Ligand profile

G4M

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

Bound to: KP13_01696 — Lipopolysaccharide biosynthesis protein rffA

Via homolog PDB 3dr4 UniProt Q9A9H3 Formula C₂₄H₃₆N₇O₁₉P₃
Mol. weight 819.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
G4M
PDB
3dr4
UniProt (similar protein)
Q9A9H3
Target protein
KP13_01696

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 819.50 Da
LogP (Crippen) -2.79
H-bond donors 12
H-bond acceptors 21
TPSA 403.17 Ų
Rotatable bonds 14
Aromatic rings 3 / 5
Heavy atoms 53
Fraction sp³ C 0.58
Formula C₂₄H₃₆N₇O₁₉P₃

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 403.2
  • −1 ≤ LogP ≤ 5 -2.79
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 819.5
  • LogP ≤ 5 -2.79
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 21
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 403.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2[C@H](O[C@@H]([C@H]([C@H]2O)O)O[P@](=O)(O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4N=C(NC5=O)N)O)O)C)O
InChI 
InChI=1S/C24H36N7O19P3/c1-8-15(32)11(10(3-26-8)5-45-51(38,39)40)4-27-13-9(2)47-23(19(36)17(13)34)49-53(43,44)50-52(41,42)46-6-12-16(33)18(35)22(48-12)31-7-28-14-20(31)29-24(25)30-21(14)37/h3,7,9,12-13,16-19,22-23,27,32-36H,4-6H2,1-2H3,(H,41,42)(H,43,44)(H2,38,39,40)(H3,25,29,30,37)/t9-,12-,13-,16-,17+,18-,19+,22-,23-/m1/s1
InChIKey 
BNJJFFPICXKOFM-VMLLIFSYSA-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
PF01041

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_01696.

PDB 7

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)