Ligand profile

LMN

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

Bound to: KP13_00007 — Ribose import ATP-binding protein rbsA

Via homolog PDB 6s8n UniProt P0A9V4 Formula C₄₇H₈₈O₂₂
Mol. weight 1005.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LMN
PDB
6s8n
UniProt (similar protein)
P0A9V4
Target protein
KP13_00007

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1005.20 Da
LogP (Crippen) -1.68
H-bond donors 14
H-bond acceptors 22
TPSA 357.06 Ų
Rotatable bonds 32
Aromatic rings 0 / 4
Heavy atoms 69
Fraction sp³ C 1.00
Formula C₄₇H₈₈O₂₂

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 357.1
  • −1 ≤ LogP ≤ 5 -1.68
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1005.2
  • LogP ≤ 5 -1.68
  • H-bond donors ≤ 5 14
  • H-bond acceptors ≤ 10 22
Veber's rules Fail
  • Rotatable bonds ≤ 10 32
  • TPSA ≤ 140 Ų 357.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCC(CCCCCCCCCC)(CO[C@@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)CO)O[C@H]2[C@H]([C@@H]([C@H]([C@@H](O2)CO)O)O)O)O)O)CO[C@@H]3[C@H]([C@@H]([C@H]([C@@H](O3)CO)O[C@H]4[C@H]([C@@H]([C@H]([C@@H](O4)CO)O)O)O)O)O
InChI 
InChI=1S/C47H88O22/c1-3-5-7-9-11-13-15-17-19-47(20-18-16-14-12-10-8-6-4-2,25-62-43-39(60)35(56)41(29(23-50)66-43)68-45-37(58)33(54)31(52)27(21-48)64-45)26-63-44-40(61)36(57)42(30(24-51)67-44)69-46-38(59)34(55)32(53)28(22-49)65-46/h27-46,48-61H,3-26H2,1-2H3/t27-,28-,29-,30-,31-,32-,33+,34+,35-,36-,37-,38-,39-,40+,41-,42-,43-,44-,45-,46-/m0/s1
InChIKey 
MADJBYLAYPCCOO-XYPZXBMFSA-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
PF03739

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_00007.

PDB 12

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)