Ligand profile

865

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

Bound to: KP13_00372 — Maltose-binding periplasmic protein

Via homolog PDB 4wmt UniProt P0AEX9 Formula C₃₇H₃₆N₆O₄
Mol. weight 628.73 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
865
PDB
4wmt
UniProt (similar protein)
P0AEX9
Target protein
KP13_00372

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 628.73 Da
LogP (Crippen) 5.49
H-bond donors 2
H-bond acceptors 8
TPSA 114.51 Ų
Rotatable bonds 10
Aromatic rings 6 / 7
Heavy atoms 47
Fraction sp³ C 0.24
Formula C₃₇H₃₆N₆O₄

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 114.5
  • −1 ≤ LogP ≤ 5 5.49
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 628.7
  • LogP ≤ 5 5.49
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 114.5
PAINS Alert

Matches PAINS filter: indol_3yl_alk(461). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccnc(c1c2cccc3c2n(c(c3CCCOc4cccc5c4cccc5)C(=O)O)CC(=O)N6CCNCC6)n7ccnc7
InChI 
InChI=1S/C37H36N6O4/c1-25-14-15-40-36(42-21-18-39-24-42)33(25)30-11-5-10-28-29(12-6-22-47-31-13-4-8-26-7-2-3-9-27(26)31)35(37(45)46)43(34(28)30)23-32(44)41-19-16-38-17-20-41/h2-5,7-11,13-15,18,21,24,38H,6,12,16-17,19-20,22-23H2,1H3,(H,45,46)
InChIKey 
ZZKICOFWGKKSRR-UHFFFAOYSA-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' '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)