Ligand profile

KAM

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

Bound to: VK055_1730 — 8-amino-7-oxononanoate synthase

Via homolog PDB 1dj9 UniProt P12998 Formula C₁₇H₂₇N₂O₈P
Mol. weight 418.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KAM
PDB
1dj9
UniProt (similar protein)
P12998
Target protein
VK055_1730

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 418.38 Da
LogP (Crippen) 1.79
H-bond donors 5
H-bond acceptors 7
TPSA 166.28 Ų
Rotatable bonds 13
Aromatic rings 1 / 1
Heavy atoms 28
Fraction sp³ C 0.59
Formula C₁₇H₂₇N₂O₈P

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 166.3
  • −1 ≤ LogP ≤ 5 1.79
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 418.4
  • LogP ≤ 5 1.79
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 166.3
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](C)C(=O)CCCCCC(=O)O)O
InChI 
InChI=1S/C17H27N2O8P/c1-11(15(20)6-4-3-5-7-16(21)22)19-9-14-13(10-27-28(24,25)26)8-18-12(2)17(14)23/h8,11,19,23H,3-7,9-10H2,1-2H3,(H,21,22)(H2,24,25,26)/t11-/m0/s1
InChIKey 
YXEXNGWPUWJMIT-NSHDSACASA-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
PF00155

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_1730.

PDB 8

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

Ligand PDB entry

ZINC 46

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

Compound Similarity (Tanimoto)