NPASS Compound

Structure

NPC158197 OpenBabel06302216162D 38 41 0 0 1 0 0 0 0 0999 V2000 0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 C 0 0 2 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 -1.7321 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 O 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 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 -2.5981 -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 -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 -5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -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 -7.7942 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -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 -3.4641 1.0000 0.0000 C 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 -0.8660 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 2 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 2 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 2 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 2 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 -2.0000 0.0000 O 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 26 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 5 6 1 0 0 0 0 6 24 2 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 25 1 0 0 0 0 9 23 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 22 1 0 0 0 0 14 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 21 1 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 27 26 1 6 0 0 0 27 28 1 0 0 0 0 27 35 1 0 0 0 0 28 29 1 0 0 0 0 28 38 1 1 0 0 0 29 30 1 0 0 0 0 29 37 1 6 0 0 0 30 31 1 0 0 0 0 30 36 1 1 0 0 0 31 32 1 6 0 0 0 31 35 1 0 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	534.1
Volume:	486.133
LogP:	1.235
LogD:	0.33
LogS:	-4.246
# Rotatable Bonds:	7
TPSA:	233.65
# H-Bond Aceptor:	14
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.123
Synthetic Accessibility Score:	4.321
Fsp3:	0.292
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.569
MDCK Permeability:	1.9219325622543693e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.972
Human Intestinal Absorption (HIA):	0.632
20% Bioavailability (F20%):	0.751
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.028
Plasma Protein Binding (PPB):	88.45276641845703%
Volume Distribution (VD):	0.466
Pgp-substrate:	9.315774917602539%

ADMET: Metabolism

CYP1A2-inhibitor:	0.067
CYP1A2-substrate:	0.029
CYP2C19-inhibitor:	0.047
CYP2C19-substrate:	0.037
CYP2C9-inhibitor:	0.039
CYP2C9-substrate:	0.224
CYP2D6-inhibitor:	0.013
CYP2D6-substrate:	0.129
CYP3A4-inhibitor:	0.053
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	1.236
Half-life (T1/2):	0.886

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.161
Drug-inuced Liver Injury (DILI):	0.976
AMES Toxicity:	0.277
Rat Oral Acute Toxicity:	0.037
Maximum Recommended Daily Dose:	0.014
Skin Sensitization:	0.606
Carcinogencity:	0.03
Eye Corrosion:	0.003
Eye Irritation:	0.084
Respiratory Toxicity:	0.085

Download Data

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

Natural Product: NPC158197

Natural Product ID:	NPC158197
*Common Name:**	MANYEARKZBQLSB-JAUKUMGQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MANYEARKZBQLSB-JAUKUMGQSA-N
Standard InCHI:	InChI=1S/C24H22O14/c1-8(35-24-20(31)18(29)19(30)21(38-24)22(32)33)23(34)36-10-5-13(27)17-14(28)7-15(37-16(17)6-10)9-2-3-11(25)12(26)4-9/h2-8,18-21,24-27,29-31H,1H3,(H,32,33)/t8-,18-,19-,20+,21-,24+/m1/s1
SMILES:	C[C@H](C(=O)Oc1cc(c2c(=O)cc(c3ccc(c(c3)O)O)oc2c1)O)O[C@@H]1[C@H]([C@@H]([C@H]([C@H](C(=O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001615] Flavones

*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
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	n.a.	twig	n.a.	PMID[14709876]
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	n.a.	leaf	n.a.	PMID[14709876]
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	Leaves; Twigs	n.a.	n.a.	PMID[15043402]
NPO23473	Cinnamomum kotoense	Species	Lauraceae	Eukaryota	stem wood	n.a.	n.a.	PMID[16180806]
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16309320]
NPO23473	Cinnamomum kotoense	Species	Lauraceae	Eukaryota	leaves	n.a.	n.a.	PMID[16792412]
NPO23769	Ainsliaea macrocephala	Species	Asteraceae	Eukaryota	n.a.	whole plant	n.a.	PMID[18484734]
NPO23473	Cinnamomum kotoense	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18489163]
NPO23557	Zanthoxylum ailanthoides	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19128011]
NPO24301	Buxus microphylla	Species	Buxaceae	Eukaryota	leaves and stems	Kunming, Yunnan, China	2007-AUG	PMID[19133780]
NPO24301	Buxus microphylla	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23264	Marrubium vulgare	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23302	Strychnos camptoneura	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25037	Nepeta cataria	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23557	Zanthoxylum ailanthoides	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23302	Strychnos camptoneura	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25037	Nepeta cataria	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23264	Marrubium vulgare	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21478	Buxus hyrcana	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24301	Buxus microphylla	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23557	Zanthoxylum ailanthoides	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25037	Nepeta cataria	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24301	Buxus microphylla	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23264	Marrubium vulgare	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23769	Ainsliaea macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21478	Buxus hyrcana	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20498	Cephalaria ambrosioides	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23474	Abies veitchii	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24301	Buxus microphylla	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23849	Dicoma anomala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25037	Nepeta cataria	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23302	Strychnos camptoneura	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22684	Enrichment culture	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO24015	Perknaster fuscus	Species	Ganeriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24258	Vellozia nivea	Species	Velloziaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23264	Marrubium vulgare	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21352	Boronia ternata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24462	Pityrogramma ebenea	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23557	Zanthoxylum ailanthoides	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18918	Lecanicillium muscarium	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28748	Aphis sambuci	Species	Aphididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23930	Luculia pinceana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23473	Cinnamomum kotoense	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24952	Galeopsis tetrahit	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24993	Conospermum teretifolium	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18735	Pinus mugo	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7197	Colchicum robustum	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23428	Tinus mamillata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO25080	Sphaeria maculans	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO23896	Cytisus ratisbonensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23721	Epidendrum rigidum	Species	Orchidaceae	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 NPC158197 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	408
0.1-0.2	1739
0.2-0.3	3958
0.3-0.4	8875
0.4-0.5	9079
0.5-0.6	4558
0.6-0.7	5254
0.7-0.8	5280
0.8-0.85	2018
0.85-0.9	927
0.9-0.95	442
0.95-1	159

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 NPC158197 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	364
0.1-0.2	940
0.2-0.3	1960
0.3-0.4	2608
0.4-0.5	1871
0.5-0.6	923
0.6-0.7	307
0.7-0.8	131
0.8-0.85	23
0.85-0.9	15
0.9-0.95	7
0.95-1	1

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