Ligand profile

LYD

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

Bound to: KP13_02286 — Thymidylate synthase

Via homolog PDB 1jut UniProt P0A884 Formula C₂₀H₂₃N₅O₄
Mol. weight 397.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LYD
PDB
1jut
UniProt (similar protein)
P0A884
Target protein
KP13_02286

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 397.44 Da
LogP (Crippen) 1.46
H-bond donors 5
H-bond acceptors 5
TPSA 153.96 Ų
Rotatable bonds 7
Aromatic rings 3 / 3
Heavy atoms 29
Fraction sp³ C 0.30
Formula C₂₀H₂₃N₅O₄

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 154.0
  • −1 ≤ LogP ≤ 5 1.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 397.4
  • LogP ≤ 5 1.46
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 154.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@@H](C(=O)O)NC(=O)c1ccc(cc1)CCc2c[nH]c3c2C(=O)NC(=N3)N
InChI 
InChI=1S/C20H23N5O4/c1-10(2)15(19(28)29)23-17(26)12-6-3-11(4-7-12)5-8-13-9-22-16-14(13)18(27)25-20(21)24-16/h3-4,6-7,9-10,15H,5,8H2,1-2H3,(H,23,26)(H,28,29)(H4,21,22,24,25,27)/t15-/m0/s1
InChIKey 
MYENGRJSPURSQB-HNNXBMFYSA-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)