Structure

Physi-Chem Properties

Molecular Weight:  428.29
Volume:  454.097
LogP:  3.887
LogD:  3.672
LogS:  -4.844
# Rotatable Bonds:  0
TPSA:  58.92
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  6
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.554
Synthetic Accessibility Score:  5.578
Fsp3:  0.852
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.833
MDCK Permeability:  9.373615284857806e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.202
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.805
30% Bioavailability (F30%):  0.394

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.359
Plasma Protein Binding (PPB):  57.62260437011719%
Volume Distribution (VD):  1.634
Pgp-substrate:  34.32433319091797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.02
CYP1A2-substrate:  0.454
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.738
CYP2C9-inhibitor:  0.084
CYP2C9-substrate:  0.067
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.28
CYP3A4-inhibitor:  0.671
CYP3A4-substrate:  0.372

ADMET: Excretion

Clearance (CL):  9.374
Half-life (T1/2):  0.348

ADMET: Toxicity

hERG Blockers:  0.708
Human Hepatotoxicity (H-HT):  0.397
Drug-inuced Liver Injury (DILI):  0.505
AMES Toxicity:  0.484
Rat Oral Acute Toxicity:  0.384
Maximum Recommended Daily Dose:  0.98
Skin Sensitization:  0.652
Carcinogencity:  0.572
Eye Corrosion:  0.006
Eye Irritation:  0.05
Respiratory Toxicity:  0.956

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  Natural Product: NPC270249

Natural Product ID:  NPC270249
Common Name*:   ALTRINCJVPIQNK-YIMFJVKZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ALTRINCJVPIQNK-YIMFJVKZSA-N
Standard InCHI:  InChI=1S/C27H40O4/c1-15-7-10-27(30-14-15)16(2)24-22(31-27)13-21-19-6-5-17-11-18(28)12-23(29)26(17,4)20(19)8-9-25(21,24)3/h5,16,18-24,28-29H,1,6-14H2,2-4H3/t16-,18+,19+,20+,21+,22-,23+,24-,25-,26-,27+/m0/s1
SMILES:  C=C1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@@H]4[C@@H]5CC=C6C[C@H](C[C@H]([C@]6(C)[C@@H]5CC[C@]34C)O)O)O2)OC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

*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
NPO25265 Sophora secundiflora Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4039(00)78784-3]
NPO26956 Crambe crambe Species Esperiopsidae Eukaryota n.a. n.a. n.a. DOI[10.1021/jo00019a049]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota Seeds n.a. n.a. PMID[11325235]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. leaf n.a. PMID[11348221]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota Seeds n.a. n.a. PMID[14575439]
NPO26173 Anomospermum grandifolium Species Menispermaceae Eukaryota Stems n.a. n.a. PMID[14695805]
NPO26683 Dichomitus squalens Species Polyporaceae Eukaryota n.a. n.a. n.a. PMID[15620268]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[15844957]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[16378361]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruits Tahiti n.a. PMID[17378609]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[17480098]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota roots n.a. n.a. PMID[18076142]
NPO24757 Meryta denhamii Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[18442289]
NPO9613 Anisomeles indica Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18547115]
NPO24883 Angiopteris caudatiformis Species Marattiaceae Eukaryota n.a. n.a. n.a. PMID[19371069]
NPO4011 Chlamydomonas reinhardtii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. PMID[20581114]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[24224843]
NPO4011 Chlamydomonas reinhardtii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. PMID[25515814]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[27196335]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[32083868]
NPO26550 Ruscus aculeatus Species Asparagaceae Eukaryota Underground parts n.a. n.a. PMID[9784168]
NPO4011 Chlamydomonas reinhardtii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO25843 Solanum chacoense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26550 Ruscus aculeatus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9613 Anisomeles indica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4011 Chlamydomonas reinhardtii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO26550 Ruscus aculeatus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26915 Erinus alpinus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9613 Anisomeles indica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25843 Solanum chacoense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26550 Ruscus aculeatus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25808 Fritillaria taipaiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26793 Trichia carnea Species Trichiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25265 Sophora secundiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26444 Mimosa invisa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26222 Gonepteryx rhamni Species Pieridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24150 Baptisia lecontii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26956 Crambe crambe Species Esperiopsidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23463 Basanacantha spinosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23068 Guettarda eximia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27000 Geranium macrorrhizum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27038 Senecio macrophyllus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26862 Pentaceraster alveolatus Species Oreasteridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25843 Solanum chacoense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27053 Maclura aurantiaca Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24594 Polypodium hastatum Species Polypodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26693 Daphne papyracea Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26843 Heliconius cydno Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25025 Gypothamnium pinifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25783 Tulipa silvestris Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26489 Arthrobacter viscosus Species Rhizobiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO26577 Clinostemon mahuba n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO9613 Anisomeles indica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24375 Micrococcus luteus Species Micrococcaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29139 Agave huachucensis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25438 Xiphophora gladiata Species Fucaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25808 Fritillaria taipaiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27027 Renilla muelleri Species Renillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20000 Adina rubescens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25592 Pedicularis densispica Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26106 Lactarius pubescens Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26020 Dahlstedtia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26173 Anomospermum grandifolium Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25729 Centaurea aemulans Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2096 Stenostomum acutatum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23570 Hypolaena fastigiata Species Restionaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26427 Heterocapsa triquetra Species Heterocapsaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26915 Erinus alpinus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26683 Dichomitus squalens Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18404 Clarkia unguiculata Species Onagraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25210 Fulmarus glacialis Species Procellariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24509 Randia longispina Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24883 Angiopteris caudatiformis Species Marattiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26300 Penianthus zenkeri Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24757 Meryta denhamii Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12552 Aloe indica Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4011 Chlamydomonas reinhardtii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26550 Ruscus aculeatus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26467 Nipaecoccus aurilanatus Species Pseudococcidae 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

☑ 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 NPC270249 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 NPC270249 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