NPASS Compound

Structure

NPC239913 OpenBabel06302215362D 32 34 0 0 1 0 0 0 0 0999 V2000 4.7553 -1.5451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5474 -0.5669 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2905 0.1022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5963 -0.2579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8532 -0.9271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0611 -1.9052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3179 -2.5743 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5258 -3.5525 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8567 -4.2956 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8622 -4.1911 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3567 -5.1616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3349 -4.9537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4394 -3.9592 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3054 -3.4592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1714 -3.9592 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0375 -3.4592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9035 -3.9592 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0375 -2.4592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1714 -1.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1714 -0.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0375 -0.4592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9035 -0.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9035 -1.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3669 -2.2653 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1590 -1.2872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9021 -0.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2079 -0.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5352 -1.6473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4863 -1.3383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6942 -0.3601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 7 6 1 1 0 0 0 7 24 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 13 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 6 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 23 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 27 32 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	438.2
Volume:	461.596
LogP:	4.951
LogD:	4.336
LogS:	-4.746
# Rotatable Bonds:	12
TPSA:	78.9
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.509
Synthetic Accessibility Score:	3.461
Fsp3:	0.423
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:	-4.783
MDCK Permeability:	3.104516144958325e-05
Pgp-inhibitor:	0.992
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.243
30% Bioavailability (F30%):	0.959

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.06
Plasma Protein Binding (PPB):	98.88809967041016%
Volume Distribution (VD):	1.271
Pgp-substrate:	1.2031739950180054%

ADMET: Metabolism

CYP1A2-inhibitor:	0.094
CYP1A2-substrate:	0.085
CYP2C19-inhibitor:	0.719
CYP2C19-substrate:	0.054
CYP2C9-inhibitor:	0.683
CYP2C9-substrate:	0.098
CYP2D6-inhibitor:	0.029
CYP2D6-substrate:	0.048
CYP3A4-inhibitor:	0.527
CYP3A4-substrate:	0.193

ADMET: Excretion

Clearance (CL):	9.908
Half-life (T1/2):	0.579

ADMET: Toxicity

hERG Blockers:	0.157
Human Hepatotoxicity (H-HT):	0.059
Drug-inuced Liver Injury (DILI):	0.937
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.074
Maximum Recommended Daily Dose:	0.01
Skin Sensitization:	0.549
Carcinogencity:	0.329
Eye Corrosion:	0.005
Eye Irritation:	0.848
Respiratory Toxicity:	0.025

Download Data

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

Natural Product: NPC239913

Natural Product ID:	NPC239913
*Common Name:**	HRJWHNUFVIACBL-KMDXXIMOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HRJWHNUFVIACBL-KMDXXIMOSA-N
Standard InCHI:	InChI=1S/C26H30O6/c1-18(2)10-9-15-22(32-26(29)20-13-7-4-8-14-20)24-21(27)16-30-23(24)17-31-25(28)19-11-5-3-6-12-19/h3-8,11-14,18,22-24H,9-10,15-17H2,1-2H3/t22-,23-,24+/m0/s1
SMILES:	CC(C)CCC[C@@H]([C@H]1C(=O)CO[C@H]1COC(=O)c1ccccc1)OC(=O)c1ccccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000176] Benzoic acids and derivatives [CHEMONTID:0001350] Benzoic acid esters

*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
NPO24105	Artemisia iwayomogi	Species	Asteraceae	Eukaryota	n.a.	aerial part	n.a.	DOI[10.1002/hlca.201300170.]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	1996-Sep	PMID[10352947]
NPO17888	Myxococcus xanthus	Species	Myxococcaceae	Bacteria	n.a.	n.a.	n.a.	PMID[12141877]
NPO24105	Artemisia iwayomogi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12735688]
NPO17888	Myxococcus xanthus	Species	Myxococcaceae	Bacteria	n.a.	n.a.	n.a.	PMID[14575429]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15877880]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	needles	Himalayan	n.a.	PMID[16480866]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18460139]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	n.a.	Northeastern Regional Plant Introduction Station at Geneva	1966, 1967, and 1968 crop seasons	PMID[18460139]
NPO24105	Artemisia iwayomogi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23510022]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	Stem Bark	n.a.	n.a.	PMID[28240909]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28581744]
NPO17888	Myxococcus xanthus	Species	Myxococcaceae	Bacteria	n.a.	n.a.	n.a.	PMID[31465225]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7264680]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	Flower	n.a.	n.a.	Database[FooDB]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18919	Helenium amarum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21175	Senecio retrorsus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19994	Scutellaria viscidula	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17801	Drimia altissima	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18919	Helenium amarum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23431	Aconitum umbrosum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19994	Scutellaria viscidula	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21175	Senecio retrorsus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19994	Scutellaria viscidula	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18919	Helenium amarum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24105	Artemisia iwayomogi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO23686	Selinum tenuifolium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19539	Uperoleia rugosa	Species	Myobatrachidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18919	Helenium amarum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9228.2	Narcissus pseudonarcissus subsp. radinganorum	Subspecies	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21915	Diospyros chloroxylon	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23781	Lemaireocereus stellatus	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23688	Lonicera nitida	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22028	Ligularia lankongensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23363	0dulisporium hinnuleum	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24105	Artemisia iwayomogi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23113	Garcinia neglecta	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23268	Xanthorrhoea reflexa	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21747	Sideritis glacialis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20290	Vernonia arkansana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17888	Myxococcus xanthus	Species	Myxococcaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO16976	Phebalium rotundifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21175	Senecio retrorsus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23611	Conyza pallidiflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13151.1	Pulsatilla vulgaris subsp. grandis	Subspecies	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6439	Lithospermum carolinense	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19994	Scutellaria viscidula	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17801	Drimia altissima	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26544	Bolboschoenus maritimus	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23981	Maytenus disticha	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24063	Evasterias retifera	Species	Asteriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23431	Aconitum umbrosum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23175	Streptomyces antibioticus	Species	Streptomycetaceae	Bacteria	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 NPC239913 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	280
0.1-0.2	1053
0.2-0.3	2356
0.3-0.4	6350
0.4-0.5	11352
0.5-0.6	9739
0.6-0.7	10275
0.7-0.8	1170
0.8-0.85	99
0.85-0.9	23
0.9-0.95	0
0.95-1	0

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 NPC239913 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	244
0.1-0.2	720
0.2-0.3	1304
0.3-0.4	2688
0.4-0.5	2522
0.5-0.6	1175
0.6-0.7	457
0.7-0.8	40
0.8-0.85	0
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