Binder profile

LMD

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

Bound to: PA3828 — hypothetical protein

Via homolog PDB 6s8g UniProt P0AFA1 C26H50O11
Mol. weight 538.68 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LMD
PDB
6s8g
UniProt (similar protein)
P0AFA1
Target protein
PA3828

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 538.68 Da
LogP (Crippen) 0.33
H-bond donors 7
H-bond acceptors 11
TPSA 178.53 Ų
Rotatable bonds 18
Aromatic rings 0 / 2
Heavy atoms 37
Fraction sp³ C 1.00
Formula C26H50O11

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 538.7
  • LogP ≤ 5 0.33
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 18
  • TPSA ≤ 140 Ų 178.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCO[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/C26H50O11/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-34-25-23(33)21(31)24(18(16-28)36-25)37-26-22(32)20(30)19(29)17(15-27)35-26/h17-33H,2-16H2,1H3/t17-,18-,19-,20+,21-,22-,23-,24-,25-,26-/m1/s1
InChIKey 
UKPROSIGWJBJGA-IWODYCRQSA-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
PF03739

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3828.

PDB 11

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)