NPASS Compound

Structure

NPC179717 OpenBabel06302215552D 65 72 0 0 1 0 0 0 0 0999 V2000 -1.3473 0.3610 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8542 -0.4932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8405 -0.4932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8542 -1.4795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9726 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8542 -1.4795 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7083 -1.9726 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5625 -1.4795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5625 -0.4932 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2708 -1.4795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7083 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7083 0.9863 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5625 1.4795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4166 0.9863 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2708 1.4795 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4166 1.9726 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2708 2.4658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1250 2.9589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9791 2.4658 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9791 1.4795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4723 0.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9654 1.4795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1250 0.9863 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1250 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2708 -0.4932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4166 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4166 -0.9863 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8333 2.9589 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6875 2.4658 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.5416 2.9589 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.3958 2.4658 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 9.3958 1.4795 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.5416 0.9863 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.5416 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6875 -0.4932 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3958 -0.4932 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6875 1.4795 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.2499 0.9863 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.1041 1.4795 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 12.0051 1.0783 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 12.6651 1.8113 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 12.1720 2.6654 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 12.5731 3.5664 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.5540 3.6695 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.2072 2.4604 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 13.6460 1.7082 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.2102 0.1135 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.2499 2.9589 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.2499 3.9452 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 11.1041 4.4384 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 11.1041 5.4247 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 10.2499 5.9178 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.3958 5.4247 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.5416 5.9178 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5416 6.9041 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3958 4.4384 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.2499 6.9041 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.9583 5.9178 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.9583 3.9452 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5416 3.9452 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8542 -0.4932 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8542 -2.4658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.9589 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7083 -2.9589 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 62 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 61 1 0 0 0 0 6 7 1 0 0 0 0 6 63 1 6 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 26 1 0 0 0 0 9 10 1 1 0 0 0 9 11 1 0 0 0 0 11 12 2 0 0 0 0 11 61 1 0 0 0 0 12 13 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 26 1 0 0 0 0 15 23 1 0 0 0 0 15 16 1 6 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 28 1 6 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 6 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 6 0 0 0 29 28 1 1 0 0 0 29 30 1 0 0 0 0 29 37 1 0 0 0 0 30 31 1 0 0 0 0 30 60 1 6 0 0 0 31 32 1 0 0 0 0 31 48 1 1 0 0 0 32 33 1 0 0 0 0 32 38 1 6 0 0 0 33 34 1 1 0 0 0 33 37 1 0 0 0 0 34 35 2 0 0 0 0 34 36 1 0 0 0 0 39 38 1 6 0 0 0 39 40 1 0 0 0 0 39 45 1 0 0 0 0 40 41 1 0 0 0 0 40 47 1 1 0 0 0 41 42 1 0 0 0 0 41 46 1 6 0 0 0 42 43 1 1 0 0 0 42 45 1 0 0 0 0 43 44 1 0 0 0 0 49 48 1 6 0 0 0 49 50 1 0 0 0 0 49 56 1 0 0 0 0 50 51 1 0 0 0 0 50 59 1 1 0 0 0 51 52 1 0 0 0 0 51 58 1 6 0 0 0 52 53 1 0 0 0 0 52 57 1 1 0 0 0 53 54 1 6 0 0 0 53 56 1 0 0 0 0 54 55 1 0 0 0 0 61 62 1 1 0 0 0 63 64 2 0 0 0 0 63 65 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	926.49
Volume:	903.331
LogP:	2.622
LogD:	1.883
LogS:	-3.261
# Rotatable Bonds:	10
TPSA:	291.82
# H-Bond Aceptor:	18
# H-Bond Donor:	10
# Rings:	8
# Heavy Atoms:	18

MedChem Properties

QED Drug-Likeness Score:	0.11
Synthetic Accessibility Score:	6.2
Fsp3:	0.915
Lipinski Rule-of-5:	Rejected
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:	-6.324
MDCK Permeability:	4.11955697927624e-05
Pgp-inhibitor:	0.719
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.961
20% Bioavailability (F20%):	0.533
30% Bioavailability (F30%):	0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.139
Plasma Protein Binding (PPB):	80.84134674072266%
Volume Distribution (VD):	0.291
Pgp-substrate:	13.47628402709961%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.098
CYP2C19-inhibitor:	0.001
CYP2C19-substrate:	0.074
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.03
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.059
CYP3A4-inhibitor:	0.031
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	0.599
Half-life (T1/2):	0.75

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.182
Drug-inuced Liver Injury (DILI):	0.038
AMES Toxicity:	0.108
Rat Oral Acute Toxicity:	0.149
Maximum Recommended Daily Dose:	0.568
Skin Sensitization:	0.026
Carcinogencity:	0.033
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.935

Download Data

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

Natural Product: NPC179717

Natural Product ID:	NPC179717
*Common Name:**	OIGBNBKGCWDSEQ-GNDIVNLPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OIGBNBKGCWDSEQ-GNDIVNLPSA-N
Standard InCHI:	InChI=1S/C47H74O18/c1-42(2)14-16-47(41(58)59)17-15-45(6)21(22(47)18-42)8-9-26-44(5)12-11-27(43(3,4)25(44)10-13-46(26,45)7)62-40-33(55)34(63-39-32(54)30(52)28(50)23(19-48)60-39)35(36(65-40)37(56)57)64-38-31(53)29(51)24(20-49)61-38/h8,22-36,38-40,48-55H,9-20H2,1-7H3,(H,56,57)(H,58,59)/t22-,23+,24-,25-,26+,27-,28+,29-,30-,31+,32+,33+,34+,35-,36-,38-,39-,40+,44-,45+,46+,47-/m0/s1
SMILES:	CC1(C)CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]34C)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O3)O[C@H]3[C@@H]([C@H]([C@H](CO)O3)O)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O)[C@@H]2C1)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11766338
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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
NPO7500	Rhodiola algida	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22964	Teucrium fruticans	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7500	Rhodiola algida	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10373	Senna pallida	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1620	Dictyopteris prolifera	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3067	Frullania nisquallensis	Species	Frullaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7500	Rhodiola algida	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10972	Lysimachia patungensis	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10387	Mandragora vernalis	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22964	Teucrium fruticans	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6196	Aralia armata	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8750	Lychnis githago	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11459	Parmelia formosana	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24581	Lobophytum catalai	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO773	Siphonaria maura	Species	Chytriomycetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25464	Uroleucon nigrotuberculatum	Species	Aphididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23790	Crinum glaucum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8494	Pteris longipes	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15071	Lissoclinum perforatum	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9554	Parthenium ligulatum	Species	Asteraceae	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 NPC179717 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	281
0.1-0.2	1830
0.2-0.3	5527
0.3-0.4	10884
0.4-0.5	10165
0.5-0.6	6714
0.6-0.7	4119
0.7-0.8	1957
0.8-0.85	498
0.85-0.9	474
0.9-0.95	172
0.95-1	76

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 NPC179717 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	244
0.1-0.2	2083
0.2-0.3	4048
0.3-0.4	1762
0.4-0.5	546
0.5-0.6	255
0.6-0.7	152
0.7-0.8	55
0.8-0.85	3
0.85-0.9	0
0.9-0.95	2
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