NPASS Compound

Structure

NPC189895 OpenBabel06302215532D 29 30 0 0 1 0 0 0 0 0999 V2000 1.7321 -0.0000 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 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 C 0 0 0 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 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2321 -2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2321 -2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 2 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 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 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 0.0000 -0.0000 0.0000 C 0 0 1 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 O 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 -0.0000 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 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 2.5000 0.0000 O 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 -0.0000 4.0000 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 0.8660 4.5000 0.0000 O 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 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 -3.4641 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 14 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 12 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 6 9 1 0 0 0 0 9 10 1 0 0 0 0 9 29 1 1 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 1 0 0 0 12 14 1 0 0 0 0 14 15 1 1 0 0 0 15 16 1 0 0 0 0 17 16 1 6 0 0 0 17 18 1 0 0 0 0 17 26 1 0 0 0 0 18 19 1 6 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	412.21
Volume:	414.435
LogP:	1.419
LogD:	5.304
LogS:	-2.373
# Rotatable Bonds:	8
TPSA:	141.36
# H-Bond Aceptor:	8
# H-Bond Donor:	4
# Rings:	2
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.445
Synthetic Accessibility Score:	4.476
Fsp3:	0.762
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.194
MDCK Permeability:	0.0009660633513703942
Pgp-inhibitor:	0.0
Pgp-substrate:	0.108
Human Intestinal Absorption (HIA):	0.577
20% Bioavailability (F20%):	0.022
30% Bioavailability (F30%):	0.057

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.096
Plasma Protein Binding (PPB):	44.31183624267578%
Volume Distribution (VD):	0.317
Pgp-substrate:	34.285552978515625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.025
CYP2C19-inhibitor:	0.006
CYP2C19-substrate:	0.036
CYP2C9-inhibitor:	0.008
CYP2C9-substrate:	0.531
CYP2D6-inhibitor:	0.01
CYP2D6-substrate:	0.074
CYP3A4-inhibitor:	0.01
CYP3A4-substrate:	0.003

ADMET: Excretion

Clearance (CL):	2.629
Half-life (T1/2):	0.735

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.133
Drug-inuced Liver Injury (DILI):	0.077
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.83
Maximum Recommended Daily Dose:	0.922
Skin Sensitization:	0.255
Carcinogencity:	0.587
Eye Corrosion:	0.151
Eye Irritation:	0.035
Respiratory Toxicity:	0.967

Download Data

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

Natural Product: NPC189895

Natural Product ID:	NPC189895
*Common Name:**	NXBOOZAQZQINMQ-BEIOMWSMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NXBOOZAQZQINMQ-BEIOMWSMSA-N
Standard InCHI:	InChI=1S/C21H32O8/c1-11-5-6-14-20(2,3)15(22)7-8-21(14,4)13(11)10-29-17(19(27)28)12(18(25)26)9-16(23)24/h12-15,17,22H,1,5-10H2,2-4H3,(H,23,24)(H,25,26)(H,27,28)/t12-,13-,14+,15-,17+,21+/m0/s1
SMILES:	C=C1CC[C@@H]2C(C)(C)[C@H](CC[C@]2(C)[C@H]1CO[C@H]([C@H](CC(=O)O)C(=O)O)C(=O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0001986] Tricarboxylic acids and derivatives

*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
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24014097]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24128451]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9917288]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	Tissue Culture	n.a.	n.a.	Database[FooDB]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	Essential Oil	n.a.	n.a.	Database[FooDB]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7276	Mitragyna macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO7276	Mitragyna macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1599	Ormosia pachycarpa	Species	Limoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5585	Cassia greggii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7276	Mitragyna macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6970	Wyethia angustifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8579	Pestalotiopsis longiseta	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO341	Xylaria obovata	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4237	Vepris madagascarica	Species	Rutaceae	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 NPC189895 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	241
0.1-0.2	1711
0.2-0.3	5358
0.3-0.4	11300
0.4-0.5	10934
0.5-0.6	6930
0.6-0.7	5477
0.7-0.8	734
0.8-0.85	12
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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 NPC189895 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	232
0.1-0.2	2248
0.2-0.3	3717
0.3-0.4	1884
0.4-0.5	634
0.5-0.6	288
0.6-0.7	133
0.7-0.8	14
0.8-0.85	0
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