Ligand profile

9RC

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

Bound to: HT085_RS00215 — oligoribonuclease

Via homolog PDB 6a4d UniProt Q47VZ4 Formula C₁₆H₁₈N₃O₁₀P
Mol. weight 443.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9RC
PDB
6a4d
UniProt (similar protein)
Q47VZ4
Target protein
HT085_RS00215

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 443.31 Da
LogP (Crippen) 0.60
H-bond donors 3
H-bond acceptors 10
TPSA 183.22 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 30
Fraction sp³ C 0.38
Formula C₁₆H₁₈N₃O₁₀P

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 183.2
  • −1 ≤ LogP ≤ 5 0.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 443.3
  • LogP ≤ 5 0.60
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 183.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)Oc3ccc(cc3)[N+](=O)[O-])O
InChI 
InChI=1S/C16H18N3O10P/c1-9-7-18(16(22)17-15(9)21)14-6-12(20)13(28-14)8-27-30(25,26)29-11-4-2-10(3-5-11)19(23)24/h2-5,7,12-14,20H,6,8H2,1H3,(H,25,26)(H,17,21,22)/t12-,13+,14+/m0/s1
InChIKey 
RWOAVOYBVRQNIZ-BFHYXJOUSA-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
PF00929

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_RS00215.

PDB 2

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)