Ligand profile

1F7

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

Bound to: KP13_00363 — LpxA-like domain-containing transferase

Via homolog PDB 4ihf UniProt P21645 Formula C₂₅H₄₉N₂O₉PS
Mol. weight 584.71 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1F7
PDB
4ihf
UniProt (similar protein)
P21645
Target protein
KP13_00363

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 584.71 Da
LogP (Crippen) 3.04
H-bond donors 6
H-bond acceptors 8
TPSA 182.49 Ų
Rotatable bonds 23
Aromatic rings 0 / 0
Heavy atoms 38
Fraction sp³ C 0.88
Formula C₂₅H₄₉N₂O₉PS

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 182.5
  • −1 ≤ LogP ≤ 5 3.04
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 584.7
  • LogP ≤ 5 3.04
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 23
  • TPSA ≤ 140 Ų 182.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCC[C@H](CC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(C)COP(=O)(O)O)O)O
InChI 
InChI=1S/C25H49N2O9PS/c1-4-5-6-7-8-9-10-11-12-13-20(28)18-22(30)38-17-16-26-21(29)14-15-27-24(32)23(31)25(2,3)19-36-37(33,34)35/h20,23,28,31H,4-19H2,1-3H3,(H,26,29)(H,27,32)(H2,33,34,35)/t20-,23-/m1/s1
InChIKey 
JYSKQPQRUCZFIQ-NFBKMPQASA-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
PF00132

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_00363.

PDB 15

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)