Binder profile

M7M

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

Bound to: PA2840 — ATP-dependent RNA helicase

Via homolog PDB 6qx9 UniProt Q9BUQ8 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
PA2840

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.

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 TPW 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 binders for this protein

Quick navigation to other ligands bound to PA2840.

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)