Structure

Physi-Chem Properties

Molecular Weight:  641.85
Volume:  425.654
LogP:  5.742
LogD:  3.9
LogS:  -4.808
# Rotatable Bonds:  13
TPSA:  89.78
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.23
Synthetic Accessibility Score:  2.864
Fsp3:  0.444
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:  -5.145
MDCK Permeability:  1.5657800759072416e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.439
20% Bioavailability (F20%):  0.013
30% Bioavailability (F30%):  0.122

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.608
Plasma Protein Binding (PPB):  98.8418960571289%
Volume Distribution (VD):  0.711
Pgp-substrate:  2.1810781955718994%

ADMET: Metabolism

CYP1A2-inhibitor:  0.86
CYP1A2-substrate:  0.14
CYP2C19-inhibitor:  0.869
CYP2C19-substrate:  0.05
CYP2C9-inhibitor:  0.891
CYP2C9-substrate:  0.864
CYP2D6-inhibitor:  0.383
CYP2D6-substrate:  0.476
CYP3A4-inhibitor:  0.613
CYP3A4-substrate:  0.069

ADMET: Excretion

Clearance (CL):  1.993
Half-life (T1/2):  0.275

ADMET: Toxicity

hERG Blockers:  0.103
Human Hepatotoxicity (H-HT):  0.128
Drug-inuced Liver Injury (DILI):  0.803
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.934
Maximum Recommended Daily Dose:  0.907
Skin Sensitization:  0.555
Carcinogencity:  0.635
Eye Corrosion:  0.003
Eye Irritation:  0.04
Respiratory Toxicity:  0.886

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

  Natural Product: NPC87232

Natural Product ID:  NPC87232
Common Name*:   FLOMIRTZSBSGEW-NBXFTRSQSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FLOMIRTZSBSGEW-NBXFTRSQSA-N
Standard InCHI:  InChI=1S/C50H67NO14/c1-29-43(53)36(58-6)25-42(60-29)65-44-30(2)61-41(26-37(44)59-7)63-35-18-19-46(4)34(24-35)17-20-49(56)38(46)27-39(64-40(52)16-15-32-12-9-8-10-13-32)47(5)48(55,21-22-50(47,49)57)31(3)62-45(54)33-14-11-23-51-28-33/h8-17,23,28-31,35-39,41-44,53,55-57H,18-22,24-27H2,1-7H3/b16-15+/t29-,30-,31+,35+,36-,37+,38-,39-,41+,42+,43-,44-,46+,47-,48-,49+,50-/m1/s1
SMILES:  C[C@@H]1[C@H]([C@@H](C[C@@H](O1)O[C@@H]1[C@@H](C)O[C@H](C[C@@H]1OC)O[C@H]1CC[C@@]2(C)C(=CC[C@@]3([C@@H]2C[C@H]([C@]2(C)[C@@](CC[C@]32O)([C@H](C)OC(=O)c2cccnc2)O)OC(=O)/C=C/c2ccccc2)O)C1)OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   102165348
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides

*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
NPO8680 Polypodium niponicum Species Polypodiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)80275-7]
NPO8809 Cynanchum wilfordii Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[10217732]
NPO626 Indigofera tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16644212]
NPO280 Dysidea chlorea Species Dysideidae Eukaryota n.a. Okinawan n.a. PMID[16872148]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota Roots n.a. n.a. PMID[24054487]
NPO55 Croton urucurana Species Euphorbiaceae Eukaryota n.a. twig n.a. PMID[24354204]
NPO55 Croton urucurana Species Euphorbiaceae Eukaryota n.a. leaf n.a. PMID[24354204]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota roots n.a. n.a. PMID[24412339]
NPO55 Croton urucurana Species Euphorbiaceae Eukaryota Latex n.a. n.a. PMID[26561866]
NPO8809 Cynanchum wilfordii Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[26716755]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8680 Polypodium niponicum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO626 Indigofera tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12693 Mesembryanthemum tortuosum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12693 Mesembryanthemum tortuosum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5745 Randia formosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8680 Polypodium niponicum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO626 Indigofera tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8680 Polypodium niponicum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8809 Cynanchum wilfordii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO626 Indigofera tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23643 Thalictrum aquilegiifolium Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7220 Artemisia latifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8942 Hedysarum coronarium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3834 Periplaneta americana Species Blattoidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5745 Randia formosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1017 Dendrobium gibsonii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5486 Helicoon richonis Species Orbiliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6312 Picea engelmannii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO280 Dysidea chlorea Species Dysideidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8809 Cynanchum wilfordii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8276 Harpullia ramiflora Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4983 Bromelia pinguin Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8680 Polypodium niponicum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28100 Jacobaea othonnae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13333 Paenibacillus thiaminolyticus Species Paenibacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2641 Marsupella aquatica Species Gymnomitriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8531 Centaurea ferox Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6086 Axinella polypoides Species Axinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO55 Croton urucurana Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8407 Polyporus fomentarius Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12693 Mesembryanthemum tortuosum Species Aizoaceae 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 NPC87232 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 NPC87232 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