Binder profile

LMT

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

Bound to: PA5366 — phosphate ABC transporter ATP-binding protein

Via homolog PDB 4mki UniProt Q8R7Y5 C24H46O11
Mol. weight 510.62 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LMT
PDB
4mki
UniProt (similar protein)
Q8R7Y5
Target protein
PA5366

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 510.62 Da
LogP (Crippen) -0.45
H-bond donors 7
H-bond acceptors 11
TPSA 178.53 Ų
Rotatable bonds 16
Aromatic rings 0 / 2
Heavy atoms 35
Fraction sp³ C 1.00
Formula C24H46O11

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.

Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 510.6
  • LogP ≤ 5 -0.45
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 178.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCO[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
InChI 
InChI=1S/C24H46O11/c1-2-3-4-5-6-7-8-9-10-11-12-32-23-21(31)19(29)22(16(14-26)34-23)35-24-20(30)18(28)17(27)15(13-25)33-24/h15-31H,2-14H2,1H3/t15-,16-,17-,18+,19-,20-,21-,22-,23-,24-/m1/s1
InChIKey 
NLEBIOOXCVAHBD-QKMCSOCLSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00005

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA5366.

PDB 6

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)