Ligand profile

TYM

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

Bound to: KP13_13547 — Tryptophanyl-tRNA synthetase

Via homolog PDB 1i6k UniProt P00953 Formula C₂₁H₂₄N₇O₈P
Mol. weight 533.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TYM
PDB
1i6k
UniProt (similar protein)
P00953
Target protein
KP13_13547

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 533.44 Da
LogP (Crippen) -0.26
H-bond donors 6
H-bond acceptors 13
TPSA 233.95 Ų
Rotatable bonds 8
Aromatic rings 4 / 5
Heavy atoms 37
Fraction sp³ C 0.33
Formula C₂₁H₂₄N₇O₈P

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 233.9
  • −1 ≤ LogP ≤ 5 -0.26
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 533.4
  • LogP ≤ 5 -0.26
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 233.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N
InChI 
InChI=1S/C21H24N7O8P/c22-12(5-10-6-24-13-4-2-1-3-11(10)13)21(31)36-37(32,33)34-7-14-16(29)17(30)20(35-14)28-9-27-15-18(23)25-8-26-19(15)28/h1-4,6,8-9,12,14,16-17,20,24,29-30H,5,7,22H2,(H,32,33)(H2,23,25,26)/t12-,14+,16+,17+,20+/m0/s1
InChIKey 
IFQVDHDRFCKAAW-SQIXAUHQSA-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
PF00579

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_13547.

PDB 6

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)