Ligand profile

M7M

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

Bound to: KP13_00803 — ATP-dependent RNA helicase srmB

Via homolog PDB 6qx9 UniProt Q9BUQ8 Formula C₁₃H₂₃N₅O₁₁P₂
Mol. weight 487.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
M7M
PDB
6qx9
UniProt (similar protein)
Q9BUQ8
Target protein
KP13_00803

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 487.30 Da
LogP (Crippen) -2.28
H-bond donors 6
H-bond acceptors 12
TPSA 218.45 Ų
Rotatable bonds 7
Aromatic rings 1 / 3
Heavy atoms 31
Fraction sp³ C 0.69
Formula C₁₃H₂₃N₅O₁₁P₂

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 218.4
  • −1 ≤ LogP ≤ 5 -2.28
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 487.3
  • LogP ≤ 5 -2.28
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 218.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CN(C2=C1C(=O)N=C(N2)N(C)C)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O)O)O
InChI 
InChI=1S/C13H23N5O11P2/c1-16(2)13-14-10-7(11(21)15-13)17(3)5-18(10)12-9(20)8(19)6(28-12)4-27-31(25,26)29-30(22,23)24/h6,8-9,12,19-20H,4-5H2,1-3H3,(H,25,26)(H,14,15,21)(H2,22,23,24)/t6-,8-,9-,12-/m1/s1
InChIKey 
DHQQIEJARUGVNZ-WOUKDFQISA-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
PF06544

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)