Ligand profile

3YA

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

Bound to: KP13_03811 — Phosphoribosylglycinamide formyltransferase

Via homolog PDB 4zyu UniProt P22102 Formula C₂₂H₂₄N₄O₆S
Mol. weight 472.52 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3YA
PDB
4zyu
UniProt (similar protein)
P22102
Target protein
KP13_03811

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 472.52 Da
LogP (Crippen) 2.18
H-bond donors 5
H-bond acceptors 7
TPSA 175.47 Ų
Rotatable bonds 11
Aromatic rings 3 / 3
Heavy atoms 33
Fraction sp³ C 0.32
Formula C₂₂H₂₄N₄O₆S

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 175.5
  • −1 ≤ LogP ≤ 5 2.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 472.5
  • LogP ≤ 5 2.18
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 175.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1CCCCc2cc3c(s2)NC(=NC3=O)N)C(=O)N[C@@H](CCC(=O)O)C(=O)O
InChI 
InChI=1S/C22H24N4O6S/c23-22-25-19(30)15-11-14(33-20(15)26-22)4-2-1-3-12-5-7-13(8-6-12)18(29)24-16(21(31)32)9-10-17(27)28/h5-8,11,16H,1-4,9-10H2,(H,24,29)(H,27,28)(H,31,32)(H3,23,25,26,30)/t16-/m0/s1
InChIKey 
KVBZUTNKUVNMNN-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
PDB
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 22

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

Ligand PDB entry

ChEMBL 74

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)