Ligand profile

F89

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

Bound to: KP13_02286 — Thymidylate synthase

Via homolog PDB 1syn UniProt P0A884 Formula C₂₇H₂₄N₄O₆
Mol. weight 500.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
F89
PDB
1syn
UniProt (similar protein)
P0A884
Target protein
KP13_02286

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 500.51 Da
LogP (Crippen) 3.27
H-bond donors 4
H-bond acceptors 6
TPSA 152.69 Ų
Rotatable bonds 8
Aromatic rings 4 / 5
Heavy atoms 37
Fraction sp³ C 0.22
Formula C₂₇H₂₄N₄O₆

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 152.7
  • −1 ≤ LogP ≤ 5 3.27
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 500.5
  • LogP ≤ 5 3.27
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 152.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=Nc2ccc3ccc(cc3c2C(=O)N1)CNc4ccc5c(c4)CN(C5=O)[C@@H](CCC(=O)O)C(=O)O
InChI 
InChI=1S/C27H24N4O6/c1-14-29-21-7-4-16-3-2-15(10-20(16)24(21)25(34)30-14)12-28-18-5-6-19-17(11-18)13-31(26(19)35)22(27(36)37)8-9-23(32)33/h2-7,10-11,22,28H,8-9,12-13H2,1H3,(H,32,33)(H,36,37)(H,29,30,34)/t22-/m0/s1
InChIKey 
BRVFNEZMTRVUGW-QFIPXVFZSA-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)