Ligand profile

CHEMBL5899780

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_3002 — na+/H+ antiporter

Via homolog UniProt P48764 Formula C₄₂H₆₆ClN₁₃O₈

pchembl 8.10 ~7.9 nM

Mol. weight 916.53 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: CHEMBL5899780
UniProt (similar protein): P48764
pchembl: 8.100 (~7.9 nM)
Target protein: VK055_3002

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 916.53 Da

LogP (Crippen) 2.11

H-bond donors 8

H-bond acceptors 13

TPSA 266.20 Å²

Rotatable bonds 30

Aromatic rings 3 / 4

Heavy atoms 64

Fraction sp³ C 0.57

Formula C₄₂H₆₆ClN₁₃O₈

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 266.2
−1 ≤ LogP ≤ 5 2.11

Lipinski's Rule of Five Fail 3 violations

MW ≤ 500 Da 916.5
LogP ≤ 5 2.11
H-bond donors ≤ 5 8
H-bond acceptors ≤ 10 13

Veber's rules Fail

Rotatable bonds ≤ 10 30
TPSA ≤ 140 Å² 266.2

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

CCCOCNC(=O)NCCCCNC(=O)NCCOCCOCCNC(=O)NCCOCCOCCN1CCN(c2cccc(-c3nc(N=C(N)N)nc4ccc(Cl)cc34)c2)CC1

InChI

InChI=1S/C42H66ClN13O8/c1-2-20-64-31-51-42(59)47-11-4-3-10-46-40(57)48-12-21-60-25-26-61-22-13-49-41(58)50-14-23-62-27-28-63-24-19-55-15-17-56(18-16-55)34-7-5-6-32(29-34)37-35-30-33(43)8-9-36(35)52-39(53-37)54-38(44)45/h5-9,29-30H,2-4,10-28,31H2,1H3,(H2,46,48,57)(H2,47,51,59)(H2,49,50,58)(H4,44,45,52,53,54)

InChIKey

SZJPDSLJJGYQGV-UHFFFAOYSA-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: 762953
Binding sites: PF00999

External resources

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

ChEMBL ChEMBL compound CHEMBL5899780 →
UniProt UniProt P48764 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “CHEMBL5899780”) →

Other ligands for this protein

Quick navigation to other ligands bound to VK055_3002.

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)