Ligand profile

3YE

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

Bound to: KP13_03811 — Phosphoribosylglycinamide formyltransferase

Via homolog PDB 4zz0 UniProt P22102 Formula C₁₉H₂₇N₅O₆
Mol. weight 421.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3YE
PDB
4zz0
UniProt (similar protein)
P22102
Target protein
KP13_03811

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 421.45 Da
LogP (Crippen) 1.15
H-bond donors 6
H-bond acceptors 6
TPSA 191.26 Ų
Rotatable bonds 13
Aromatic rings 2 / 2
Heavy atoms 30
Fraction sp³ C 0.53
Formula C₁₉H₂₇N₅O₆

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 1.15
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 421.5
  • LogP ≤ 5 1.15
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 191.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c([nH]c2c1C(=O)NC(=N2)N)CCCCCCCC(=O)N[C@@H](CCC(=O)O)C(=O)O
InChI 
InChI=1S/C19H27N5O6/c20-19-23-16-12(17(28)24-19)10-11(21-16)6-4-2-1-3-5-7-14(25)22-13(18(29)30)8-9-15(26)27/h10,13H,1-9H2,(H,22,25)(H,26,27)(H,29,30)(H4,20,21,23,24,28)/t13-/m0/s1
InChIKey 
MZFFIVGWDCAMQT-ZDUSSCGKSA-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)