)21/h3-4,6,11-14,17-18H,5H2,1-2H3,(H2,19,20,21)/t11-,12-,13-,14+/m1/s1
InChIKey 
ZMRGXEJKZPRBPJ-SYQHCUMBSA-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
PF02277

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_02342.

PDB 25

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)