Ligand profile

ZINC3870259

Virtual-screening candidate from ZINC.

Bound to: KP13_00870 — GMP synthase

Via homolog UniProt Q8IJR9 Formula C₉H₁₃N₂O₉P
Tanimoto 0.55
Mol. weight 324.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3870259
UniProt (similar protein)
Q8IJR9
Tanimoto
0.554
Target protein
KP13_00870

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 324.18 Da
LogP (Crippen) -2.73
H-bond donors 5
H-bond acceptors 8
TPSA 171.31 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 21
Fraction sp³ C 0.56
Formula C₉H₁₃N₂O₉P

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 171.3
  • −1 ≤ LogP ≤ 5 -2.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 324.2
  • LogP ≤ 5 -2.73
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 171.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@H]2O)c(=O)[nH]1
InChI 
InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6+,7-,8-/m0/s1
InChIKey 
DJJCXFVJDGTHFX-UCVXFZOQSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
XMP
Homolog
Q8IJR9

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_00870.

PDB 3

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)