Ligand profile

C84

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

Bound to: KP13_05440 — Peptide transport periplasmic protein sapA

Via homolog PDB 4zec UniProt Q52012 Formula C₂₁H₃₄N₆O₁₆P₂
Mol. weight 688.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C84
PDB
4zec
UniProt (similar protein)
Q52012
Target protein
KP13_05440

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 688.48 Da
LogP (Crippen) -3.63
H-bond donors 11
H-bond acceptors 18
TPSA 337.86 Ų
Rotatable bonds 12
Aromatic rings 2 / 4
Heavy atoms 45
Fraction sp³ C 0.71
Formula C₂₁H₃₄N₆O₁₆P₂

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 337.9
  • −1 ≤ LogP ≤ 5 -3.63
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 688.5
  • LogP ≤ 5 -3.63
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 337.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@@H]([C@H](C(=O)NP(=O)(O)O[C@@H]1C[C@@H]([C@@H](O1)n2cnc3c2ncnc3NP(=O)(O)O[C@@H]4[C@H]([C@@H]([C@H](O[C@H]4O)CO)O)O)O)O)O
InChI 
InChI=1S/C21H34N6O16P2/c1-7(2)12(30)15(33)19(34)26-45(38,39)42-10-3-8(29)20(41-10)27-6-24-11-17(22-5-23-18(11)27)25-44(36,37)43-16-14(32)13(31)9(4-28)40-21(16)35/h5-10,12-16,20-21,28-33,35H,3-4H2,1-2H3,(H2,26,34,38,39)(H2,22,23,25,36,37)/t8-,9+,10+,12-,13+,14-,15+,16+,20+,21+/m0/s1
InChIKey 
KOMSNTWZRZGGEF-AIJJVVIGSA-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
PF00496

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_05440.

PDB 4

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)