Ligand profile

ZMP

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

Bound to: KP13_00989 — NADH-quinone oxidoreductase subunit F

Via homolog PDB 5gup UniProt A0A4X1SZP7 Formula C₂₅H₄₉N₂O₈PS
Mol. weight 568.71 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZMP
PDB
5gup
UniProt (similar protein)
A0A4X1SZP7
Target protein
KP13_00989

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 568.71 Da
LogP (Crippen) 4.07
H-bond donors 5
H-bond acceptors 7
TPSA 162.26 Ų
Rotatable bonds 23
Aromatic rings 0 / 0
Heavy atoms 37
Fraction sp³ C 0.88
Formula C₂₅H₄₉N₂O₈PS

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 162.3
  • −1 ≤ LogP ≤ 5 4.07
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 568.7
  • LogP ≤ 5 4.07
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 23
  • TPSA ≤ 140 Ų 162.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(C)COP(=O)(O)O)O
InChI 
InChI=1S/C25H49N2O8PS/c1-4-5-6-7-8-9-10-11-12-13-14-15-22(29)37-19-18-26-21(28)16-17-27-24(31)23(30)25(2,3)20-35-36(32,33)34/h23,30H,4-20H2,1-3H3,(H,26,28)(H,27,31)(H2,32,33,34)/t23-/m1/s1
InChIKey 
HDTINWYIVVMRIN-HSZRJFAPSA-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
PF05347

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_00989.

PDB 19

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)