Ligand profile

CHEMBL3978115

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_5137 — na+/H+ antiporter

Via homolog UniProt P48764 Formula C₅₆H₇₄F₄N₁₂O₁₆S₂

pchembl 8.10 ~7.9 nM

Mol. weight 1311.40 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: CHEMBL3978115
UniProt (similar protein): P48764
pchembl: 8.100 (~7.9 nM)
Target protein: VK055_5137

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1311.40 Da

LogP (Crippen) 2.97

H-bond donors 10

H-bond acceptors 16

TPSA 411.38 Å²

Rotatable bonds 41

Aromatic rings 4 / 4

Heavy atoms 90

Fraction sp³ C 0.39

Formula C₅₆H₇₄F₄N₁₂O₁₆S₂

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 Å² and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

TPSA ≤ 90 Å² 411.4
−1 ≤ LogP ≤ 5 2.97

Lipinski's Rule of Five Fail 3 violations

MW ≤ 500 Da 1311.4
LogP ≤ 5 2.97
H-bond donors ≤ 5 10
H-bond acceptors ≤ 10 16

Veber's rules Fail

Rotatable bonds ≤ 10 41
TPSA ≤ 140 Å² 411.4

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

C/C(=C\c1cc(F)c(Oc2ccc(S(=O)(=O)NCCOCCOCCOCCNC(=O)NCCCCNC(=O)NCCOCCOCCOCCNS(=O)(=O)c3ccc(Oc4c(F)cc(/C=C(\C)C(=O)N=C(N)N)cc4F)cc3)cc2)c(F)c1)C(=O)N=C(N)N

InChI

InChI=1S/C56H74F4N12O16S2/c1-37(51(73)71-53(61)62)31-39-33-45(57)49(46(58)34-39)87-41-5-9-43(10-6-41)89(77,78)69-17-21-83-25-29-85-27-23-81-19-15-67-55(75)65-13-3-4-14-66-56(76)68-16-20-82-24-28-86-30-26-84-22-18-70-90(79,80)44-11-7-42(8-12-44)88-50-47(59)35-40(36-48(50)60)32-38(2)52(74)72-54(63)64/h5-12,31-36,69-70H,3-4,13-30H2,1-2H3,(H2,65,67,75)(H2,66,68,76)(H4,61,62,71,73)(H4,63,64,72,74)/b37-31+,38-32+

InChIKey

IRDRZJHGMWFMDK-CBSZVXRSSA-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: 762955
Binding sites: PF00999

External resources

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

ChEMBL ChEMBL compound CHEMBL3978115 →
UniProt UniProt P48764 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “CHEMBL3978115”) →

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)