Ligand profile

8OD

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

Bound to: KP13_00803 — ATP-dependent RNA helicase srmB

Via homolog PDB 3nbf UniProt Q72GF3 Formula C₁₀H₁₅N₅O₁₁P₂
Mol. weight 443.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8OD
PDB
3nbf
UniProt (similar protein)
Q72GF3
Target protein
KP13_00803

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 443.20 Da
LogP (Crippen) -2.45
H-bond donors 7
H-bond acceptors 12
TPSA 252.57 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 28
Fraction sp³ C 0.50
Formula C₁₀H₁₅N₅O₁₁P₂

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 252.6
  • −1 ≤ LogP ≤ 5 -2.45
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 443.2
  • LogP ≤ 5 -2.45
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 252.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)N(C(=O)N2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
InChI 
InChI=1S/C10H15N5O11P2/c11-7-4-8(13-2-12-7)15(10(18)14-4)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,14,18)(H,22,23)(H2,11,12,13)(H2,19,20,21)/t3-,5-,6-,9-/m1/s1
InChIKey 
RKHXUJRVBUXHAN-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
PF00270

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to KP13_00803.

PDB 7

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)