Ligand profile

PD8

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

Bound to: VK055_4808 — folyl-polyglutamate synthetase

Via homolog PDB 1w78 UniProt P08192 Formula C₁₄H₁₃N₆O₆P
Mol. weight 392.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PD8
PDB
1w78
UniProt (similar protein)
P08192
Target protein
VK055_4808

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 392.27 Da
LogP (Crippen) 0.16
H-bond donors 5
H-bond acceptors 9
TPSA 193.41 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 27
Fraction sp³ C 0.07
Formula C₁₄H₁₃N₆O₆P

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 193.4
  • −1 ≤ LogP ≤ 5 0.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 392.3
  • LogP ≤ 5 0.16
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 193.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C(=O)OP(=O)(O)O)NCc2cnc3c(n2)C(=O)NC(=N3)N
InChI 
InChI=1S/C14H13N6O6P/c15-14-19-11-10(12(21)20-14)18-9(6-17-11)5-16-8-3-1-7(2-4-8)13(22)26-27(23,24)25/h1-4,6,16H,5H2,(H2,23,24,25)(H3,15,17,19,20,21)
InChIKey 
DNKVHXNVVYQUDC-UHFFFAOYSA-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
PF02875' 'PF08245

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4808.

PDB 6

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

Ligand PDB entry

ChEMBL 1

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)