Ligand profile

RMB

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

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

Via homolog PDB 1jho UniProt Q05603 Formula C₁₃H₁₇N₂O₇P
Mol. weight 344.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RMB
PDB
1jho
UniProt (similar protein)
Q05603
Target protein
KP13_04750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 344.26 Da
LogP (Crippen) 0.07
H-bond donors 4
H-bond acceptors 7
TPSA 134.27 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.46
Formula C₁₃H₁₇N₂O₇P

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 0.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 344.3
  • LogP ≤ 5 0.07
  • 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 
Cc1ccc2c(c1)ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O
InChI 
InChI=1S/C13H17N2O7P/c1-7-2-3-9-8(4-7)14-6-15(9)13-12(17)11(16)10(22-13)5-21-23(18,19)20/h2-4,6,10-13,16-17H,5H2,1H3,(H2,18,19,20)/t10-,11-,12-,13+/m1/s1
InChIKey 
HGUDFQQPANTQEU-LPWJVIDDSA-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)