Ligand profile

H3T

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

Bound to: KP13_01124 — putative phospholipid-binding protein mlaC

Via homolog PDB 6hsy UniProt Q9HVW4 Formula C₃₉H₇₅O₁₀P
Mol. weight 734.99 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
H3T
PDB
6hsy
UniProt (similar protein)
Q9HVW4
Target protein
KP13_01124

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 734.99 Da
LogP (Crippen) 9.75
H-bond donors 3
H-bond acceptors 9
TPSA 148.82 Ų
Rotatable bonds 37
Aromatic rings 0 / 1
Heavy atoms 50
Fraction sp³ C 0.95
Formula C₃₉H₇₅O₁₀P

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 148.8
  • −1 ≤ LogP ≤ 5 9.75
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 735.0
  • LogP ≤ 5 9.75
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 37
  • TPSA ≤ 140 Ų 148.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC[C@H](CO)O)OC(=O)CCCCCCC[C@@H]1C[C@@H]1CCCCCC
InChI 
InChI=1S/C39H75O10P/c1-3-5-7-9-10-11-12-13-14-15-16-19-23-27-38(42)46-32-37(33-48-50(44,45)47-31-36(41)30-40)49-39(43)28-24-20-17-18-22-26-35-29-34(35)25-21-8-6-4-2/h34-37,40-41H,3-33H2,1-2H3,(H,44,45)/t34-,35+,36-,37+/m0/s1
InChIKey 
JWIOKCJPLNKYBQ-TWHRXLCVSA-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
PF05494

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_01124.

PDB 3

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)