Ligand profile

3ZE

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

Bound to: VK055_2316 — gpt

Via homolog PDB 4jls UniProt P0A9M5 Formula C₁₁H₁₅N₆O₆P
Mol. weight 358.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3ZE
PDB
4jls
UniProt (similar protein)
P0A9M5
Target protein
VK055_2316

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 358.25 Da
LogP (Crippen) -2.38
H-bond donors 5
H-bond acceptors 8
TPSA 187.66 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.45
Formula C₁₁H₁₅N₆O₆P

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 187.7
  • −1 ≤ LogP ≤ 5 -2.38
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 358.3
  • LogP ≤ 5 -2.38
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 187.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3CN(C[C@H]3O)C(=O)CP(=O)(O)O)N=C(NC2=O)N
InChI 
InChI=1S/C11H15N6O6P/c12-11-14-9-8(10(20)15-11)13-4-17(9)5-1-16(2-6(5)18)7(19)3-24(21,22)23/h4-6,18H,1-3H2,(H2,21,22,23)(H3,12,14,15,20)/t5-,6+/m0/s1
InChIKey 
PIHCTBQWWHFPNB-NTSWFWBYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00156

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_2316.

PDB 14

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

Ligand PDB entry

ChEMBL 2

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)