Structure

Physi-Chem Properties

Molecular Weight:  758.58
Volume:  838.309
LogP:  9.522
LogD:  6.228
LogS:  -5.573
# Rotatable Bonds:  8
TPSA:  91.67
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  8
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.241
Synthetic Accessibility Score:  6.674
Fsp3:  0.9
Lipinski Rule-of-5:  Rejected
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:  -5.323
MDCK Permeability:  8.57143459143117e-06
Pgp-inhibitor:  0.009
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.991
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.101
Plasma Protein Binding (PPB):  90.75981903076172%
Volume Distribution (VD):  1.131
Pgp-substrate:  1.631245732307434%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.215
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.927
CYP2C9-inhibitor:  0.087
CYP2C9-substrate:  0.707
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.235
CYP3A4-inhibitor:  0.386
CYP3A4-substrate:  0.381

ADMET: Excretion

Clearance (CL):  4.19
Half-life (T1/2):  0.05

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.432
Drug-inuced Liver Injury (DILI):  0.054
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.452
Maximum Recommended Daily Dose:  0.797
Skin Sensitization:  0.156
Carcinogencity:  0.307
Eye Corrosion:  0.004
Eye Irritation:  0.036
Respiratory Toxicity:  0.971

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General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC124513

Natural Product ID:  NPC124513
Common Name*:   AOUGNCPHJBSCDC-WUUBZBNVSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  AOUGNCPHJBSCDC-WUUBZBNVSA-N
Standard InCHI:  InChI=1S/C50H78O5/c1-31(33-18-23-47(9)39-17-16-37-43(4,5)40(52)20-25-49(37)30-50(39,49)27-26-46(33,47)8)28-35(51)34-14-12-32(29-45(34,7)41(53)54)13-15-38-44(6)22-11-21-42(2,3)36(44)19-24-48(38,10)55/h12,31,33-34,36-39,55H,11,13-30H2,1-10H3,(H,53,54)/t31-,33-,34-,36+,37+,38-,39+,44+,45+,46-,47+,48-,49-,50+/m1/s1
SMILES:  C[C@H](CC(=O)[C@H]1CC=C(CC[C@@H]2[C@@]3(C)CCCC(C)(C)[C@@H]3CC[C@@]2(C)O)C[C@]1(C)C(=O)O)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@H]4C(C)(C)C(=O)CC[C@]54C[C@@]35CC[C@]12C
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:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002321] Cycloartanols 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
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. tuber n.a. PMID[15180301]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[17381154]
NPO385 Bipolaris oryzae Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[23668986]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[25843525]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20140 Aloe perryi Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22239 Hibiscus vitifolius Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5178 Pelophylax nigromaculatus Species Ranidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22239 Hibiscus vitifolius Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20140 Aloe perryi Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20140 Aloe perryi Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22563 Sclerocarya birrea Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22239 Hibiscus vitifolius Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22700 Dacrydium comosum Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21914 Turnera angustifolia Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO385 Bipolaris oryzae Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20328 Plumeria acutifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21090 Chrysanthemum ornatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20772 Pedalium murex Species Pedaliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5178 Pelophylax nigromaculatus Species Ranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20262 Delia paludosa Species Anthomyiidae 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 NPC124513 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 NPC124513 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