NPASS Compound

Structure

NPC218798 OpenBabel06302215422D 30 32 0 0 1 0 0 0 0 0999 V2000 6.9282 -1.0000 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 5.1962 -1.0000 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 0 0 0 0 0 0 0 0 0 0 6.9282 -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 3.4641 -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 1.7321 -0.0000 0.0000 O 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 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 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 -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 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 2 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 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 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 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 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 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 7 1 0 0 0 0 5 6 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 27 1 0 0 0 0 12 13 1 0 0 0 0 12 30 1 1 0 0 0 13 14 1 0 0 0 0 13 29 1 6 0 0 0 14 15 1 0 0 0 0 14 28 1 1 0 0 0 15 16 1 6 0 0 0 15 27 1 0 0 0 0 16 17 1 0 0 0 0 18 17 1 6 0 0 0 18 19 1 0 0 0 0 18 23 1 0 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 0 0 0 0 21 24 1 6 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	428.17
Volume:	406.163
LogP:	-0.406
LogD:	-0.252
LogS:	-1.54
# Rotatable Bonds:	7
TPSA:	158.3
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.286
Synthetic Accessibility Score:	4.291
Fsp3:	0.6
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.39
MDCK Permeability:	1.6812828107504174e-05
Pgp-inhibitor:	0.127
Pgp-substrate:	0.812
Human Intestinal Absorption (HIA):	0.925
20% Bioavailability (F20%):	0.795
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.169
Plasma Protein Binding (PPB):	57.140777587890625%
Volume Distribution (VD):	0.396
Pgp-substrate:	25.004344940185547%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.054
CYP2C19-inhibitor:	0.031
CYP2C19-substrate:	0.081
CYP2C9-inhibitor:	0.004
CYP2C9-substrate:	0.042
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.104
CYP3A4-inhibitor:	0.009
CYP3A4-substrate:	0.021

ADMET: Excretion

Clearance (CL):	1.071
Half-life (T1/2):	0.746

ADMET: Toxicity

hERG Blockers:	0.465
Human Hepatotoxicity (H-HT):	0.03
Drug-inuced Liver Injury (DILI):	0.044
AMES Toxicity:	0.419
Rat Oral Acute Toxicity:	0.117
Maximum Recommended Daily Dose:	0.001
Skin Sensitization:	0.924
Carcinogencity:	0.251
Eye Corrosion:	0.004
Eye Irritation:	0.527
Respiratory Toxicity:	0.028

Download Data

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

Natural Product: NPC218798

Natural Product ID:	NPC218798
*Common Name:**	RINHYCZCUGCZAJ-IPXOVKFZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RINHYCZCUGCZAJ-IPXOVKFZSA-N
Standard InCHI:	InChI=1S/C20H28O10/c21-12-9-28-19(17(25)14(12)22)29-10-13-15(23)16(24)18(26)20(30-13)27-8-4-7-11-5-2-1-3-6-11/h1-7,12-26H,8-10H2/b7-4+/t12-,13+,14-,15+,16-,17+,18+,19-,20+/m0/s1
SMILES:	c1ccc(cc1)/C=C/CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@H](CO2)O)O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	9823887
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
NPO29535	Samadera indica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1039/C39770000295]
NPO29535	Samadera indica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11429258]
NPO29535	Samadera indica	Species	Simaroubaceae	Eukaryota	n.a.	stem	n.a.	PMID[8945767]
NPO574	Rumex nepalensis	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1279	Fritillaria cirrhosa	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22230	Rhodiola crenulata	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO574	Rumex nepalensis	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO292	Aglaia elliptica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1279	Fritillaria cirrhosa	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22230	Rhodiola crenulata	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO574	Rumex nepalensis	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22230	Rhodiola crenulata	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22230	Rhodiola crenulata	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1279	Fritillaria cirrhosa	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17074	Trichosurus vulpecula	Species	Phalangeridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6134	Vitis betulifolia	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1906	Catananche caerulea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1279	Fritillaria cirrhosa	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5424	Phebalium whitei	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22230	Rhodiola crenulata	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3758	Stiretrus anchorago	Species	Pentatomidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5266	Strychnos ligustrina	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7912	Salvia urolepis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO574	Rumex nepalensis	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO718	Corydalis calliantha	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5984	Rosa agrestis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4566	Solanderia secunda	Species	Hydractiniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4295	Agarum cribrosum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2570	Cirsium wallichii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2426	Corynascus setosus	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4819	Dryocosmus kuriphilus	Species	Cynipidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7469	Veronica kellereri	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO292	Aglaia elliptica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29535	Samadera indica	Species	Simaroubaceae	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 NPC218798 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	240
0.1-0.2	1082
0.2-0.3	2982
0.3-0.4	9143
0.4-0.5	15775
0.5-0.6	10916
0.6-0.7	2191
0.7-0.8	339
0.8-0.85	13
0.85-0.9	10
0.9-0.95	5
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 NPC218798 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	202
0.1-0.2	729
0.2-0.3	1563
0.3-0.4	3500
0.4-0.5	2248
0.5-0.6	851
0.6-0.7	53
0.7-0.8	4
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