Ligand profile

1EI

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

Bound to: KP13_05059 — putative murein peptide carboxypeptidase

Via homolog PDB 4iiy UniProt Q47511 Formula C₁₅H₂₀N₆O₁₀S
Mol. weight 476.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1EI
PDB
4iiy
UniProt (similar protein)
Q47511
Target protein
KP13_05059

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 476.42 Da
LogP (Crippen) -3.69
H-bond donors 6
H-bond acceptors 13
TPSA 249.05 Ų
Rotatable bonds 9
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.53
Formula C₁₅H₂₀N₆O₁₀S

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 249.0
  • −1 ≤ LogP ≤ 5 -3.69
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 476.4
  • LogP ≤ 5 -3.69
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 249.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CCC(=O)O)N)O)O)N=CNC2=O
InChI 
InChI=1S/C15H20N6O10S/c16-6(1-2-8(22)23)13(26)20-32(28,29)30-3-7-10(24)11(25)15(31-7)21-5-19-9-12(21)17-4-18-14(9)27/h4-7,10-11,15,24-25H,1-3,16H2,(H,20,26)(H,22,23)(H,17,18,27)/t6-,7+,10+,11+,15+/m0/s1
InChIKey 
CVAFSXWGULKSTF-WERHYGNASA-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
PF02016' 'PF17676

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_05059.

PDB 7

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)