NPASS Compound

Structure

NPC174249 OpenBabel06302216222D 27 29 0 0 1 0 0 0 0 0999 V2000 2.5981 -0.5000 0.0000 C 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 0.8660 -0.5000 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 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 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 -0.8660 -0.5000 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 -2.5981 -0.5000 0.0000 C 0 0 3 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 -2.1913 -1.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9345 -2.0827 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8005 -1.5827 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -3.5926 -0.6045 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -4.2617 0.1386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2399 -0.0693 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7141 -1.9894 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8186 -2.9839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7321 -3.3907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8367 -4.3852 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7502 -4.7919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5411 -2.8029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4547 -3.2096 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4366 -1.8084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5231 -1.4016 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 3 27 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 27 2 0 0 0 0 9 10 1 0 0 0 0 10 15 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 18 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 18 26 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 23 2 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 25 26 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	376.15
Volume:	374.52
LogP:	1.152
LogD:	1.743
LogS:	-2.63
# Rotatable Bonds:	6
TPSA:	108.61
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.608
Synthetic Accessibility Score:	3.656
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.992
MDCK Permeability:	5.771043106506113e-06
Pgp-inhibitor:	0.007
Pgp-substrate:	0.178
Human Intestinal Absorption (HIA):	0.417
20% Bioavailability (F20%):	0.232
30% Bioavailability (F30%):	0.054

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.105
Plasma Protein Binding (PPB):	90.16019439697266%
Volume Distribution (VD):	1.033
Pgp-substrate:	10.34300708770752%

ADMET: Metabolism

CYP1A2-inhibitor:	0.045
CYP1A2-substrate:	0.637
CYP2C19-inhibitor:	0.057
CYP2C19-substrate:	0.681
CYP2C9-inhibitor:	0.136
CYP2C9-substrate:	0.795
CYP2D6-inhibitor:	0.272
CYP2D6-substrate:	0.87
CYP3A4-inhibitor:	0.675
CYP3A4-substrate:	0.497

ADMET: Excretion

Clearance (CL):	14.512
Half-life (T1/2):	0.802

ADMET: Toxicity

hERG Blockers:	0.033
Human Hepatotoxicity (H-HT):	0.313
Drug-inuced Liver Injury (DILI):	0.052
AMES Toxicity:	0.396
Rat Oral Acute Toxicity:	0.528
Maximum Recommended Daily Dose:	0.062
Skin Sensitization:	0.437
Carcinogencity:	0.151
Eye Corrosion:	0.003
Eye Irritation:	0.038
Respiratory Toxicity:	0.02

Download Data

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

Natural Product: NPC174249

Natural Product ID:	NPC174249
*Common Name:**	BVHIKUCXNBQDEM-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BVHIKUCXNBQDEM-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C20H24O7/c1-25-17-7-12(3-5-15(17)22)9-20(24)11-27-19(14(20)10-21)13-4-6-16(23)18(8-13)26-2/h3-8,14,19,21-24H,9-11H2,1-2H3
SMILES:	COc1cc(ccc1O)CC1(COC(c2ccc(c(c2)OC)O)C1CO)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	586733
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003422] 7,9'-epoxylignans

*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
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[12802735]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[18384095]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014120]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[22014120]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014168]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23540838]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24295708]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[25102361]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[25306330]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26767291]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	bark	n.a.	PMID[26767291]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	leaf	n.a.	PMID[8699184]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO18827	Aspidosperma olivaceum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22383	Aspidosperma nigricans	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14143	Aspidosperma campus-belus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18827	Aspidosperma olivaceum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22383	Aspidosperma nigricans	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14143	Aspidosperma campus-belus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18827	Aspidosperma olivaceum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	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 NPC174249 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	375
0.1-0.2	1221
0.2-0.3	3311
0.3-0.4	8918
0.4-0.5	10128
0.5-0.6	4675
0.6-0.7	9272
0.7-0.8	3409
0.8-0.85	810
0.85-0.9	438
0.9-0.95	104
0.95-1	36

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 NPC174249 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	296
0.1-0.2	764
0.2-0.3	1690
0.3-0.4	2639
0.4-0.5	1909
0.5-0.6	1036
0.6-0.7	658
0.7-0.8	150
0.8-0.85	7
0.85-0.9	1
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