Ligand profile

TXT

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

Bound to: KP13_00372 — Maltose-binding periplasmic protein

Via homolog PDB 3k02 UniProt B0B0V1 Formula C₃₁H₅₅NO₂₃
Mol. weight 809.77 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TXT
PDB
3k02
UniProt (similar protein)
B0B0V1
Target protein
KP13_00372

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 809.77 Da
LogP (Crippen) -10.66
H-bond donors 17
H-bond acceptors 24
TPSA 400.32 Ų
Rotatable bonds 12
Aromatic rings 0 / 5
Heavy atoms 55
Fraction sp³ C 1.00
Formula C₃₁H₅₅NO₂₃

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 400.3
  • −1 ≤ LogP ≤ 5 -10.66
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 809.8
  • LogP ≤ 5 -10.66
  • H-bond donors ≤ 5 17
  • H-bond acceptors ≤ 10 24
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 400.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1[C@H]([C@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O[C@@H]3[C@H](O[C@@H]([C@@H]([C@H]3O)O)O[C@@H]4[C@H](O[C@@H]([C@@H]([C@H]4O)O)O)CO)CO)CO)O)O)N[C@H]5CC([C@@H]([C@H]([C@@H]5O)O)O)CO
InChI 
InChI=1S/C31H55NO23/c1-7-13(32-9-2-8(3-33)14(37)17(40)15(9)38)16(39)22(45)29(49-7)53-26-11(5-35)51-31(23(46)19(26)42)55-27-12(6-36)52-30(24(47)20(27)43)54-25-10(4-34)50-28(48)21(44)18(25)41/h7-48H,2-6H2,1H3/t7-,8?,9+,10-,11-,12-,13-,14+,15-,16-,17-,18-,19-,20-,21-,22-,23-,24-,25-,26-,27-,28+,29-,30-,31-/m1/s1
InChIKey 
IVFOOIPIJGLQPY-VDZAKWEDSA-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
PF01547

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_00372.

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)