Ligand profile

3YD

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

Bound to: KP13_03811 — Phosphoribosylglycinamide formyltransferase

Via homolog PDB 4zyz UniProt P22102 Formula C₁₈H₂₅N₅O₆
Mol. weight 407.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3YD
PDB
4zyz
UniProt (similar protein)
P22102
Target protein
KP13_03811

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 407.43 Da
LogP (Crippen) 0.76
H-bond donors 6
H-bond acceptors 6
TPSA 191.26 Ų
Rotatable bonds 12
Aromatic rings 2 / 2
Heavy atoms 29
Fraction sp³ C 0.50
Formula C₁₈H₂₅N₅O₆

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 0.76
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 407.4
  • LogP ≤ 5 0.76
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • 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)CCCCCCC(=O)N[C@@H](CCC(=O)O)C(=O)O
InChI 
InChI=1S/C18H25N5O6/c19-18-22-15-11(16(27)23-18)9-10(20-15)5-3-1-2-4-6-13(24)21-12(17(28)29)7-8-14(25)26/h9,12H,1-8H2,(H,21,24)(H,25,26)(H,28,29)(H4,19,20,22,23,27)/t12-/m0/s1
InChIKey 
YFTJOYZLYVUUOD-LBPRGKRZSA-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)