Ligand profile

ZINC53188920

Virtual-screening candidate from ZINC.

Bound to: KP13_04672 — Phenylalanyl-tRNA synthetase beta chain

Via homolog UniProt Q5SGX1 Formula C₂₃H₃₁N₇O₅
Tanimoto 0.75
Mol. weight 485.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC53188920
UniProt (similar protein)
Q5SGX1
Tanimoto
0.753
Target protein
KP13_04672

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 485.55 Da
LogP (Crippen) -0.45
H-bond donors 3
H-bond acceptors 11
TPSA 152.09 Ų
Rotatable bonds 8
Aromatic rings 3 / 4
Heavy atoms 35
Fraction sp³ C 0.48
Formula C₂₃H₃₁N₇O₅

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 152.1
  • −1 ≤ LogP ≤ 5 -0.45
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 485.5
  • LogP ≤ 5 -0.45
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 152.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(C[C@@H](N)C(=O)N(C)[C@H]2[C@H](O)[C@H](n3cnc4c(N(C)C)ncnc43)O[C@H]2CO)cc1
InChI 
InChI=1S/C23H31N7O5/c1-28(2)20-17-21(26-11-25-20)30(12-27-17)23-19(32)18(16(10-31)35-23)29(3)22(33)15(24)9-13-5-7-14(34-4)8-6-13/h5-8,11-12,15-16,18-19,23,31-32H,9-10,24H2,1-4H3/t15-,16+,18-,19+,23-/m1/s1
InChIKey 
VZPOYHASKSFENZ-FWSLATNXSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
PUY
Homolog
Q5SGX1

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_04672.

PDB 4

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)