Ligand profile

N5G

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

Bound to: VK055_4136 — 5-formyltetrahydrofolate cyclo-ligase

Via homolog PDB 3hy4 UniProt P49914 Formula C₂₀H₃₈N₇O₁₀P
Mol. weight 567.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
N5G
PDB
3hy4
UniProt (similar protein)
P49914
Target protein
VK055_4136

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 567.54 Da
LogP (Crippen) -3.64
H-bond donors 11
H-bond acceptors 12
TPSA 268.07 Ų
Rotatable bonds 12
Aromatic rings 0 / 3
Heavy atoms 38
Fraction sp³ C 0.85
Formula C₂₀H₃₈N₇O₁₀P

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 268.1
  • −1 ≤ LogP ≤ 5 -3.64
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 567.5
  • LogP ≤ 5 -3.64
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 268.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CC(CCC1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2CN[C@@H]3[C@H]([N@@]2COP(=O)(O)O)[C@H](N[C@@H](N3)N)O
InChI 
InChI=1S/C20H38N7O10P/c21-20-25-16-15(18(31)26-20)27(9-37-38(34,35)36)12(8-23-16)7-22-11-3-1-10(2-4-11)17(30)24-13(19(32)33)5-6-14(28)29/h10-13,15-16,18,20,22-23,25-26,31H,1-9,21H2,(H,24,30)(H,28,29)(H,32,33)(H2,34,35,36)/t10?,11?,12-,13-,15-,16-,18+,20+/m0/s1
InChIKey 
YEQBTMZGNSUQID-LJERSSFRSA-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
PF01812

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_4136.

PDB 1

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

Ligand PDB entry

ZINC 2

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)