Ligand profile

8ND

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

Bound to: KP13_01124 — putative phospholipid-binding protein mlaC

Via homolog PDB 5uwa UniProt P0ADV7 Formula C₃₇H₇₃NO₅
Mol. weight 611.99 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8ND
PDB
5uwa
UniProt (similar protein)
P0ADV7
Target protein
KP13_01124

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 611.99 Da
LogP (Crippen) 10.38
H-bond donors 1
H-bond acceptors 6
TPSA 87.85 Ų
Rotatable bonds 35
Aromatic rings 0 / 0
Heavy atoms 43
Fraction sp³ C 0.95
Formula C₃₇H₇₃NO₅

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 87.8
  • −1 ≤ LogP ≤ 5 10.38
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 612.0
  • LogP ≤ 5 10.38
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 35
  • TPSA ≤ 140 Ų 87.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCC(=O)OC[C@H](COCCN)OC(=O)CCCCCCCCCCCCCCC
InChI 
InChI=1S/C37H73NO5/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-36(39)42-34-35(33-41-32-31-38)43-37(40)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h35H,3-34,38H2,1-2H3/t35-/m0/s1
InChIKey 
UWTLPHGXKLBELN-DHUJRADRSA-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)