Ligand profile

6ZL

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

Bound to: KP13_03756 — Nucleoside permease nupC

Via homolog PDB 5l24 UniProt G4CRQ5 Formula C₄₃H₈₀O₂₂
Mol. weight 949.09 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6ZL
PDB
5l24
UniProt (similar protein)
G4CRQ5
Target protein
KP13_03756

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 949.09 Da
LogP (Crippen) -3.24
H-bond donors 14
H-bond acceptors 22
TPSA 357.06 Ų
Rotatable bonds 28
Aromatic rings 0 / 4
Heavy atoms 65
Fraction sp³ C 1.00
Formula C₄₃H₈₀O₂₂

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 357.1
  • −1 ≤ LogP ≤ 5 -3.24
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 949.1
  • LogP ≤ 5 -3.24
  • H-bond donors ≤ 5 14
  • H-bond acceptors ≤ 10 22
Veber's rules Fail
  • Rotatable bonds ≤ 10 28
  • TPSA ≤ 140 Ų 357.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCC(CCCCCCCC)(CO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O)CO[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O[C@@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)O)O
InChI 
InChI=1S/C43H80O22/c1-3-5-7-9-11-13-15-43(16-14-12-10-8-6-4-2,21-58-39-35(56)31(52)37(25(19-46)62-39)64-41-33(54)29(50)27(48)23(17-44)60-41)22-59-40-36(57)32(53)38(26(20-47)63-40)65-42-34(55)30(51)28(49)24(18-45)61-42/h23-42,44-57H,3-22H2,1-2H3/t23-,24-,25-,26-,27-,28-,29+,30+,31-,32-,33-,34-,35-,36-,37-,38-,39-,40-,41-,42-/m1/s1
InChIKey 
GDAZOFIUKHGYGD-VLJUBQHSSA-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
PF01773' 'PF07662' 'PF07670

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_03756.

PDB 9

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)