NPASS Compound

Structure

NPC191926 OpenBabel06302215282D 31 32 0 0 1 0 0 0 0 0999 V2000 5.6831 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1831 1.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1831 1.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6831 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1831 -0.5570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1831 -0.5570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6831 -1.4230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1831 -2.2891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6831 -1.4230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -1.1910 0.0000 O 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 0.9511 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 1.8090 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1.8171 2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 3.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 3.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 4.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 4.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 4.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 0.8090 0.0000 C 0 0 2 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 -1.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4538 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5878 1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0878 -0.0570 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6831 2.0411 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 1 0 0 0 0 5 16 1 0 0 0 0 5 6 1 0 0 0 0 5 11 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 26 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 24 1 0 0 0 0 15 16 2 0 0 0 0 15 18 1 0 0 0 0 16 17 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 25 27 1 6 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 M CHG 1 17 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	430.27
Volume:	469.272
LogP:	5.357
LogD:	4.359
LogS:	-4.951
# Rotatable Bonds:	8
TPSA:	80.67
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.337
Synthetic Accessibility Score:	4.511
Fsp3:	0.654
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.525
MDCK Permeability:	1.9881428670487367e-05
Pgp-inhibitor:	0.771
Pgp-substrate:	0.009
Human Intestinal Absorption (HIA):	0.036
20% Bioavailability (F20%):	0.467
30% Bioavailability (F30%):	0.172

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.009
Plasma Protein Binding (PPB):	89.84903717041016%
Volume Distribution (VD):	2.466
Pgp-substrate:	7.044622421264648%

ADMET: Metabolism

CYP1A2-inhibitor:	0.052
CYP1A2-substrate:	0.086
CYP2C19-inhibitor:	0.505
CYP2C19-substrate:	0.796
CYP2C9-inhibitor:	0.676
CYP2C9-substrate:	0.117
CYP2D6-inhibitor:	0.024
CYP2D6-substrate:	0.032
CYP3A4-inhibitor:	0.389
CYP3A4-substrate:	0.322

ADMET: Excretion

Clearance (CL):	8.322
Half-life (T1/2):	0.063

ADMET: Toxicity

hERG Blockers:	0.002
Human Hepatotoxicity (H-HT):	0.923
Drug-inuced Liver Injury (DILI):	0.871
AMES Toxicity:	0.099
Rat Oral Acute Toxicity:	0.539
Maximum Recommended Daily Dose:	0.03
Skin Sensitization:	0.113
Carcinogencity:	0.491
Eye Corrosion:	0.003
Eye Irritation:	0.021
Respiratory Toxicity:	0.887

Download Data

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

Natural Product: NPC191926

Natural Product ID:	NPC191926
*Common Name:**	HWYZDQMASKCQDN-HXUWFJFHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HWYZDQMASKCQDN-HXUWFJFHSA-N
Standard InCHI:	InChI=1S/C26H38O5/c1-15(2)9-11-26(12-10-16(3)4)23(28)18-14-20(25(7,8)30)31-22(18)21(24(26)29)19(27)13-17(5)6/h9-10,17,20,29-30H,11-14H2,1-8H3/p-1/t20-/m1/s1
SMILES:	CC(=CCC1(CC=C(C)C)C(=O)C2=C(C(=C1[O-])C(=O)CC(C)C)O[C@H](C2)C(C)(C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000301] Benzofurans

*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
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		DOI[10.1002/ejlt.201100207]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		DOI[10.1007/s11746-010-1670-2]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		DOI[10.1016/j.foodcont.2016.09.002]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		DOI[10.1016/j.jfca.2010.08.006]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		DOI[10.1016/j.supflu.2010.06.003]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		DOI[10.1016/j.supflu.2010.12.007]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		DOI[10.1016/j.supflu.2016.02.010]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		DOI[10.1016/j.supflu.2018.06.017]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		DOI[10.12691/jfnr-2-5-9]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		DOI[10.5219/332]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	cone	n.a.	PMID[10336650]
NPO3492	Negombata magnifica	Species	Latrunculiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15217296]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679315]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16252923]
NPO3492	Negombata magnifica	Species	Latrunculiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16499319]
NPO13478	Scorzonera pseudodivaricata	Species	Asteraceae	Eukaryota	n.a.	Mongolian	n.a.	PMID[17542634]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	cone	n.a.	PMID[17624889]
NPO3492	Negombata magnifica	Species	Latrunculiidae	Eukaryota	n.a.	sand-covered bottom at -10 to -15 m at Hurghada, on the Egyptian Red Sea coast	2003-JUN	PMID[18298079]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18611049]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18768384]
NPO3492	Negombata magnifica	Species	Latrunculiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18942825]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19476340]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[19628108]
NPO12855	Alkanna cappadocica	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20405844]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21912858]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	cone	n.a.	PMID[22111577]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	flower	n.a.	PMID[22166201]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[22538527]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23790907]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[24811150]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24948953]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25564559]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[28274428]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29154541]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[30236698]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	Guangzhou, China		PMID[30563201]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[30583361]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[30599958]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[31159190]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	Seeds	n.a.		PMID[31861466]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2398	Millettia erythrocalyx	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24390.1	Juniperus rigida var. conferta	Varieties	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1834	Atalantia racemosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9313	Fritillaria ningguoensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2398	Millettia erythrocalyx	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9313	Fritillaria ningguoensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24390.1	Juniperus rigida var. conferta	Varieties	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13671	Ononis vaginalis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9313	Fritillaria ningguoensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13478	Scorzonera pseudodivaricata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO252	Hoffmannia strigillosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8928	Pteris semipinnata	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9934	Mycobacterium leprae	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO14578	Prorocentrum micans	Species	Prorocentraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10783	Syncarpia hillii	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13281	Salvia hispanica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13585	Rapanea lancifolia	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5930	Crambe tatarica	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13030	Artemisia dentata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12196	Buphane fischeri	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO21830	Buddleja cordata	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1834	Atalantia racemosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12855	Alkanna cappadocica	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2398	Millettia erythrocalyx	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12700	Diospyros eriantha	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6360	Xenoacremonium recifei	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11848	Lemaireocereus griseus	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3492	Negombata magnifica	Species	Latrunculiidae	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 NPC191926 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	202
0.1-0.2	1136
0.2-0.3	4063
0.3-0.4	8063
0.4-0.5	16401
0.5-0.6	8366
0.6-0.7	3968
0.7-0.8	460
0.8-0.85	33
0.85-0.9	3
0.9-0.95	0
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 NPC191926 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	179
0.1-0.2	1538
0.2-0.3	3601
0.3-0.4	2468
0.4-0.5	964
0.5-0.6	349
0.6-0.7	50
0.7-0.8	1
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