Ligand profile

A

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

Bound to: KP13_01352 — Elongation factor Tu

Via homolog PDB 4v5g UniProt Q5SHN6 Formula C₁₀H₁₄N₅O₇P
Mol. weight 347.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A
PDB
4v5g
UniProt (similar protein)
Q5SHN6
Target protein
KP13_01352

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 347.22 Da
LogP (Crippen) -1.86
H-bond donors 5
H-bond acceptors 10
TPSA 186.07 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.50
Formula C₁₀H₁₄N₅O₇P

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 186.1
  • −1 ≤ LogP ≤ 5 -1.86
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 347.2
  • LogP ≤ 5 -1.86
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 186.1
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)COP(=O)(O)O)O)O)N
InChI 
InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKey 
UDMBCSSLTHHNCD-KQYNXXCUSA-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
PF03144

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)