Ligand profile

3M6

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

Bound to: KP13_00372 — Maltose-binding periplasmic protein

Via homolog PDB 4wgi UniProt P0AEY0 Formula C₃₀H₃₀F₄N₄O₇S
Mol. weight 666.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3M6
PDB
4wgi
UniProt (similar protein)
P0AEY0
Target protein
KP13_00372

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 666.65 Da
LogP (Crippen) 5.12
H-bond donors 3
H-bond acceptors 6
TPSA 145.35 Ų
Rotatable bonds 8
Aromatic rings 3 / 4
Heavy atoms 46
Fraction sp³ C 0.30
Formula C₃₀H₃₀F₄N₄O₇S

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 145.3
  • −1 ≤ LogP ≤ 5 5.12
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 666.7
  • LogP ≤ 5 5.12
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 145.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1CN(C(=O)c2cccc(c2O[C@@H]1CN(C)C(=O)Nc3ccc(cc3)C(F)(F)F)NS(=O)(=O)c4ccc(cc4)F)[C@@H](C)C(=O)O
InChI 
InChI=1S/C30H30F4N4O7S/c1-17-15-38(18(2)28(40)41)27(39)23-5-4-6-24(36-46(43,44)22-13-9-20(31)10-14-22)26(23)45-25(17)16-37(3)29(42)35-21-11-7-19(8-12-21)30(32,33)34/h4-14,17-18,25,36H,15-16H2,1-3H3,(H,35,42)(H,40,41)/t17-,18+,25-/m1/s1
InChIKey 
XAEPMFMCFFIZDH-FUMQJTLXSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF00452

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)