NPASS Compound

Structure

NPC243870 OpenBabel06302216042D 27 29 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 -1.7321 1.0000 0.0000 C 0 0 1 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 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 2 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 -3.8301 -0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3301 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 -6.0622 0.5000 0.0000 C 0 0 1 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 -5.1962 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 O 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 -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 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 1 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 -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 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 16 1 0 0 0 0 3 4 2 0 0 0 0 5 4 1 6 0 0 0 5 12 1 0 0 0 0 5 14 1 0 0 0 0 5 6 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 10 11 1 0 0 0 0 10 15 1 6 0 0 0 11 12 1 0 0 0 0 12 13 1 6 0 0 0 12 14 1 0 0 0 0 17 16 1 1 0 0 0 17 18 1 0 0 0 0 17 24 1 0 0 0 0 18 19 1 0 0 0 0 18 27 1 6 0 0 0 19 20 1 0 0 0 0 19 26 1 1 0 0 0 20 21 1 0 0 0 0 20 25 1 6 0 0 0 21 22 1 1 0 0 0 21 24 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	388.21
Volume:	379.196
LogP:	0.716
LogD:	0.352
LogS:	-2.445
# Rotatable Bonds:	5
TPSA:	132.14
# H-Bond Aceptor:	8
# H-Bond Donor:	5
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.313
Synthetic Accessibility Score:	4.946
Fsp3:	0.895
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.901
MDCK Permeability:	0.00015508639626204967
Pgp-inhibitor:	0.014
Pgp-substrate:	0.996
Human Intestinal Absorption (HIA):	0.879
20% Bioavailability (F20%):	0.636
30% Bioavailability (F30%):	0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.085
Plasma Protein Binding (PPB):	67.73033905029297%
Volume Distribution (VD):	0.471
Pgp-substrate:	33.14980697631836%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.859
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.826
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.035
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.098
CYP3A4-inhibitor:	0.01
CYP3A4-substrate:	0.252

ADMET: Excretion

Clearance (CL):	2.178
Half-life (T1/2):	0.748

ADMET: Toxicity

hERG Blockers:	0.024
Human Hepatotoxicity (H-HT):	0.217
Drug-inuced Liver Injury (DILI):	0.05
AMES Toxicity:	0.678
Rat Oral Acute Toxicity:	0.175
Maximum Recommended Daily Dose:	0.925
Skin Sensitization:	0.218
Carcinogencity:	0.891
Eye Corrosion:	0.003
Eye Irritation:	0.022
Respiratory Toxicity:	0.93

Download Data

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

Natural Product: NPC243870

Natural Product ID:	NPC243870
*Common Name:**	RIUMIKAUMHZQMP-DBCWZAFBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RIUMIKAUMHZQMP-DBCWZAFBSA-N
Standard InCHI:	InChI=1S/C19H32O8/c1-10(25-16-15(24)14(23)13(22)12(9-20)26-16)5-6-19-17(2,3)7-11(21)8-18(19,4)27-19/h5-6,10-16,20-24H,7-9H2,1-4H3/b6-5+/t10-,11-,12+,13+,14-,15+,16+,18+,19-/m0/s1
SMILES:	C[C@@H](/C=C/[C@]12C(C)(C)C[C@@H](C[C@@]1(C)O2)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6325144
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001766] Fatty acyl glycosides [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

*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
NPO14524	Delisea pulchra	Species	Bonnemaisoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16933872]
NPO11394	Dichroa febrifuga	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19467876]
NPO11394	Dichroa febrifuga	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11394	Dichroa febrifuga	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5546	Calycophyllum spruceanum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11394	Dichroa febrifuga	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5051	Lobelia urens	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12937	Tithonia pedunculata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11394	Dichroa febrifuga	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5546	Calycophyllum spruceanum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21864	Agathis alba	Species	Araucariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14524	Delisea pulchra	Species	Bonnemaisoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3224	Chloridium virescens	Species	Chaetosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13240	Pinguipes brasilianus	Species	Pinguipedidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8396	Quercus macrocarpa	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9459	Piper hoffmannseggianum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14017	Bulbine abyssinica	Species	Asphodelaceae	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 NPC243870 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	247
0.1-0.2	1836
0.2-0.3	5134
0.3-0.4	10347
0.4-0.5	12944
0.5-0.6	7166
0.6-0.7	4205
0.7-0.8	790
0.8-0.85	26
0.85-0.9	0
0.9-0.95	1
0.95-1	1

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 NPC243870 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	208
0.1-0.2	2088
0.2-0.3	3830
0.3-0.4	2026
0.4-0.5	687
0.5-0.6	243
0.6-0.7	61
0.7-0.8	7
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