Ligand profile

SMA

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

Bound to: KP13_00989 — NADH-quinone oxidoreductase subunit F

Via homolog PDB 2ybb UniProt Q56222 Formula C₃₀H₄₂O₇
Mol. weight 514.66 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SMA
PDB
2ybb
UniProt (similar protein)
Q56222
Target protein
KP13_00989

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 514.66 Da
LogP (Crippen) 6.14
H-bond donors 1
H-bond acceptors 7
TPSA 87.36 Ų
Rotatable bonds 13
Aromatic rings 2 / 2
Heavy atoms 37
Fraction sp³ C 0.50
Formula C₃₀H₄₂O₇

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 87.4
  • −1 ≤ LogP ≤ 5 6.14
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 514.7
  • LogP ≤ 5 6.14
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 87.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C/C=C(\C)/C=C/C=C[C@@H]([C@@H](C)[C@H]([C@@H](C)CCC1=C(C(=O)c2c(cc(c(c2O1)O)OC)OC)C)OC)OC
InChI 
InChI=1S/C30H42O7/c1-10-18(2)13-11-12-14-22(33-6)21(5)29(36-9)19(3)15-16-23-20(4)27(31)26-24(34-7)17-25(35-8)28(32)30(26)37-23/h10-14,17,19,21-22,29,32H,15-16H2,1-9H3/b13-11+,14-12?,18-10+/t19-,21+,22-,29-/m0/s1
InChIKey 
UZHDGDDPOPDJGM-WPPYOTIYSA-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
PF00032' 'PF00033' 'PF00355

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)