Ligand profile

CHEMBL3987020

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_5137 — na+/H+ antiporter

Via homolog UniProt P48764 Formula C₅₈H₇₈Cl₄N₈O₁₆S₂
pchembl 8.70 ~2.0 nM
Mol. weight 1349.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3987020
UniProt (similar protein)
P48764
pchembl
8.700 (~2.0 nM)
Target protein
VK055_5137

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1349.25 Da
LogP (Crippen) 3.82
H-bond donors 6
H-bond acceptors 18
TPSA 293.48 Ų
Rotatable bonds 41
Aromatic rings 4 / 6
Heavy atoms 88
Fraction sp³ C 0.52
Formula C₅₈H₇₈Cl₄N₈O₁₆S₂

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 293.5
  • −1 ≤ LogP ≤ 5 3.82
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1349.2
  • LogP ≤ 5 3.82
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 41
  • TPSA ≤ 140 Ų 293.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1Cc2c(Cl)cc(Cl)cc2[C@H](c2cccc(S(=O)(=O)NCCOCCOCCOCCNC(=O)CN(CCN(CC(=O)O)CC(=O)NCCOCCOCCOCCNS(=O)(=O)c3cccc([C@@H]4CN(C)Cc5c(Cl)cc(Cl)cc54)c3)CC(=O)O)c2)C1
InChI 
InChI=1S/C58H78Cl4N8O16S2/c1-67-33-49(47-29-43(59)31-53(61)51(47)35-67)41-5-3-7-45(27-41)87(77,78)65-11-17-83-21-25-85-23-19-81-15-9-63-55(71)37-69(39-57(73)74)13-14-70(40-58(75)76)38-56(72)64-10-16-82-20-24-86-26-22-84-18-12-66-88(79,80)46-8-4-6-42(28-46)50-34-68(2)36-52-48(50)30-44(60)32-54(52)62/h3-8,27-32,49-50,65-66H,9-26,33-40H2,1-2H3,(H,63,71)(H,64,72)(H,73,74)(H,75,76)/t49-,50-/m0/s1
InChIKey 
RGKGUYUTRZOCGU-WLTNIFSVSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
ChEMBL
Activity
763030
Binding sites
PF00999

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_5137.

PDB 2

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 99

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)