Ligand profile

FDA

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

Bound to: KP13_03430 — Choline dehydrogenase

Via homolog PDB 4ynt UniProt B8MX95 Formula C₂₇H₃₅N₉O₁₅P₂
Mol. weight 787.57 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
FDA
PDB
4ynt
UniProt (similar protein)
B8MX95
Target protein
KP13_03430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 787.57 Da
LogP (Crippen) -1.75
H-bond donors 11
H-bond acceptors 20
TPSA 363.28 Ų
Rotatable bonds 13
Aromatic rings 4 / 6
Heavy atoms 53
Fraction sp³ C 0.44
Formula C₂₇H₃₅N₉O₁₅P₂

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 363.3
  • −1 ≤ LogP ≤ 5 -1.75
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 787.6
  • LogP ≤ 5 -1.75
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 363.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
InChI 
InChI=1S/C27H35N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,32,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H2,33,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKey 
YPZRHBJKEMOYQH-UYBVJOGSSA-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
PF00732' 'PF05199

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_03430.

PDB 6

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)