Ligand profile

P2P

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

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

Via homolog PDB 1jhr UniProt Q05603 Formula C₁₀H₁₃N₄O₈P
Mol. weight 348.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
P2P
PDB
1jhr
UniProt (similar protein)
Q05603
Target protein
KP13_04750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 348.21 Da
LogP (Crippen) -1.74
H-bond donors 5
H-bond acceptors 10
TPSA 180.28 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.50
Formula C₁₀H₁₃N₄O₈P

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 180.3
  • −1 ≤ LogP ≤ 5 -1.74
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 348.2
  • LogP ≤ 5 -1.74
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 180.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c2c(ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)nc(n1)O
InChI 
InChI=1S/C10H13N4O8P/c15-6-5(2-21-23(18,19)20)22-9(7(6)16)14-3-12-8-4(14)1-11-10(17)13-8/h1,3,5-7,9,15-16H,2H2,(H,11,13,17)(H2,18,19,20)/t5-,6-,7-,9+/m1/s1
InChIKey 
BVZASCINAVSQNO-PULFBKJNSA-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)