NPASS Compound

Structure

NPC18297 OpenBabel06302215342D 42 47 0 0 0 0 0 0 0 0999 V2000 1.7321 -2.0000 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 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -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 0 0 0 0 0 0 0 0 0 0 -6.9282 -0.0000 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 -1.7321 -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 -1.7321 1.0000 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 -0.0000 1.0000 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 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 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 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 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 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 5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 O 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 -0.8660 2.5000 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 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -4.5000 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 20 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 5 42 1 0 0 0 0 6 19 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 18 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 38 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 40 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 39 1 0 0 0 0 25 38 1 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 29 37 1 0 0 0 0 30 35 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 36 1 0 0 0 0 34 35 1 0 0 0 0 37 38 1 0 0 0 0 40 41 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	180.04
Volume:	177.642
LogP:	0.687
LogD:	0.375
LogS:	-0.456
# Rotatable Bonds:	3
TPSA:	74.6
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.667
Synthetic Accessibility Score:	1.985
Fsp3:	0.111
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.357
MDCK Permeability:	1.2178135875728913e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.04
20% Bioavailability (F20%):	0.4
30% Bioavailability (F30%):	0.203

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.205
Plasma Protein Binding (PPB):	53.693843841552734%
Volume Distribution (VD):	0.287
Pgp-substrate:	49.260406494140625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.099
CYP1A2-substrate:	0.057
CYP2C19-inhibitor:	0.052
CYP2C19-substrate:	0.051
CYP2C9-inhibitor:	0.199
CYP2C9-substrate:	0.646
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.197
CYP3A4-inhibitor:	0.025
CYP3A4-substrate:	0.162

ADMET: Excretion

Clearance (CL):	8.918
Half-life (T1/2):	0.925

ADMET: Toxicity

hERG Blockers:	0.058
Human Hepatotoxicity (H-HT):	0.384
Drug-inuced Liver Injury (DILI):	0.835
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.038
Maximum Recommended Daily Dose:	0.004
Skin Sensitization:	0.337
Carcinogencity:	0.029
Eye Corrosion:	0.53
Eye Irritation:	0.965
Respiratory Toxicity:	0.061

Download Data

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

Natural Product: NPC18297

Natural Product ID:	NPC18297
*Common Name:**	RVOYIHAAPJNILN-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RVOYIHAAPJNILN-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C32H22O10/c1-39-25-13-21(37)27-19(35)11-23(15-3-7-17(33)8-4-15)41-31(27)29(25)30-26(40-2)14-22(38)28-20(36)12-24(42-32(28)30)16-5-9-18(34)10-6-16/h3-14,33-34,37-38H,1-2H3
SMILES:	COc1cc(c2c(=O)cc(c3ccc(cc3)O)oc2c1c1c(cc(c2c(=O)cc(c3ccc(cc3)O)oc12)O)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5316884
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

*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
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	Leaves and branches	Soorkesh Valley, Gollestan, Iran	n.a.	PMID[15104493]
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	leaves	Soorkesh Valley, Gollestan, Iran	n.a.	PMID[15104493]
NPO28430	Biota orientalis	n.a.	n.a.	n.a.	n.a.	leaf	n.a.	PMID[21793559]
NPO28430	Biota orientalis	n.a.	n.a.	n.a.	n.a.	twig	n.a.	PMID[21793559]
NPO23434	Fissistigma latifolium	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29160716]
NPO13468.1	Cryptomeria japonica var. sinensis	Varieties	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30485090]
NPO28430	Biota orientalis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO23814	Elsholtzia splendens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22216	Chimonanthus fragrans	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5174	Helenium mexicanum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28430	Biota orientalis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO13468.1	Cryptomeria japonica var. sinensis	Varieties	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13513	Agathis palmerstonii	Species	Araucariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5174	Helenium mexicanum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22216	Chimonanthus fragrans	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11495	Pellia epiphylla	Species	Pelliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11353	Viscaria vulgaris	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21146	Aloidendron sabaea	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20124	Xylopia discreta	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11328	Juniperus chinensis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23814	Elsholtzia splendens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22216	Chimonanthus fragrans	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28430	Biota orientalis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11495	Pellia epiphylla	Species	Pelliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14674	Vallesia glabra	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23153	Eria smithii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28430	Biota orientalis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO24155	Nepeta annua	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5174	Helenium mexicanum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13513	Agathis palmerstonii	Species	Araucariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20124	Xylopia discreta	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7689	Cota triumfettii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13599	Dryopteris abbreviata	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24429	Cestrum pallidissimum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22365	Osbeckia chinensis	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12500	Inga umbellifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14835	Lepraria chlorina	Species	Stereocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23434	Fissistigma latifolium	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15446	Quercus coccifera	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24234	Agrocybe aegerita	Species	Bolbitiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22216	Chimonanthus fragrans	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11353	Viscaria vulgaris	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23575	Aspergillus restrictus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23814	Elsholtzia splendens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24351	Sclerotinia libertiana	Species	Sclerotiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21146	Aloidendron sabaea	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13468.1	Cryptomeria japonica var. sinensis	Varieties	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25084	Dasiphora fruticosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11328	Juniperus chinensis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24272	Akania lucens	Species	Akaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8387	Lactarius flavidulus	Species	Lactariidae	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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Individual Protein	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT78	Individual Protein	Beta amyloid A4 protein	Homo sapiens	IC50	=	17300.0	nM	PMID[559760]

☑ 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 NPC18297 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	469
0.1-0.2	1956
0.2-0.3	4328
0.3-0.4	10853
0.4-0.5	7419
0.5-0.6	4208
0.6-0.7	5617
0.7-0.8	4139
0.8-0.85	2568
0.85-0.9	944
0.9-0.95	161
0.95-1	35

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 NPC18297 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	443
0.1-0.2	996
0.2-0.3	1588
0.3-0.4	2742
0.4-0.5	1921
0.5-0.6	993
0.6-0.7	289
0.7-0.8	117
0.8-0.85	47
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