Ligand profile

GNP

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

Bound to: HT085_RS00320 — redox-regulated ATPase YchF

Via homolog PDB 5ee9 UniProt Q6Z1J6 Formula C₁₀H₁₇N₆O₁₃P₃
Mol. weight 522.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GNP
PDB
5ee9
UniProt (similar protein)
Q6Z1J6
Target protein
HT085_RS00320

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 522.20 Da
LogP (Crippen) -2.76
H-bond donors 9
H-bond acceptors 13
TPSA 301.90 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.50
Formula C₁₀H₁₇N₆O₁₃P₃

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 301.9
  • −1 ≤ LogP ≤ 5 -2.76
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 522.2
  • LogP ≤ 5 -2.76
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 301.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKey 
UQABYHGXWYXDTK-UUOKFMHZSA-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
PF01926

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to HT085_RS00320.

PDB 3

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)