NPASS Compound

Structure

NPC3945 OpenBabel06302215192D 44 49 0 0 0 0 0 0 0 0999 V2000 5.0922 0.9800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2435 1.4700 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3948 0.9800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3948 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5461 -0.4900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6974 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6974 0.9800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5461 1.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8487 -0.4900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8487 -1.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.9600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.9400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 -1.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 -0.4900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5461 -0.4900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5461 -1.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2435 -2.4500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0922 -1.9600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0922 -0.9800 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9409 -2.4500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7896 -1.9600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6383 -2.4500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6383 -3.4300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7896 -3.9200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9409 -3.4300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0922 -3.9200 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2435 -3.4300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3948 -3.9200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3948 -4.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5461 -5.3900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 -4.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 -3.9200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5461 -3.4300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 -5.3900 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 -6.3700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4870 -3.9200 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.3358 -3.4300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7896 -0.9800 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 -1.9600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 -2.9400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3948 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3948 0.9800 0.0000 C 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 9 1 0 0 0 0 7 8 1 0 0 0 0 9 44 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 40 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 44 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 42 1 0 0 0 0 17 18 1 0 0 0 0 17 40 1 0 0 0 0 18 28 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 26 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 39 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 37 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 34 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 32 33 2 0 0 0 0 32 35 1 0 0 0 0 33 34 1 0 0 0 0 35 36 1 0 0 0 0 37 38 1 0 0 0 0 40 41 1 0 0 0 0 42 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	594.15
Volume:	591.0
LogP:	6.296
LogD:	2.43
LogS:	-4.769
# Rotatable Bonds:	7
TPSA:	137.8
# H-Bond Aceptor:	10
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.215
Synthetic Accessibility Score:	2.892
Fsp3:	0.118
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.867
MDCK Permeability:	4.85759082948789e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.029
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.916

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0
Plasma Protein Binding (PPB):	87.40142822265625%
Volume Distribution (VD):	0.363
Pgp-substrate:	12.947421073913574%

ADMET: Metabolism

CYP1A2-inhibitor:	0.422
CYP1A2-substrate:	0.929
CYP2C19-inhibitor:	0.581
CYP2C19-substrate:	0.059
CYP2C9-inhibitor:	0.772
CYP2C9-substrate:	0.964
CYP2D6-inhibitor:	0.013
CYP2D6-substrate:	0.953
CYP3A4-inhibitor:	0.267
CYP3A4-substrate:	0.181

ADMET: Excretion

Clearance (CL):	2.505
Half-life (T1/2):	0.049

ADMET: Toxicity

hERG Blockers:	0.057
Human Hepatotoxicity (H-HT):	0.342
Drug-inuced Liver Injury (DILI):	0.989
AMES Toxicity:	0.357
Rat Oral Acute Toxicity:	0.034
Maximum Recommended Daily Dose:	0.71
Skin Sensitization:	0.052
Carcinogencity:	0.035
Eye Corrosion:	0.003
Eye Irritation:	0.423
Respiratory Toxicity:	0.138

Download Data

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

Natural Product: NPC3945

Natural Product ID:	NPC3945
*Common Name:**	HOAUCAJOHGDHDA-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HOAUCAJOHGDHDA-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C34H26O10/c1-39-19-9-5-17(6-10-19)24-15-23(36)29-27(43-24)16-25(42-4)30(32(29)37)31-33(38)28-22(35)13-21(41-3)14-26(28)44-34(31)18-7-11-20(40-2)12-8-18/h5-16,35,37H,1-4H3
SMILES:	COc1ccc(cc1)c1cc(=O)c2c(cc(c(c3c(=O)c4c(cc(cc4oc3c3ccc(cc3)OC)OC)O)c2O)OC)o1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	12087758
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0003530] Pyranoisoflavonoids

*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
NPO1179	Anaxagorea luzonensis	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10959592]
NPO755	Phoradendron reichenbachianum	Species	Viscaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[11488459]
NPO12773	Stephania tetrandra	Species	Menispermaceae	Eukaryota	n.a.	root	n.a.	PMID[20030508]
NPO3148	Melianthus major	Species	Melianthaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[32663024]
NPO12773	Stephania tetrandra	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3728032]
NPO12773	Stephania tetrandra	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO7698	Elettaria cardamomum	Species	Zingiberaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO7698	Elettaria cardamomum	Species	Zingiberaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO7698	Elettaria cardamomum	Species	Zingiberaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO7698	Elettaria cardamomum	Species	Zingiberaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7698	Elettaria cardamomum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO12183	Argyreia nervosa	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1484	Bupleurum scorzonerifolium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11802	Physeter catodon	Species	Physeteridae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12773	Stephania tetrandra	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7698	Elettaria cardamomum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO12773	Stephania tetrandra	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12183	Argyreia nervosa	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1484	Bupleurum scorzonerifolium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2690	Carapichea ipecacuanha	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11802	Physeter catodon	Species	Physeteridae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12773	Stephania tetrandra	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1484	Bupleurum scorzonerifolium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11802	Physeter catodon	Species	Physeteridae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12183	Argyreia nervosa	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7698	Elettaria cardamomum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2690	Carapichea ipecacuanha	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12773	Stephania tetrandra	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1484	Bupleurum scorzonerifolium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7698	Elettaria cardamomum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12663	Penicillium implicatum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18003	Leptolyngbya lurida	Species	Leptolyngbyaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO1484	Bupleurum scorzonerifolium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12430	Erythrina chiriquensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2679	Dictyota bartayresiana	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28111	Lathyrus aphaca	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11802	Physeter catodon	Species	Physeteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3148	Melianthus major	Species	Melianthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22389	Phelipanche arenaria	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5377	Tapinoma erraticum	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12183	Argyreia nervosa	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2690	Carapichea ipecacuanha	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12773	Stephania tetrandra	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5783	Acronychia muelleri	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO755	Phoradendron reichenbachianum	Species	Viscaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12882	Clitocybe fasciculata	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1179	Anaxagorea luzonensis	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15367	Croton regelianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21826	Vulpicida juniperinus	Species	Parmeliaceae	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 NPC3945 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	433
0.1-0.2	1842
0.2-0.3	4073
0.3-0.4	10298
0.4-0.5	8143
0.5-0.6	3975
0.6-0.7	5768
0.7-0.8	4064
0.8-0.85	2550
0.85-0.9	1273
0.9-0.95	242
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 NPC3945 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	395
0.1-0.2	992
0.2-0.3	1537
0.3-0.4	2686
0.4-0.5	1987
0.5-0.6	1048
0.6-0.7	318
0.7-0.8	119
0.8-0.85	54
0.85-0.9	12
0.9-0.95	2
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