Ligand profile

45A

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

Bound to: KP13_02199 — Lysyl-tRNA synthetase

Via homolog PDB 6ild UniProt Q15046 Formula C₁₁H₁₆N₅O₆P
Mol. weight 345.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
45A
PDB
6ild
UniProt (similar protein)
Q15046
Target protein
KP13_02199

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 345.25 Da
LogP (Crippen) -1.14
H-bond donors 4
H-bond acceptors 10
TPSA 165.84 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.55
Formula C₁₁H₁₆N₅O₆P

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 165.8
  • −1 ≤ LogP ≤ 5 -1.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 345.3
  • LogP ≤ 5 -1.14
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 165.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
InChI 
InChI=1S/C11H16N5O6P/c1-23(19,20)21-2-5-7(17)8(18)11(22-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H,19,20)(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
InChIKey 
PXSSQXBLDTZHLF-IOSLPCCCSA-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
PF00152

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_02199.

PDB 17

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 2

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)