Structure

Physi-Chem Properties

Molecular Weight:  576.33
Volume:  581.892
LogP:  4.136
LogD:  3.54
LogS:  -4.611
# Rotatable Bonds:  6
TPSA:  127.82
# H-Bond Aceptor:  9
# H-Bond Donor:  3
# Rings:  6
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.339
Synthetic Accessibility Score:  5.373
Fsp3:  0.844
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.297
MDCK Permeability:  6.866941839689389e-05
Pgp-inhibitor:  0.193
Pgp-substrate:  0.996
Human Intestinal Absorption (HIA):  0.03
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.21

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.113
Plasma Protein Binding (PPB):  92.042236328125%
Volume Distribution (VD):  1.054
Pgp-substrate:  6.966650485992432%

ADMET: Metabolism

CYP1A2-inhibitor:  0.005
CYP1A2-substrate:  0.35
CYP2C19-inhibitor:  0.011
CYP2C19-substrate:  0.632
CYP2C9-inhibitor:  0.088
CYP2C9-substrate:  0.047
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.166
CYP3A4-inhibitor:  0.477
CYP3A4-substrate:  0.61

ADMET: Excretion

Clearance (CL):  11.338
Half-life (T1/2):  0.086

ADMET: Toxicity

hERG Blockers:  0.672
Human Hepatotoxicity (H-HT):  0.333
Drug-inuced Liver Injury (DILI):  0.695
AMES Toxicity:  0.201
Rat Oral Acute Toxicity:  0.918
Maximum Recommended Daily Dose:  0.957
Skin Sensitization:  0.874
Carcinogencity:  0.522
Eye Corrosion:  0.003
Eye Irritation:  0.013
Respiratory Toxicity:  0.965

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  Natural Product: NPC103534

Natural Product ID:  NPC103534
Common Name*:   JLPDBLFIVFSOCC-XYXFTTADSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JLPDBLFIVFSOCC-XYXFTTADSA-N
Standard InCHI:  InChI=1S/C32H48O9/c1-17-29(35)24(37-5)14-27(39-17)41-21-8-10-30(3)20(13-21)6-7-23-22(30)9-11-31(4)28(19-12-26(34)38-16-19)25(40-18(2)33)15-32(23,31)36/h12,17,20-25,27-29,35-36H,6-11,13-16H2,1-5H3/t17-,20+,21-,22-,23+,24-,25-,27-,28-,29-,30-,31+,32-/m0/s1
SMILES:  C[C@H]1[C@@H]([C@H](C[C@@H](O1)O[C@H]1CC[C@@]2(C)[C@H](CC[C@@H]3[C@@H]2CC[C@]2(C)[C@@H](C4=CC(=O)OC4)[C@H](C[C@]32O)OC(=O)C)C1)OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11541511
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001125] Steroid lactones
          • [CHEMONTID:0001555] Cardenolides and derivatives
            • [CHEMONTID:0001559] Cardenolide glycosides and derivatives

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/C39730000707]
NPO1071 Parerythropodium fulvum Species n.a. n.a. n.a. n.a. n.a. PMID[11277760]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota leaves Niigata City, Niigata Province, Japan 2000-Nov PMID[15730243]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota leaves n.a. n.a. PMID[16933868]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[17253842]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota stems and twigs Niigata City, Niigata Province, Japan 2001-NOV PMID[17595134]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota stems and twigs n.a. n.a. PMID[17595134]
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18491868]
NPO3936 Malva sylvestris Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[19731587]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[29693393]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota Leaves; Stems n.a. n.a. PMID[9214727]
NPO2747 Hypericum triquetrifolium Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13325 Plantago lanceolata Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6520 Myrica multiflora Species Myricaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3664 Mesembryanthemum anatomicum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3936 Malva sylvestris Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24652 Toxicodendron succedaneum Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14048 Cryptotaenia japonica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14048 Cryptotaenia japonica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6520 Myrica multiflora Species Myricaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3664 Mesembryanthemum anatomicum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2518 Crinum kirkii Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2747 Hypericum triquetrifolium Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13325 Plantago lanceolata Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3936 Malva sylvestris Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24652 Toxicodendron succedaneum Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14048 Cryptotaenia japonica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24652 Toxicodendron succedaneum Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1607 Croton rhamnifolius Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20132 Scutellaria seleriana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6520 Myrica multiflora Species Myricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2747 Hypericum triquetrifolium Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO715 Teucrium pestalozzae Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24652 Toxicodendron succedaneum Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15583 Tripodanthus acutifolius Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5980 Eria subsessilis Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8472 Knightia deplanchei Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1071 Parerythropodium fulvum Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO3146 Ammodendron conollyi Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3936 Malva sylvestris Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO351 Cirsium dipsacolepis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2518 Crinum kirkii Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5197 Streptomyces eurythermus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4253 Viguiera annua Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3664 Mesembryanthemum anatomicum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6776 Trifolium apertum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1308 Veronica pectinata Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8585 Verpa digitaliformis Species Morchellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2361 Aconitum brevicalcaratum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6377 Cocculus diversifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14048 Cryptotaenia japonica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7097 Rhynchosporium orthosporum Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4082 Ophiarthrum elegans Species Ophiocomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12987 Rhododendron farrerae Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18054 Curvularia coicis Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6974 Solanum racemigerum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8840 Ptilidium ciliare Species Ptilidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13325 Plantago lanceolata Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5591 Fucus spiralis Species Fucaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT71 Cell Line HEK293 Homo sapiens IC50 = 28.0 nM PMID[29693393]
NPT404 Cell Line CCRF-CEM Homo sapiens IC50 = 19.0 nM PMID[31325787]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 33.0 nM PMID[31325787]
NPT165 Cell Line HeLa Homo sapiens IC50 = 62.0 nM PMID[31325787]
NPT1160 Cell Line BJ Homo sapiens IC50 = 26.0 nM PMID[31325787]
NPT404 Cell Line CCRF-CEM Homo sapiens IC50 = 19.0 nM PMID[32645647]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 33.0 nM PMID[32645647]
NPT165 Cell Line HeLa Homo sapiens IC50 = 62.0 nM PMID[32645647]
NPT1160 Cell Line BJ Homo sapiens IC50 = 26.0 nM PMID[32645647]
NPT24787 SINGLE PROTEIN Neurogenic locus notch homolog protein 1 Mus musculus IC50 = 120.0 nM PMID[29693393]
NPT18515 CELL-LINE HPBALL Homo sapiens IC50 = 14.0 nM PMID[29693393]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 49.78 % DOI[10.21203/rs.3.rs-23951/v1]
NPT22588 PROTEIN COMPLEX GROUP Sodium/potassium-transporting ATPase Sus scrofa Activity = 49.0 % PMID[31325787]
NPT22588 PROTEIN COMPLEX GROUP Sodium/potassium-transporting ATPase Sus scrofa Inhibition = 25.0 % PMID[31325787]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 11.04 % DOI[10.6019/CHEMBL4495564]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -0.02 % DOI[10.6019/CHEMBL4495565]
NPT2 Others Unspecified Activity = 59.2 % PMID[32645647]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC103534 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC103534 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data