Structure

Physi-Chem Properties

Molecular Weight:  750.35
Volume:  718.66
LogP:  2.298
LogD:  2.629
LogS:  -3.919
# Rotatable Bonds:  10
TPSA:  223.57
# H-Bond Aceptor:  15
# H-Bond Donor:  5
# Rings:  8
# Heavy Atoms:  15

MedChem Properties

QED Drug-Likeness Score:  0.096
Synthetic Accessibility Score:  6.345
Fsp3:  0.868
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:  -5.898
MDCK Permeability:  0.0002387831045780331
Pgp-inhibitor:  0.991
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.966
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.042
Plasma Protein Binding (PPB):  33.26664733886719%
Volume Distribution (VD):  0.666
Pgp-substrate:  35.006717681884766%

ADMET: Metabolism

CYP1A2-inhibitor:  0.004
CYP1A2-substrate:  0.056
CYP2C19-inhibitor:  0.006
CYP2C19-substrate:  0.103
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.005
CYP2D6-inhibitor:  0.021
CYP2D6-substrate:  0.054
CYP3A4-inhibitor:  0.108
CYP3A4-substrate:  0.203

ADMET: Excretion

Clearance (CL):  1.258
Half-life (T1/2):  0.697

ADMET: Toxicity

hERG Blockers:  0.515
Human Hepatotoxicity (H-HT):  0.239
Drug-inuced Liver Injury (DILI):  0.458
AMES Toxicity:  0.051
Rat Oral Acute Toxicity:  0.365
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.144
Carcinogencity:  0.107
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.967

Download Data

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

  Natural Product: NPC273247

Natural Product ID:  NPC273247
Common Name*:   QKJMGMVEODCHCQ-PKIWOSNNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QKJMGMVEODCHCQ-PKIWOSNNSA-N
Standard InCHI:  InChI=1S/C38H54O15/c1-14-9-22(51-34(45)18(14)13-47-35-29(44)28(43)27(42)24(12-39)52-35)15(2)19-7-8-20-26-21(10-25(36(19,20)5)48-16(3)40)37(6)32(49-17(4)41)30-23(50-30)11-38(37,46)33-31(26)53-33/h15,19-33,35,39,42-44,46H,7-13H2,1-6H3/t15-,19+,20-,21-,22+,23-,24+,25-,26-,27+,28-,29+,30-,31-,32-,33-,35+,36+,37-,38-/m0/s1
SMILES:  CC1=C(CO[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)C(=O)O[C@H](C1)[C@@H](C)[C@H]1CC[C@H]2[C@H]3[C@H](C[C@@H]([C@]12C)OC(=O)C)[C@@]1(C)[C@H]([C@@H]2[C@H](C[C@@]1([C@@H]1[C@H]3O1)O)O2)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   101489538
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001125] Steroid lactones
          • [CHEMONTID:0001560] Withanolides 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
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. root n.a. PMID[10230514]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota rhizomes SiMao City, Yunnan Province, China 1996-OCT PMID[11908966]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota Rhizomes n.a. n.a. PMID[12350150]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[12956064]
NPO12186 Oplopanax chironium Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[15104479]
NPO11157 Corydalis saxicola Species Papaveraceae Eukaryota n.a. root n.a. PMID[17611928]
NPO11157 Corydalis saxicola Species Papaveraceae Eukaryota n.a. leaf n.a. PMID[18649321]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. PMID[20715765]
NPO7143 Acacia jacquemontii Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21894904]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25608854]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. PMID[33253561]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13831 Cephalotaxus oliveri Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13426 Lemmaphyllum microphyllum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13426 Lemmaphyllum microphyllum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13831 Cephalotaxus oliveri Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12093 Papaver orientale Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13426 Lemmaphyllum microphyllum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11585 Geijera salicifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10094 Daphne gnidioides Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3227 Androsace umbellata Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8399 Psiadia trinervia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11157 Corydalis saxicola Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7143 Acacia jacquemontii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14634 Artemisia balchanorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6266 Anzia hypoleucoides Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1133 Zieria laevigata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11753 Sideroxylon foetidissimum Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9487 Penicillium flexuosum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5551 Podocarpus sylvestris Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13831 Cephalotaxus oliveri Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11396 Metzgeria furcata Species Metzgeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14018 Pleurotus salmoneostramineus Species Pleurotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11909 Othonna arborescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14308 Coleonema pulchrum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9126 Stevia maimarensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12268 Aloe littoralis Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12093 Papaver orientale Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12186 Oplopanax chironium Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13723 Salvia eriophora Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13527 Solanum ecuadorense Species Solanaceae 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 NPC273247 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 NPC273247 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