NPASS Compound

Structure

CID186668 OpenBabel06191715562D 29 33 0 0 1 0 0 0 0 0999 V2000 -0.8124 -2.4513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7161 -0.9908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5291 -0.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6860 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0005 -1.9466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8425 -1.4599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6293 -1.4530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3718 -1.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6849 0.9728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6858 -2.9199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4160 -0.0904 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5277 -0.4859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5291 -1.4602 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8430 -1.4602 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8430 -0.4867 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6855 0.0003 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3715 -2.9194 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5285 -3.4061 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8425 1.4592 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.5805 -1.6552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6861 -1.9469 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8425 -0.4864 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2376 -3.4194 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5287 -4.4061 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5836 2.4251 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9760 -2.5435 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0667 -0.8130 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 22 1 0 0 0 0 3 4 1 0 0 0 0 3 13 1 0 0 0 0 4 15 1 0 0 0 0 5 6 1 0 0 0 0 5 14 1 0 0 0 0 6 22 1 0 0 0 0 7 12 2 0 0 0 0 7 20 1 0 0 0 0 8 13 1 0 0 0 0 8 17 1 0 0 0 0 9 16 1 0 0 0 0 9 19 1 0 0 0 0 10 18 1 0 0 0 0 10 21 1 0 0 0 0 11 12 1 0 0 0 0 11 29 1 0 0 0 0 12 16 1 0 0 0 0 13 21 1 6 0 0 0 14 15 1 0 0 0 0 14 21 1 6 0 0 0 15 23 1 1 0 0 0 16 22 1 6 0 0 0 17 18 1 0 0 0 0 17 24 1 6 0 0 0 18 25 1 1 0 0 0 19 23 1 6 0 0 0 19 26 1 0 0 0 0 20 27 2 0 0 0 0 20 29 1 0 0 0 0 21 1 1 6 0 0 0 22 23 1 6 0 0 0 23 28 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	406.24
Volume:	411.05
LogP:	2.728
LogD:	2.227
LogS:	-3.429
# Rotatable Bonds:	1
TPSA:	114.29
# H-Bond Aceptor:	6
# H-Bond Donor:	5
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.49
Synthetic Accessibility Score:	5.13
Fsp3:	0.826
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:	-5.61
MDCK Permeability:	8.668546797707677e-06
Pgp-inhibitor:	0.004
Pgp-substrate:	0.995
Human Intestinal Absorption (HIA):	0.464
20% Bioavailability (F20%):	0.902
30% Bioavailability (F30%):	0.968

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.269
Plasma Protein Binding (PPB):	93.01378631591797%
Volume Distribution (VD):	0.901
Pgp-substrate:	9.21058177947998%

ADMET: Metabolism

CYP1A2-inhibitor:	0.018
CYP1A2-substrate:	0.109
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.396
CYP2C9-inhibitor:	0.051
CYP2C9-substrate:	0.296
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.254
CYP3A4-inhibitor:	0.081
CYP3A4-substrate:	0.132

ADMET: Excretion

Clearance (CL):	7.822
Half-life (T1/2):	0.615

ADMET: Toxicity

hERG Blockers:	0.211
Human Hepatotoxicity (H-HT):	0.443
Drug-inuced Liver Injury (DILI):	0.073
AMES Toxicity:	0.013
Rat Oral Acute Toxicity:	0.848
Maximum Recommended Daily Dose:	0.933
Skin Sensitization:	0.866
Carcinogencity:	0.517
Eye Corrosion:	0.004
Eye Irritation:	0.062
Respiratory Toxicity:	0.953

Download Data

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

Natural Product: NPC186668

Natural Product ID:	NPC186668
*Common Name:**	Afrogenin
IUPAC Name:	3-[(2R,3R,5S,8R,9S,10S,13R,14S,15R,17R)-2,3,14,15-tetrahydroxy-10,13-dimethyl-1,2,3,4,5,6,7,8,9,11,12,15,16,17-tetradecahydrocyclopenta[a]phenanthren-17-yl]-2H-furan-5-one
Synonyms:
Standard InCHIKey:	PPMVAFKDEJNUOY-WGIKCKTPSA-N
Standard InCHI:	InChI=1S/C23H34O6/c1-21-10-18(25)17(24)8-13(21)3-4-15-14(21)5-6-22(2)16(9-19(26)23(15,22)28)12-7-20(27)29-11-12/h7,13-19,24-26,28H,3-6,8-11H2,1-2H3/t13-,14-,15+,16+,17+,18+,19+,21-,22+,23+/m0/s1
SMILES:	C[C@]12C[C@H]([C@@H](C[C@@H]1CC[C@@H]1[C@@H]2CC[C@]2(C)[C@H](C[C@H]([C@]12O)O)C1=CC(=O)OC1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3617466
PubChem CID:	23252526
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001555] Cardenolides 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO9165	Asclepias curassavica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19251412]
NPO9165	Asclepias curassavica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16252914]
NPO3369	Anemone narcissiflora	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2175	Hyperbaena columbica	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8349	Uga sinensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26375	Viburnum grandifolium	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9165	Asclepias curassavica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9165	Asclepias curassavica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9165	Asclepias curassavica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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	2
MIC	5

Activity Type	# Activity
Cell Line	2
Organism	5

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	2472.0	nM	PMID[509499]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	1693.0	nM	PMID[509499]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	>	100.0	ug.mL-1	PMID[509499]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	100.0	ug.mL-1	PMID[509499]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	100.0	ug.mL-1	PMID[509499]
NPT1108	Organism	Mycobacterium bovis BCG	Mycobacterium bovis BCG	MIC	>	80.0	ug.mL-1	PMID[509499]
NPT20	Organism	Candida albicans	Candida albicans	MIC	>	100.0	ug.mL-1	PMID[509499]

Showing 1 to 7 of 7 entries

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☑ 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 NPC186668 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	200
0.1-0.2	1426
0.2-0.3	4613
0.3-0.4	10817
0.4-0.5	10916
0.5-0.6	5957
0.6-0.7	6061
0.7-0.8	2421
0.8-0.85	199
0.85-0.9	63
0.9-0.95	16
0.95-1	8

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Similarity Score	Similarity Level	Natural Product ID
0.9592	High Similarity	NPC472821
0.9588	High Similarity	NPC25177
0.9588	High Similarity	NPC247701
0.9588	High Similarity	NPC268829
0.9588	High Similarity	NPC295110

Showing 1 to 5 of 200 entries

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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 NPC186668 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	163
0.1-0.2	1542
0.2-0.3	4056
0.3-0.4	2313
0.4-0.5	605
0.5-0.6	200
0.6-0.7	199
0.7-0.8	56
0.8-0.85	11
0.85-0.9	5
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.88	High Similarity	NPD7638	Approved
0.8727	High Similarity	NPD7516	Approved
0.8713	High Similarity	NPD7639	Approved
0.8713	High Similarity	NPD7640	Approved
0.8636	High Similarity	NPD7327	Approved

Showing 1 to 5 of 200 entries

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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