Ligand profile

3Y9

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_03811 — Phosphoribosylglycinamide formyltransferase

Via homolog UniProt Q64737 Formula C₂₂H₂₅N₅O₆
pchembl 6.82 ~151.4 nM
Mol. weight 455.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3Y9
UniProt (similar protein)
Q64737
pchembl
6.820 (~151.4 nM)
Target protein
KP13_03811

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 455.47 Da
LogP (Crippen) 1.45
H-bond donors 6
H-bond acceptors 6
TPSA 191.26 Ų
Rotatable bonds 11
Aromatic rings 3 / 3
Heavy atoms 33
Fraction sp³ C 0.32
Formula C₂₂H₂₅N₅O₆

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 191.3
  • −1 ≤ LogP ≤ 5 1.45
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 455.5
  • LogP ≤ 5 1.45
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 191.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1CCCCc2cc3c([nH]2)N=C(NC3=O)N)C(=O)N[C@@H](CCC(=O)O)C(=O)O
InChI 
InChI=1S/C22H25N5O6/c23-22-26-18-15(20(31)27-22)11-14(24-18)4-2-1-3-12-5-7-13(8-6-12)19(30)25-16(21(32)33)9-10-17(28)29/h5-8,11,16H,1-4,9-10H2,(H,25,30)(H,28,29)(H,32,33)(H4,23,24,26,27,31)/t16-/m0/s1
InChIKey 
CEPQCJFDTGQKDN-INIZCTEOSA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00551

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_03811.

PDB 23

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

Ligand PDB entry

ChEMBL 73

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)