Ligand profile

1RB

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

Bound to: KP13_04750 — Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase

Via homolog PDB 1l5k UniProt Q05603 Formula C₁₂H₁₅N₂O₇P
Mol. weight 330.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1RB
PDB
1l5k
UniProt (similar protein)
Q05603
Target protein
KP13_04750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 330.23 Da
LogP (Crippen) -0.24
H-bond donors 4
H-bond acceptors 7
TPSA 134.27 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 22
Fraction sp³ C 0.42
Formula C₁₂H₁₅N₂O₇P

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 -0.24
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 330.2
  • LogP ≤ 5 -0.24
  • 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 
c1ccc2c(c1)ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O
InChI 
InChI=1S/C12H15N2O7P/c15-10-9(5-20-22(17,18)19)21-12(11(10)16)14-6-13-7-3-1-2-4-8(7)14/h1-4,6,9-12,15-16H,5H2,(H2,17,18,19)/t9-,10-,11-,12+/m1/s1
InChIKey 
YPYFPLLZCVEYCS-KKOKHZNYSA-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_04750.

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)