Ligand profile

LYB

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

Bound to: KP13_02286 — Thymidylate synthase

Via homolog PDB 1jtu UniProt P0A884 Formula C₃₅H₄₂N₈O₁₅
Mol. weight 814.76 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LYB
PDB
1jtu
UniProt (similar protein)
P0A884
Target protein
KP13_02286

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 814.76 Da
LogP (Crippen) -1.28
H-bond donors 12
H-bond acceptors 12
TPSA 390.46 Ų
Rotatable bonds 24
Aromatic rings 3 / 3
Heavy atoms 58
Fraction sp³ C 0.40
Formula C₃₅H₄₂N₈O₁₅

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 390.5
  • −1 ≤ LogP ≤ 5 -1.28
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 814.8
  • LogP ≤ 5 -1.28
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 24
  • TPSA ≤ 140 Ų 390.5
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](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)C(=O)O
InChI 
InChI=1S/C35H42N8O15/c36-35-42-28-27(30(50)43-35)18(15-37-28)6-3-16-1-4-17(5-2-16)29(49)41-22(34(57)58)9-13-25(46)39-20(32(53)54)7-11-23(44)38-19(31(51)52)8-12-24(45)40-21(33(55)56)10-14-26(47)48/h1-2,4-5,15,19-22H,3,6-14H2,(H,38,44)(H,39,46)(H,40,45)(H,41,49)(H,47,48)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H4,36,37,42,43,50)/t19-,20-,21+,22-/m0/s1
InChIKey 
DICHBVJYDUDAIQ-KJJMTIBFSA-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)