Ligand profile

1R3

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

Bound to: KP13_03868 — 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

Via homolog PDB 4keh UniProt P0A6Q3 Formula C₂₁H₄₅N₂O₉PS
Mol. weight 532.64 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1R3
PDB
4keh
UniProt (similar protein)
P0A6Q3
Target protein
KP13_03868

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 532.64 Da
LogP (Crippen) 3.00
H-bond donors 7
H-bond acceptors 7
TPSA 185.65 Ų
Rotatable bonds 20
Aromatic rings 0 / 0
Heavy atoms 34
Fraction sp³ C 0.90
Formula C₂₁H₄₅N₂O₉PS

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 185.6
  • −1 ≤ LogP ≤ 5 3.00
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 532.6
  • LogP ≤ 5 3.00
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 185.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCS(CCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)O)O)(O)O
InChI 
InChI=1S/C21H45N2O9PS/c1-4-5-6-7-8-9-10-15-34(30,31)16-11-13-22-18(24)12-14-23-20(26)19(25)21(2,3)17-32-33(27,28)29/h19,25,30-31H,4-17H2,1-3H3,(H,22,24)(H,23,26)(H2,27,28,29)/t19-/m0/s1
InChIKey 
ZGCXUZRDGZYOOW-IBGZPJMESA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF07977

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_03868.

PDB 12

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)