Ligand profile

ZINC12612383

Virtual-screening candidate from ZINC.

Bound to: KP13_01311 — Methylmalonate semialdehyde dehydrogenase acylating

Via homolog UniProt P00352 Formula C₂₅H₂₆N₂O₃

Tanimoto 1.00

Mol. weight 402.49 Da

Permeability High

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: ZINC12612383
UniProt (similar protein): P00352
Tanimoto: 1.000
Target protein: KP13_01311

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 402.49 Da

LogP (Crippen) 3.74

H-bond donors 0

H-bond acceptors 4

TPSA 42.01 Å²

Rotatable bonds 3

Aromatic rings 2 / 6

Heavy atoms 30

Fraction sp³ C 0.40

Formula C₂₅H₂₆N₂O₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 42.0
−1 ≤ LogP ≤ 5 3.74

Lipinski's Rule of Five Pass 0 violations

MW ≤ 500 Da 402.5
LogP ≤ 5 3.74
H-bond donors ≤ 5 0
H-bond acceptors ≤ 10 4

Veber's rules Pass

Rotatable bonds ≤ 10 3
TPSA ≤ 140 Å² 42.0

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

COc1ccc2c(c1)C=C([C@@H]1C[C@H]3CN(c4ccccc4)C(=O)[C@]34CCCN14)CO2

InChI

InChI=1S/C25H26N2O3/c1-29-21-8-9-23-17(13-21)12-18(16-30-23)22-14-19-15-26(20-6-3-2-4-7-20)24(28)25(19)10-5-11-27(22)25/h2-4,6-9,12-13,19,22H,5,10-11,14-16H2,1H3/t19-,22-,25-/m0/s1

InChIKey

MDQKNUCUTOGXNR-JTJYXVOQSA-N

Provenance

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

Method: LigQ nearest_k
Query: CHEMBL600769
Homolog: P00352

External resources

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

ZINC ZINC15 ZINC12612383 →
ZINC ZINC20 ZINC12612383 →
UniProt UniProt P00352 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “ZINC12612383”) →

Other ligands for this protein

Quick navigation to other ligands bound to KP13_01311.

PDB 11

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

Ligand PDB entry

ChEMBL 100

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

Compound Potency (pchembl)

ZINC 49

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

Compound Similarity (Tanimoto)