Structure

Physi-Chem Properties

Molecular Weight:  412.37
Volume:  479.432
LogP:  7.231
LogD:  6.24
LogS:  -7.098
# Rotatable Bonds:  5
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.457
Synthetic Accessibility Score:  4.733
Fsp3:  0.862
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.615
MDCK Permeability:  7.995460691745393e-06
Pgp-inhibitor:  0.009
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.034
30% Bioavailability (F30%):  0.387

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.883
Plasma Protein Binding (PPB):  98.96309661865234%
Volume Distribution (VD):  1.585
Pgp-substrate:  1.1483583450317383%

ADMET: Metabolism

CYP1A2-inhibitor:  0.048
CYP1A2-substrate:  0.599
CYP2C19-inhibitor:  0.076
CYP2C19-substrate:  0.927
CYP2C9-inhibitor:  0.126
CYP2C9-substrate:  0.105
CYP2D6-inhibitor:  0.038
CYP2D6-substrate:  0.64
CYP3A4-inhibitor:  0.469
CYP3A4-substrate:  0.736

ADMET: Excretion

Clearance (CL):  16.356
Half-life (T1/2):  0.01

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.007
Drug-inuced Liver Injury (DILI):  0.018
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.052
Maximum Recommended Daily Dose:  0.637
Skin Sensitization:  0.015
Carcinogencity:  0.028
Eye Corrosion:  0.003
Eye Irritation:  0.015
Respiratory Toxicity:  0.595

Download Data

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  Natural Product: NPC318696

Natural Product ID:  NPC318696
Common Name*:   JZVFJDZBLUFKCA-CMDGGOBGSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JZVFJDZBLUFKCA-CMDGGOBGSA-N
Standard InCHI:  InChI=1S/C29H48O/c1-7-21(19(2)3)9-8-20(4)25-12-13-26-24-11-10-22-18-23(30)14-16-28(22,5)27(24)15-17-29(25,26)6/h8-9,11,19-23,25-27,30H,7,10,12-18H2,1-6H3/b9-8+
SMILES:  CCC(C=CC(C)C1CCC2C1(CCC3C2=CCC4C3(CCC(C4)O)C)C)C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5315190
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002031] Stigmastanes 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
NPO6108 Cocos nucifera Species Arecaceae Eukaryota n.a. Mysore, India n.a. DOI[10.1007/s11746-009-1435-y]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. seed n.a. DOI[10.1016/S0031-9422(00)97029-8]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. PMID[11430011]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[11975490]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[12232319]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota n.a. n.a. n.a. PMID[15453426]
NPO29808 Platycodon grandiflorum Species Campanulaceae Eukaryota n.a. root n.a. PMID[17851435]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota roots n.a. n.a. PMID[18177012]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota seeds n.a. n.a. PMID[18603435]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[18679750]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota Seeds n.a. n.a. PMID[20469887]
NPO29808 Platycodon grandiflorum Species Campanulaceae Eukaryota n.a. root n.a. PMID[20939516]
NPO29808 Platycodon grandiflorum Species Campanulaceae Eukaryota Roots n.a. n.a. PMID[20939516]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22208890]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota Seeds n.a. n.a. PMID[26595875]
NPO1592 Citrullus colocynthis Species Cucurbitaceae Eukaryota Fruits n.a. n.a. PMID[30183289]
NPO21876 Trichosanthes cucumeroides Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[33269591]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. leaf n.a. PMID[9433811]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota n.a. n.a. Database[FooDB]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Leaves n.a. Database[FooDB]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota Endosperm n.a. n.a. Database[FooDB]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota Hull Husk n.a. n.a. Database[FooDB]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota Juice n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO30744 Equisetum hiemale Species Equisetaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21170 Embelia parviflora Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30998 Conyza blinii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30404 Luffa cylindrica Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29808 Platycodon grandiflorum Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21876 Trichosanthes cucumeroides Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16412 Menyanthes trifoliata Species Menyanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1592 Citrullus colocynthis Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7805 Vallisneria spiralis Species Hydrocharitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO16412 Menyanthes trifoliata Species Menyanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1592 Citrullus colocynthis Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15723 Bupleurum aureum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21170 Embelia parviflora Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21876 Trichosanthes cucumeroides Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7805 Vallisneria spiralis Species Hydrocharitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30998 Conyza blinii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21170 Embelia parviflora Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31067 Impatiens sicullfer Species Balsaminaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1592 Citrullus colocynthis Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30404 Luffa cylindrica Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7805 Vallisneria spiralis Species Hydrocharitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29808 Platycodon grandiflorum Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21876 Trichosanthes cucumeroides Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30744 Equisetum hiemale Species Equisetaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15723 Bupleurum aureum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16412 Menyanthes trifoliata Species Menyanthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21876 Trichosanthes cucumeroides Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1592 Citrullus colocynthis Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21170 Embelia parviflora Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15723 Bupleurum aureum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6108 Cocos nucifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16412 Menyanthes trifoliata Species Menyanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29401 Bupleurum chinense Species Apiaceae 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 NPC318696 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 NPC318696 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