NPASS Compound

Structure

NPC112016 OpenBabel06302215162D 31 31 0 0 1 0 0 0 0 0999 V2000 4.5549 -0.6020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9916 0.2242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4255 1.1252 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8622 1.9514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2961 2.8524 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8650 1.8767 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4311 0.9757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4339 0.9010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6235 -0.7818 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5984 -0.5593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2786 -1.2924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9838 -2.2479 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2535 -1.0698 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4010 -1.7568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1828 -2.3802 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -2.1906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4010 -1.7568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6235 -0.7818 0.0000 C 0 0 0 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 0.0747 0.9972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8262 0.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7272 0.1294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8019 -0.8678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7029 -1.3017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2662 -2.1279 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2690 -2.2026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5291 -0.7383 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -3.1906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3660 -3.6906 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9944 0.1495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 31 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 20 1 0 0 0 0 10 11 1 6 0 0 0 10 15 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 2 0 0 0 0 17 29 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 1 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 25 27 1 0 0 0 0 25 28 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	432.25
Volume:	466.686
LogP:	2.463
LogD:	1.658
LogS:	-3.81
# Rotatable Bonds:	10
TPSA:	97.74
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.148
Synthetic Accessibility Score:	4.786
Fsp3:	0.6
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.664
MDCK Permeability:	2.52292647928698e-05
Pgp-inhibitor:	0.994
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.166
20% Bioavailability (F20%):	0.935
30% Bioavailability (F30%):	0.889

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.814
Plasma Protein Binding (PPB):	78.31632232666016%
Volume Distribution (VD):	1.519
Pgp-substrate:	12.548724174499512%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.134
CYP2C19-inhibitor:	0.484
CYP2C19-substrate:	0.62
CYP2C9-inhibitor:	0.692
CYP2C9-substrate:	0.26
CYP2D6-inhibitor:	0.351
CYP2D6-substrate:	0.139
CYP3A4-inhibitor:	0.775
CYP3A4-substrate:	0.415

ADMET: Excretion

Clearance (CL):	3.185
Half-life (T1/2):	0.887

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.106
Drug-inuced Liver Injury (DILI):	0.102
AMES Toxicity:	0.119
Rat Oral Acute Toxicity:	0.023
Maximum Recommended Daily Dose:	0.942
Skin Sensitization:	0.979
Carcinogencity:	0.629
Eye Corrosion:	0.022
Eye Irritation:	0.242
Respiratory Toxicity:	0.864

Download Data

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

Natural Product: NPC112016

Natural Product ID:	NPC112016
*Common Name:**	IKQKKJHNBJMDBL-TVMFGEKRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IKQKKJHNBJMDBL-TVMFGEKRSA-N
Standard InCHI:	InChI=1S/C25H36O6/c1-17(2)14-22(28)31-13-9-21-20(15-18(3)27)23(29)19(16-26)8-12-25(21,6)11-7-10-24(4,5)30/h7-10,13-14,20-21,26,30H,11-12,15-16H2,1-6H3/b10-7+,13-9+/t20-,21-,25-/m0/s1
SMILES:	CC(=CC(=O)O/C=C/[C@H]1[C@H](CC(=O)C)C(=O)C(=CC[C@]1(C)C/C=C/C(C)(C)O)CO)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10550692
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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO6082	Centaurium pulchellum	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0031-9422(00)83457-3]
NPO8911	Aspergillus aculeatus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075772]
NPO8404	Isodon xerophilus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10843567]
NPO6717	Viburnum awabuki	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15043405]
NPO8911	Aspergillus aculeatus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16155971]
NPO4979	Elysia grandifolia	Species	Placobranchidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17125219]
NPO8404	Isodon xerophilus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17665952]
NPO8269	Isodon nervosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18345641]
NPO8911	Aspergillus aculeatus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19824618]
NPO8911	Aspergillus aculeatus	Species	Aspergillaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[21667999]
NPO8911	Aspergillus aculeatus	Species	Aspergillaceae	Eukaryota	n.a.	latex	n.a.	PMID[21854017]
NPO7935	Strychnos angustiflora	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27592135]
NPO8911	Aspergillus aculeatus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[324959]
NPO8404	Isodon xerophilus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33325237]
NPO6717	Viburnum awabuki	Species	Adoxaceae	Eukaryota	n.a.	leaf	n.a.	Database[Article]
NPO8404	Isodon xerophilus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2476	Lonicera fulvotomentosa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7935	Strychnos angustiflora	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO149	Heliotropium europaeum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5144	Berberis japonica	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9228.1	Narcissus pseudonarcissus subsp. leonensis	Subspecies	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO149	Heliotropium europaeum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6717	Viburnum awabuki	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2476	Lonicera fulvotomentosa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7935	Strychnos angustiflora	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2637	Agave rigidissima	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8404	Isodon xerophilus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2476	Lonicera fulvotomentosa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO149	Heliotropium europaeum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8911	Aspergillus aculeatus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Title]
NPO2476	Lonicera fulvotomentosa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10806	Achillea roseoalba	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24370	Crassocephalum crepidioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2476	Lonicera fulvotomentosa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6082	Centaurium pulchellum	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5319	Ulmus thomasii	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3830	Euplotes rariseta	Species	Euplotidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6310	Ruta bracteosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7935	Strychnos angustiflora	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO149	Heliotropium europaeum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8269	Isodon nervosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7766	Pericopsis schliebenii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4516	Fasciospongia rimosa	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9228.1	Narcissus pseudonarcissus subsp. leonensis	Subspecies	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8103	Lecanora melanophthalma	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1355	Urechis caupo	Species	Urechidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9903	Engelhardia spicata	Species	Juglandaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8404	Isodon xerophilus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8911	Aspergillus aculeatus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2304	Byssovorax cruenta	Species	Polyangiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6717	Viburnum awabuki	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25481	Lonchocarpus oaxacensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7060	Ficus ruficaulis	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2637	Agave rigidissima	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4979	Elysia grandifolia	Species	Placobranchidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO276	Miscanthus sacchariflorus	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5144	Berberis japonica	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15610	Citrus trifolia	Species	Rutaceae	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 NPC112016 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	212
0.1-0.2	1188
0.2-0.3	4677
0.3-0.4	10634
0.4-0.5	14487
0.5-0.6	6957
0.6-0.7	3900
0.7-0.8	627
0.8-0.85	9
0.85-0.9	3
0.9-0.95	1
0.95-1	2

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 NPC112016 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	193
0.1-0.2	1774
0.2-0.3	3582
0.3-0.4	2360
0.4-0.5	846
0.5-0.6	317
0.6-0.7	67
0.7-0.8	10
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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