NPASS Compound

Structure

NPC105609 OpenBabel06302216152D 46 52 0 0 1 0 0 0 0 0999 V2000 -8.0118 1.9752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0118 0.9752 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1458 0.4752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1458 -0.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2798 -1.0248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4137 -0.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4137 0.4752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2798 0.9752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2798 1.9752 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1458 2.4752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5477 -1.0248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5477 -2.0248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8046 -2.6939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2113 -3.6074 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2058 -3.5029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8750 -4.2461 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4137 -2.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2798 -2.0248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1458 -2.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1458 -3.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0118 -4.0248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8778 -3.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8778 -2.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0118 -2.0248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.8289 -2.2158 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.4167 -3.0248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.8289 -3.8338 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6817 -0.5248 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8157 -1.0248 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9021 -0.6180 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2330 -1.3612 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3194 -1.7679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2149 -2.7624 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7330 -2.2272 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7111 -2.0193 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4240 -0.7734 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6942 0.3601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 0.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5352 1.6473 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4158 1.9563 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1590 1.2872 0.0000 C 0 0 2 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 2.1100 1.5962 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6237 2.9344 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2784 2.3164 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 18 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 11 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 11 12 2 0 0 0 0 11 28 1 0 0 0 0 12 17 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 27 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 29 28 1 1 0 0 0 29 30 1 0 0 0 0 29 35 1 0 0 0 0 30 31 1 0 0 0 0 30 37 1 6 0 0 0 31 32 1 0 0 0 0 31 34 1 0 0 0 0 31 36 1 6 0 0 0 32 33 1 0 0 0 0 34 35 1 0 0 0 0 38 37 1 1 0 0 0 38 39 1 0 0 0 0 38 43 1 0 0 0 0 39 40 1 0 0 0 0 39 46 1 6 0 0 0 40 41 1 0 0 0 0 40 45 1 6 0 0 0 41 42 1 0 0 0 0 41 44 1 1 0 0 0 42 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	644.17
Volume:	592.962
LogP:	1.245
LogD:	1.219
LogS:	-5.239
# Rotatable Bonds:	8
TPSA:	201.29
# H-Bond Aceptor:	15
# H-Bond Donor:	5
# Rings:	7
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.208
Synthetic Accessibility Score:	4.856
Fsp3:	0.452
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.064
MDCK Permeability:	1.9078774130321108e-05
Pgp-inhibitor:	0.024
Pgp-substrate:	0.996
Human Intestinal Absorption (HIA):	0.039
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.206

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.07
Plasma Protein Binding (PPB):	80.25794219970703%
Volume Distribution (VD):	0.571
Pgp-substrate:	3.8894574642181396%

ADMET: Metabolism

CYP1A2-inhibitor:	0.063
CYP1A2-substrate:	0.895
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.233
CYP2C9-inhibitor:	0.01
CYP2C9-substrate:	0.17
CYP2D6-inhibitor:	0.193
CYP2D6-substrate:	0.191
CYP3A4-inhibitor:	0.549
CYP3A4-substrate:	0.1

ADMET: Excretion

Clearance (CL):	3.09
Half-life (T1/2):	0.484

ADMET: Toxicity

hERG Blockers:	0.315
Human Hepatotoxicity (H-HT):	0.177
Drug-inuced Liver Injury (DILI):	0.945
AMES Toxicity:	0.817
Rat Oral Acute Toxicity:	0.018
Maximum Recommended Daily Dose:	0.037
Skin Sensitization:	0.077
Carcinogencity:	0.906
Eye Corrosion:	0.003
Eye Irritation:	0.02
Respiratory Toxicity:	0.03

Download Data

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

Natural Product: NPC105609

Natural Product ID:	NPC105609
*Common Name:**	HBUCXSOGVZJQHH-HMODPNIESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HBUCXSOGVZJQHH-HMODPNIESA-N
Standard InCHI:	InChI=1S/C31H32O15/c1-38-19-6-14-15(7-20(19)39-2)26(16-8-40-28(36)23(16)22(14)13-3-4-18-21(5-13)44-12-43-18)45-30-27(31(37,10-32)11-42-30)46-29-25(35)24(34)17(33)9-41-29/h3-7,17,24-25,27,29-30,32-35,37H,8-12H2,1-2H3/t17-,24+,25+,27-,29-,30-,31+/m0/s1
SMILES:	COc1cc2c(cc1OC)c(c1COC(=O)c1c2c1ccc2c(c1)OCO2)O[C@H]1[C@@H]([C@@](CO)(CO1)O)O[C@H]1[C@@H]([C@@H]([C@H](CO1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001511] Lignan glycosides

*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
NPO13775	Polygala amarella	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10395523]
NPO18042	Geranium nepalense	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23006989]
NPO23835	Swertia angustifolia	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO23659	Rostellularia procumbens	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO23835	Swertia angustifolia	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18042	Geranium nepalense	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23659	Rostellularia procumbens	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO13775	Polygala amarella	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24094	Pelargonium reniforme	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18042	Geranium nepalense	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23835	Swertia angustifolia	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23659	Rostellularia procumbens	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23835	Swertia angustifolia	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24448	Haplopappus ciliatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13775	Polygala amarella	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23835	Swertia angustifolia	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22467	Kippistia suaedifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23325	Doris verrucosa	Species	Dorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19177	Euphorbia franckiana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25670	Aspergillus foveolatus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23369	Hertia intermedia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23659	Rostellularia procumbens	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO20023	Uncaria gambier	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24094	Pelargonium reniforme	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO796	Diphasiastrum alpinum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18042	Geranium nepalense	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24192	Piptoporus australiensis	Species	Fomitopsidaceae	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 NPC105609 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	379
0.1-0.2	1525
0.2-0.3	3071
0.3-0.4	7132
0.4-0.5	10216
0.5-0.6	5803
0.6-0.7	6773
0.7-0.8	7160
0.8-0.85	561
0.85-0.9	52
0.9-0.95	11
0.95-1	14

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 NPC105609 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	323
0.1-0.2	852
0.2-0.3	1648
0.3-0.4	2597
0.4-0.5	2100
0.5-0.6	1042
0.6-0.7	445
0.7-0.8	124
0.8-0.85	19
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