Ligand profile

L3W

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

Bound to: KP13_00989 — NADH-quinone oxidoreductase subunit F

Via homolog PDB 6saq UniProt O66841 Formula C₂₁H₂₉N₇O₁₆P₂
Mol. weight 697.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
L3W
PDB
6saq
UniProt (similar protein)
O66841
Target protein
KP13_00989

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 697.44 Da
LogP (Crippen) -3.38
H-bond donors 9
H-bond acceptors 19
TPSA 354.92 Ų
Rotatable bonds 14
Aromatic rings 2 / 4
Heavy atoms 46
Fraction sp³ C 0.48
Formula C₂₁H₂₉N₇O₁₆P₂

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 354.9
  • −1 ≤ LogP ≤ 5 -3.38
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 697.4
  • LogP ≤ 5 -3.38
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 354.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N(/C=C/C=C(/C(=O)N)\O)C=O)O)O)O)O)N
InChI 
InChI=1S/C21H29N7O16P2/c22-17-12-19(25-6-24-17)28(7-26-12)21-16(34)14(32)11(43-21)5-41-46(38,39)44-45(36,37)40-4-10-13(31)15(33)20(42-10)27(8-29)3-1-2-9(30)18(23)35/h1-3,6-8,10-11,13-16,20-21,30-34H,4-5H2,(H2,23,35)(H,36,37)(H,38,39)(H2,22,24,25)/b3-1+,9-2-/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKey 
QSTZUQWNOOUKGF-OTTADCDWSA-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
PF01512

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_00989.

PDB 19

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)