Ligand profile

1JY

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

Bound to: KP13_02286 — Thymidylate synthase

Via homolog PDB 4isk UniProt P0A884 Formula C₃₂H₃₃N₅O₁₀
Mol. weight 647.64 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1JY
PDB
4isk
UniProt (similar protein)
P0A884
Target protein
KP13_02286

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 647.64 Da
LogP (Crippen) 0.94
H-bond donors 7
H-bond acceptors 9
TPSA 239.32 Ų
Rotatable bonds 15
Aromatic rings 3 / 4
Heavy atoms 47
Fraction sp³ C 0.34
Formula C₃₂H₃₃N₅O₁₀

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 239.3
  • −1 ≤ LogP ≤ 5 0.94
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 647.6
  • LogP ≤ 5 0.94
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 239.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C#CCN(c1ccc(cc1)C(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O)C2CCc3c2cc4c(c3)NC(=NC4=O)CO
InChI 
InChI=1S/C32H33N5O10/c1-2-13-37(25-10-5-18-14-24-21(15-20(18)25)30(43)36-26(16-38)33-24)19-6-3-17(4-7-19)29(42)35-23(32(46)47)8-11-27(39)34-22(31(44)45)9-12-28(40)41/h1,3-4,6-7,14-15,22-23,25,38H,5,8-13,16H2,(H,34,39)(H,35,42)(H,40,41)(H,44,45)(H,46,47)(H,33,36,43)
InChIKey 
NVHRBQOZEMFKLD-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF00303

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_02286.

PDB 32

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

Ligand PDB entry

ChEMBL 100

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)