NPASS Compound

Structure

NPC179634 OpenBabel06302215212D 34 39 0 0 1 0 0 0 0 0999 V2000 8.3114 0.0687 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3544 0.2721 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0521 1.2026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7068 1.9298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0950 1.4061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7927 2.3366 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4403 0.6790 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7426 -0.2516 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.6997 -0.4550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0879 -0.9787 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.3903 -1.9092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2406 -0.4894 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2400 0.4890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3923 0.9784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5447 -0.4897 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6964 -0.9795 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6964 -1.9589 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5441 -2.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3923 -1.9586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3924 -0.9792 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2584 -1.4792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8482 -2.4486 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7142 -2.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 -3.4276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7144 -3.9276 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0005 -3.9168 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8477 -3.4271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8480 -2.4481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9589 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -0.9795 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8482 -0.4897 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8661 -1.4589 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1066 0.0106 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 9 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 6 0 0 0 10 11 1 1 0 0 0 10 12 1 0 0 0 0 12 20 1 0 0 0 0 12 13 1 0 0 0 0 12 34 1 0 0 0 0 13 14 1 0 0 0 0 15 14 1 6 0 0 0 15 16 1 0 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 16 31 1 0 0 0 0 17 18 1 6 0 0 0 17 22 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 22 29 1 0 0 0 0 22 23 1 6 0 0 0 22 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 2 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 29 33 1 1 0 0 0 30 31 1 0 0 0 0 30 32 1 1 0 0 0 31 32 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	470.27
Volume:	483.701
LogP:	3.606
LogD:	3.091
LogS:	-4.523
# Rotatable Bonds:	2
TPSA:	96.36
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.364
Synthetic Accessibility Score:	5.658
Fsp3:	0.786
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.872
MDCK Permeability:	2.05203741643345e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.699
Human Intestinal Absorption (HIA):	0.012
20% Bioavailability (F20%):	0.022
30% Bioavailability (F30%):	0.468

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.957
Plasma Protein Binding (PPB):	56.96612548828125%
Volume Distribution (VD):	0.911
Pgp-substrate:	18.239412307739258%

ADMET: Metabolism

CYP1A2-inhibitor:	0.038
CYP1A2-substrate:	0.714
CYP2C19-inhibitor:	0.335
CYP2C19-substrate:	0.784
CYP2C9-inhibitor:	0.195
CYP2C9-substrate:	0.054
CYP2D6-inhibitor:	0.04
CYP2D6-substrate:	0.125
CYP3A4-inhibitor:	0.837
CYP3A4-substrate:	0.727

ADMET: Excretion

Clearance (CL):	10.388
Half-life (T1/2):	0.598

ADMET: Toxicity

hERG Blockers:	0.176
Human Hepatotoxicity (H-HT):	0.296
Drug-inuced Liver Injury (DILI):	0.312
AMES Toxicity:	0.025
Rat Oral Acute Toxicity:	0.86
Maximum Recommended Daily Dose:	0.556
Skin Sensitization:	0.259
Carcinogencity:	0.865
Eye Corrosion:	0.013
Eye Irritation:	0.033
Respiratory Toxicity:	0.972

Download Data

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

Natural Product: NPC179634

Natural Product ID:	NPC179634
*Common Name:**	FAZIYUIDUNHZRG-PCTWTJKKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FAZIYUIDUNHZRG-PCTWTJKKSA-N
Standard InCHI:	InChI=1S/C28H38O6/c1-14-13-19(33-24(30)15(14)2)16(3)27(31)12-9-17-21-18(8-11-25(17,27)4)26(5)20(29)7-6-10-28(26,32)23-22(21)34-23/h6-7,16-19,21-23,31-32H,8-13H2,1-5H3/t16-,17+,18+,19-,21+,22+,23+,25+,26+,27+,28+/m1/s1
SMILES:	CC1=C(C)C(=O)O[C@H](C1)[C@@H](C)[C@]1(CC[C@H]2[C@H]3[C@H](CC[C@]12C)[C@@]1(C)C(=O)C=CC[C@@]1([C@@H]1[C@H]3O1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	21679027
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
NPO15698	Withania somnifera	Species	Solanaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/0031-9422(75)85035-7]
NPO13655	Physalis philadelphica	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12027740]
NPO32637	exodeconus maritimus	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12027740]
NPO15698	Withania somnifera	Species	Solanaceae	Eukaryota	roots	n.a.	n.a.	PMID[17190461]
NPO15698	Withania somnifera	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19056281]
NPO15698	Withania somnifera	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24079846]
NPO15698	Withania somnifera	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26169123]
NPO15698	Withania somnifera	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30776236]
NPO15698	Withania somnifera	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO13655	Physalis philadelphica	Species	Solanaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO13655	Physalis philadelphica	Species	Solanaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO13655	Physalis philadelphica	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15698	Withania somnifera	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13655	Physalis philadelphica	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15698	Withania somnifera	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15698	Withania somnifera	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1004	Consolida scleroclada	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13655	Physalis philadelphica	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3822	Rhodophiala bifida	Species	Amaryllidaceae	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

Activity Type	# Activity
IC50	4

Activity Type	# Activity
Cell Line	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT148	Cell Line	HCT-15	Homo sapiens	IC50	=	5900.0	nM	PMID[30776236]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	IC50	=	6100.0	nM	PMID[30776236]
NPT146	Cell Line	SK-OV-3	Homo sapiens	IC50	>	10000.0	nM	PMID[30776236]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[30776236]

☑ 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 NPC179634 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 NPC179634 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