Ligand profile

APR

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

Bound to: KP13_01352 — Elongation factor Tu

Via homolog PDB 2p8z UniProt P60339 Formula C₁₅H₂₃N₅O₁₄P₂
Mol. weight 559.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
APR
PDB
2p8z
UniProt (similar protein)
P60339
Target protein
KP13_01352

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 559.32 Da
LogP (Crippen) -3.28
H-bond donors 8
H-bond acceptors 17
TPSA 291.52 Ų
Rotatable bonds 9
Aromatic rings 2 / 4
Heavy atoms 36
Fraction sp³ C 0.67
Formula C₁₅H₂₃N₅O₁₄P₂

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 291.5
  • −1 ≤ LogP ≤ 5 -3.28
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 559.3
  • LogP ≤ 5 -3.28
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 291.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N
InChI 
InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
InChIKey 
SRNWOUGRCWSEMX-KEOHHSTQSA-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
PF03764

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_01352.

PDB 19

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)