Ligand profile

GPD

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

Bound to: KP13_01696 — Lipopolysaccharide biosynthesis protein rffA

Via homolog PDB 3dr7 UniProt Q9A9H3 Formula C₁₆H₂₆N₆O₁₃P₂
Mol. weight 572.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GPD
PDB
3dr7
UniProt (similar protein)
Q9A9H3
Target protein
KP13_01696

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 572.36 Da
LogP (Crippen) -2.61
H-bond donors 8
H-bond acceptors 16
TPSA 297.05 Ų
Rotatable bonds 8
Aromatic rings 2 / 4
Heavy atoms 37
Fraction sp³ C 0.69
Formula C₁₆H₂₆N₆O₁₃P₂

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 297.0
  • −1 ≤ LogP ≤ 5 -2.61
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 572.4
  • LogP ≤ 5 -2.61
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 297.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1[C@H](C[C@@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O)O)N
InChI 
InChI=1S/C16H26N6O13P2/c1-5-6(17)2-7(23)15(32-5)34-37(29,30)35-36(27,28)31-3-8-10(24)11(25)14(33-8)22-4-19-9-12(22)20-16(18)21-13(9)26/h4-8,10-11,14-15,23-25H,2-3,17H2,1H3,(H,27,28)(H,29,30)(H3,18,20,21,26)/t5-,6+,7+,8-,10-,11-,14-,15-/m1/s1
InChIKey 
DRNSMVBRYJDNAT-CYCRINRGSA-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)