Ligand profile

LY3

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

Bound to: KP13_02286 — Thymidylate synthase

Via homolog PDB 1jtq UniProt P0A884 Formula C₂₀H₂₁N₉O₄
Mol. weight 451.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LY3
PDB
1jtq
UniProt (similar protein)
P0A884
Target protein
KP13_02286

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 451.45 Da
LogP (Crippen) -0.05
H-bond donors 6
H-bond acceptors 8
TPSA 208.42 Ų
Rotatable bonds 9
Aromatic rings 4 / 4
Heavy atoms 33
Fraction sp³ C 0.25
Formula C₂₀H₂₁N₉O₄

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 208.4
  • −1 ≤ LogP ≤ 5 -0.05
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 451.4
  • LogP ≤ 5 -0.05
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 208.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1CCc2c[nH]c3c2C(=O)NC(=N3)N)C(=O)N[C@@H](CCc4n[nH]nn4)C(=O)O
InChI 
InChI=1S/C20H21N9O4/c21-20-24-16-15(18(31)25-20)12(9-22-16)6-3-10-1-4-11(5-2-10)17(30)23-13(19(32)33)7-8-14-26-28-29-27-14/h1-2,4-5,9,13H,3,6-8H2,(H,23,30)(H,32,33)(H,26,27,28,29)(H4,21,22,24,25,31)/t13-/m0/s1
InChIKey 
MXAFDBCLWLMXSI-ZDUSSCGKSA-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)