NPASS Compound

Structure

CID7059 OpenBabel06191715332D 31 35 0 0 1 0 0 0 0 0999 V2000 -0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 -1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0739 4.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0685 4.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 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 -3.4641 -0.0000 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 2.4752 3.6691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 17 2 0 0 0 0 2 25 1 0 0 0 0 3 25 1 0 0 0 0 4 26 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 6 9 1 0 0 0 0 7 10 2 0 0 0 0 8 12 1 0 0 0 0 8 13 1 0 0 0 0 9 18 2 0 0 0 0 10 18 1 0 0 0 0 11 14 2 0 0 0 0 11 19 1 0 0 0 0 12 25 1 0 0 0 0 13 26 1 0 0 0 0 14 30 1 0 0 0 0 15 23 1 0 0 0 0 16 21 1 0 0 0 0 16 22 1 0 0 0 0 17 19 1 0 0 0 0 17 20 1 0 0 0 0 18 24 1 0 0 0 0 19 22 2 0 0 0 0 20 15 1 1 0 0 0 20 21 1 0 0 0 0 21 26 1 6 0 0 0 22 30 1 0 0 0 0 23 27 1 6 0 0 0 23 31 1 0 0 0 0 24 28 2 0 0 0 0 24 31 1 0 0 0 0 25 27 1 0 0 0 0 26 27 1 6 0 0 0 27 29 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	304.13
Volume:	307.688
LogP:	1.221
LogD:	1.275
LogS:	-3.162
# Rotatable Bonds:	2
TPSA:	69.67
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.421
Synthetic Accessibility Score:	4.635
Fsp3:	0.588
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.656
MDCK Permeability:	2.6167876058025286e-05
Pgp-inhibitor:	0.798
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.758
20% Bioavailability (F20%):	0.721
30% Bioavailability (F30%):	0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.946
Plasma Protein Binding (PPB):	62.534034729003906%
Volume Distribution (VD):	0.867
Pgp-substrate:	40.84164810180664%

ADMET: Metabolism

CYP1A2-inhibitor:	0.066
CYP1A2-substrate:	0.075
CYP2C19-inhibitor:	0.032
CYP2C19-substrate:	0.552
CYP2C9-inhibitor:	0.044
CYP2C9-substrate:	0.087
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.086
CYP3A4-inhibitor:	0.637
CYP3A4-substrate:	0.321

ADMET: Excretion

Clearance (CL):	7.148
Half-life (T1/2):	0.857

ADMET: Toxicity

hERG Blockers:	0.005
Human Hepatotoxicity (H-HT):	0.267
Drug-inuced Liver Injury (DILI):	0.881
AMES Toxicity:	0.035
Rat Oral Acute Toxicity:	0.735
Maximum Recommended Daily Dose:	0.326
Skin Sensitization:	0.584
Carcinogencity:	0.772
Eye Corrosion:	0.91
Eye Irritation:	0.68
Respiratory Toxicity:	0.964

Download Data

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

Natural Product: NPC7059

Natural Product ID:	NPC7059
*Common Name:**	Isovouacapenol A
IUPAC Name:	[(4aR,5R,6aR,11aS,11bR)-4a-hydroxy-4,4,11b-trimethyl-7-methylidene-1,2,3,5,6,6a,11,11a-octahydronaphtho[2,1-f][1]benzofuran-5-yl] benzoate
Synonyms:
Standard InCHIKey:	CAKOAOJDETWCQH-BSMIGITPSA-N
Standard InCHI:	InChI=1S/C27H32O4/c1-17-19-11-14-30-22(19)16-21-20(17)15-23(31-24(28)18-9-6-5-7-10-18)27(29)25(2,3)12-8-13-26(21,27)4/h5-7,9-11,14,20-21,23,29H,1,8,12-13,15-16H2,2-4H3/t20-,21-,23+,26+,27+/m0/s1
SMILES:	O=C(c1ccccc1)O[C@@H]1C[C@H]2C(=C)c3ccoc3C[C@@H]2[C@@]2([C@]1(O)C(C)(C)CCC2)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL491583
PubChem CID:	636673
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8722541]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8699928]
NPO19747	Maytenus emarginata	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8176403]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7304185]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7102323]
NPO17333	Valeriana officinalis	Species	Caprifoliaceae	Eukaryota	n.a.	root	n.a.	PMID[547813]
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3783154]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	Leaves	n.a.	n.a.	PMID[31556299]
NPO1534	Jatropha gossypiifolia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30106289]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	Leaves	n.a.	n.a.	PMID[29355322]

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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
Others	13

Activity Type	# Activity
Organism	13

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	16.0	mm	PMID[487502]
NPT19	Organism	Escherichia coli	Escherichia coli	IZ	=	12.0	mm	PMID[487502]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	IZ	=	12.0	mm	PMID[487502]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	IZ	=	15.0	mm	PMID[487502]
NPT20	Organism	Candida albicans	Candida albicans	IZ	=	14.0	mm	PMID[487502]
NPT330	Organism	Trichophyton mentagrophytes	Trichophyton mentagrophytes	IZ	=	12.0	mm	PMID[487502]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	Activity	=	0.6	n.a.	PMID[487502]
NPT19	Organism	Escherichia coli	Escherichia coli	Activity	=	0.2	n.a.	PMID[487502]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Activity	=	0.2	n.a.	PMID[487502]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	Activity	=	0.5	n.a.	PMID[487502]

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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 NPC7059 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	340
0.1-0.2	1322
0.2-0.3	2522
0.3-0.4	5101
0.4-0.5	10050
0.5-0.6	8441
0.6-0.7	7430
0.7-0.8	6873
0.8-0.85	452
0.85-0.9	139
0.9-0.95	20
0.95-1	7

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Similarity Score	Similarity Level	Natural Product ID
0.9867	High Similarity	NPC8389
0.9801	High Similarity	NPC79571
0.961	High Similarity	NPC277618
0.9597	High Similarity	NPC121615
0.9597	High Similarity	NPC294511

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 NPC7059 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	300
0.1-0.2	825
0.2-0.3	1402
0.3-0.4	2463
0.4-0.5	2233
0.5-0.6	1270
0.6-0.7	517
0.7-0.8	136
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.858	High Similarity	NPD8434	Phase 2
0.8431	Intermediate Similarity	NPD4628	Phase 3
0.8165	Intermediate Similarity	NPD6273	Approved
0.8125	Intermediate Similarity	NPD7458	Discontinued
0.807	Intermediate Similarity	NPD6764	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