NPASS Compound

Structure

NPC186858 OpenBabel06302215552D 26 30 0 0 1 0 0 0 0 0999 V2000 -5.5066 0.8014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8375 1.5446 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8594 1.3367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5503 0.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5722 0.1777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9031 0.9209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2121 1.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1902 2.0798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4992 3.0309 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9249 0.7129 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5182 -0.2006 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7261 -1.1787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1399 -1.6787 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8831 -1.0096 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3198 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3198 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4538 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5878 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4538 0.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3633 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 -0.3090 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 0.4763 -0.0961 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6843 0.8821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1818 1.3821 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 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 6 1 1 0 0 0 10 11 1 0 0 0 0 10 26 1 0 0 0 0 11 12 1 6 0 0 0 11 24 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 6 0 0 0 14 24 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 23 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 24 25 1 6 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	356.13
Volume:	348.616
LogP:	3.089
LogD:	3.126
LogS:	-4.918
# Rotatable Bonds:	3
TPSA:	66.38
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.911
Synthetic Accessibility Score:	3.745
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.826
MDCK Permeability:	3.814394949586131e-05
Pgp-inhibitor:	0.029
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.126
Plasma Protein Binding (PPB):	95.3409652709961%
Volume Distribution (VD):	0.814
Pgp-substrate:	5.088672637939453%

ADMET: Metabolism

CYP1A2-inhibitor:	0.255
CYP1A2-substrate:	0.839
CYP2C19-inhibitor:	0.739
CYP2C19-substrate:	0.497
CYP2C9-inhibitor:	0.622
CYP2C9-substrate:	0.612
CYP2D6-inhibitor:	0.926
CYP2D6-substrate:	0.879
CYP3A4-inhibitor:	0.876
CYP3A4-substrate:	0.541

ADMET: Excretion

Clearance (CL):	15.076
Half-life (T1/2):	0.238

ADMET: Toxicity

hERG Blockers:	0.545
Human Hepatotoxicity (H-HT):	0.257
Drug-inuced Liver Injury (DILI):	0.871
AMES Toxicity:	0.497
Rat Oral Acute Toxicity:	0.084
Maximum Recommended Daily Dose:	0.841
Skin Sensitization:	0.932
Carcinogencity:	0.766
Eye Corrosion:	0.003
Eye Irritation:	0.632
Respiratory Toxicity:	0.862

Download Data

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

Natural Product: NPC186858

Natural Product ID:	NPC186858
*Common Name:**	BURBOJZOZGMMQF-LHHVKLHASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BURBOJZOZGMMQF-LHHVKLHASA-N
Standard InCHI:	InChI=1S/C20H20O6/c1-22-16-4-2-11(6-15(16)21)19-13-8-24-20(14(13)9-23-19)12-3-5-17-18(7-12)26-10-25-17/h2-7,13-14,19-21H,8-10H2,1H3/t13-,14-,19+,20-/m0/s1
SMILES:	COc1ccc(cc1O)[C@@H]1[C@H]2CO[C@@H](c3ccc4c(c3)OCO4)[C@H]2CO1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101389128
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans

*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
NPO1768	Sansevieria ehrenbergii	Species	Asparagaceae	Eukaryota	n.a.	African	n.a.	PMID[15921418]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	whole plants	Sendai, Miyagi Prefecture, Japan	2000-Sep	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17397219]
NPO8160	Diospyros montana	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17400463]
NPO11451	Lespedeza cyrtobotrya	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19102656]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	aerial parts	Kego Nature Reserve, Hatinh Province, Vietnam	2008-DEC	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	Kego Nature Reserve, Hatinh Province, Vietnam	2008-DEC	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	twig	n.a.	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	stem	n.a.	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	inflorescence	n.a.	PMID[21973101]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22940450]
NPO4720	Aglaia perviridis	Species	Meliaceae	Eukaryota	leaves, twigs, and fruits	Nui Chua National Park (11 43' N; 109 08' E; 730 m alt.), Ninh Thuan Province, Vietnam	2010-Jan	PMID[23301897]
NPO4720	Aglaia perviridis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31621322]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11451	Lespedeza cyrtobotrya	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2517	Radix zanthoxyli	Species	Lymnaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11451	Lespedeza cyrtobotrya	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1912	Acanthosyris paulo-alvinii	Species	Cervantesiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO61	Phoebe grandis	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22851	Kryptoperidinium foliaceum	Species	Peridiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1768	Sansevieria ehrenbergii	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14332	Uvaria ferruginea	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO992	Betula alnoides	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4720	Aglaia perviridis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11451	Lespedeza cyrtobotrya	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO668	Cnidoscolus texanus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17618	Flaveria bidentis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2535	Bunodactis xanthogrammica	Species	Actiniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6614	Rubus pileatus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8160	Diospyros montana	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14611	Teucrium fragile	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5657	Oocystis polymorpha	Species	Oocystaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16062	Trichilia dregeana	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17154	Hymenaea oblongifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17009	Ptelea crenulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12642	Podadenia thwaitesii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO9374	Veronica anagallis-aquatica	Species	Plantaginaceae	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 NPC186858 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	393
0.1-0.2	1333
0.2-0.3	3581
0.3-0.4	9609
0.4-0.5	9548
0.5-0.6	5848
0.6-0.7	8734
0.7-0.8	2715
0.8-0.85	628
0.85-0.9	205
0.9-0.95	93
0.95-1	10

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 NPC186858 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	305
0.1-0.2	793
0.2-0.3	1806
0.3-0.4	2817
0.4-0.5	1790
0.5-0.6	1073
0.6-0.7	501
0.7-0.8	62
0.8-0.85	3
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