Ligand profile

GN3

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

Bound to: KP13_00164 — Bifunctional (p)ppGpp synthase/hydrolase SpoT

Via homolog PDB 6s2u UniProt Q5SHL3 Formula C₁₀H₁₈N₆O₁₆P₄
Mol. weight 602.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GN3
PDB
6s2u
UniProt (similar protein)
Q5SHL3
Target protein
KP13_00164

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 602.18 Da
LogP (Crippen) -2.65
H-bond donors 10
H-bond acceptors 14
TPSA 348.43 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 36
Fraction sp³ C 0.50
Formula C₁₀H₁₈N₆O₁₆P₄

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 348.4
  • −1 ≤ LogP ≤ 5 -2.65
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 602.2
  • LogP ≤ 5 -2.65
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 348.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(NP(=O)(O)O)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C10H18N6O16P4/c11-10-13-7-4(8(18)14-10)12-2-16(7)9-5(17)6(31-34(22,23)15-33(19,20)21)3(30-9)1-29-36(27,28)32-35(24,25)26/h2-3,5-6,9,17H,1H2,(H,27,28)(H2,24,25,26)(H3,11,13,14,18)(H4,15,19,20,21,22,23)/t3-,5-,6-,9-/m1/s1
InChIKey 
XBDJLYDZMOIGRH-UUOKFMHZSA-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
PF04607

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_00164.

PDB 4

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

Ligand PDB entry

ChEMBL 7

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)