NPASS Compound

Structure

NPC74604 OpenBabel06302215072D 27 29 0 0 1 0 0 0 0 0999 V2000 -2.5981 -1.5000 0.0000 C 0 0 0 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 -3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.8301 -1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3301 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1962 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9641 1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4641 1.0000 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 -1.7321 1.0000 0.0000 C 0 0 1 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 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 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 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 1 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 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 15 1 0 0 0 0 2 3 2 0 0 0 0 3 10 1 0 0 0 0 4 3 1 6 0 0 0 4 5 1 0 0 0 0 4 6 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 1 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 10 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 16 1 6 0 0 0 17 16 1 1 0 0 0 17 18 1 0 0 0 0 17 24 1 0 0 0 0 18 19 1 0 0 0 0 18 27 1 6 0 0 0 19 20 1 0 0 0 0 19 26 1 1 0 0 0 20 21 1 0 0 0 0 20 25 1 6 0 0 0 21 22 1 1 0 0 0 21 24 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	384.21
Volume:	385.065
LogP:	1.337
LogD:	1.314
LogS:	-2.27
# Rotatable Bonds:	5
TPSA:	116.45
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.511
Synthetic Accessibility Score:	4.675
Fsp3:	0.85
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.135
MDCK Permeability:	5.478080129250884e-05
Pgp-inhibitor:	0.091
Pgp-substrate:	0.962
Human Intestinal Absorption (HIA):	0.24
20% Bioavailability (F20%):	0.225
30% Bioavailability (F30%):	0.037

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.058
Plasma Protein Binding (PPB):	85.36966705322266%
Volume Distribution (VD):	1.295
Pgp-substrate:	8.437614440917969%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.112
CYP2C19-inhibitor:	0.01
CYP2C19-substrate:	0.701
CYP2C9-inhibitor:	0.004
CYP2C9-substrate:	0.144
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.142
CYP3A4-inhibitor:	0.009
CYP3A4-substrate:	0.173

ADMET: Excretion

Clearance (CL):	5.359
Half-life (T1/2):	0.698

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.284
Drug-inuced Liver Injury (DILI):	0.25
AMES Toxicity:	0.332
Rat Oral Acute Toxicity:	0.163
Maximum Recommended Daily Dose:	0.252
Skin Sensitization:	0.079
Carcinogencity:	0.272
Eye Corrosion:	0.004
Eye Irritation:	0.051
Respiratory Toxicity:	0.064

Download Data

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

Natural Product: NPC74604

Natural Product ID:	NPC74604
*Common Name:**	IBNSTGIITWSRAW-BAVSQXHGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IBNSTGIITWSRAW-BAVSQXHGSA-N
Standard InCHI:	InChI=1S/C20H32O7/c1-9-5-11(7-20(3,4)15(9)13-6-12(13)10(2)22)26-19-18(25)17(24)16(23)14(8-21)27-19/h11-14,16-19,21,23-25H,5-8H2,1-4H3/t11-,12+,13-,14-,16-,17+,18-,19-/m1/s1
SMILES:	CC1=C([C@@H]2C[C@H]2C(=O)C)C(C)(C)C[C@@H](C1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002207] O-glycosyl compounds

*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
NPO19975	Pycnandra acuminata	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.phytochem.2007.07.001]
NPO5140	Dipteryx odorata	Species	Fabaceae	Eukaryota	seeds	n.a.	n.a.	PMID[12762787]
NPO5140	Dipteryx odorata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12762809]
NPO6412	Echinacea pallida	Species	Asteraceae	Eukaryota	root	n.a.	n.a.	PMID[15921428]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[25340465]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25340465]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25577087]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	leaf	n.a.	PMID[8699184]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO5140	Dipteryx odorata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7088	Staphylea bumalda	Species	Staphyleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO633	Mesembryanthemum expansum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20569	Psychotria serpens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO633	Mesembryanthemum expansum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20569	Psychotria serpens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6856.1	Artemisia ludoviciana subsp. mexicana	Subspecies	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7088	Staphylea bumalda	Species	Staphyleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5140	Dipteryx odorata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20569	Psychotria serpens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7088	Staphylea bumalda	Species	Staphyleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26095	Hypericum revolutum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8129	Inocybe geophylla	Species	Inocybaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20569	Psychotria serpens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7874	Helichrysum lepidissimum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5534	Alternaria kikuchiana	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4322	Scabiosa succisa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19975	Pycnandra acuminata	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO633	Mesembryanthemum expansum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2345	Coriandrum sativum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1695	Monascus pilosus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6856.1	Artemisia ludoviciana subsp. mexicana	Subspecies	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5140	Dipteryx odorata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8609	Hopea utilis	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6412	Echinacea pallida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7088	Staphylea bumalda	Species	Staphyleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12118	Cleistopholis staudtii	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11339	Litsea salicifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10010	Evernia vulpina	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12602	Leuzea centauroides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO940	Vernonia anisochaetoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6861	Galium dasypodum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12828	Dysidea tupha	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO218	Acer carpinifolium	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4759	Helleborus multifidus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11506	Stipa vaseyi	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10970	Osmorhiza aristata	Species	Apiaceae	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 NPC74604 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	227
0.1-0.2	1665
0.2-0.3	5527
0.3-0.4	12821
0.4-0.5	9854
0.5-0.6	8211
0.6-0.7	4108
0.7-0.8	271
0.8-0.85	12
0.85-0.9	1
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 NPC74604 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	205
0.1-0.2	2248
0.2-0.3	3816
0.3-0.4	1914
0.4-0.5	523
0.5-0.6	390
0.6-0.7	50
0.7-0.8	4
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