NPASS Compound

Structure

NPC143251 OpenBabel06302215132D 53 60 0 0 1 0 0 0 0 0999 V2000 -8.4759 1.3415 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4978 1.1336 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.1888 0.1826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2106 -0.0253 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.5415 0.7178 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1348 -0.1957 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.6348 -1.0618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1402 -0.0912 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.9323 0.8869 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9378 0.9915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5311 0.0779 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5800 -0.2311 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8369 0.4380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1142 0.1290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3221 -0.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2732 -1.1581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4811 -2.1363 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7379 -2.8054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2131 -2.4964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4210 -1.5183 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1642 -2.1874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3721 -1.2092 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1152 -1.8784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0663 -1.5694 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2742 -0.5912 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.6809 -1.5048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8094 -2.2385 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 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 3.4641 -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 2 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 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 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 2.5981 0.5000 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 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 2 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 -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 2.5981 -2.5000 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 -4.7984 1.3869 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8505 1.6689 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8287 1.8768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9016 -0.9764 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 2 52 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 53 1 1 0 0 0 5 50 1 0 0 0 0 5 6 1 0 0 0 0 5 51 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 25 1 0 0 0 0 9 10 1 1 0 0 0 9 50 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 25 1 0 0 0 0 12 13 1 0 0 0 0 12 22 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 20 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 28 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 27 1 0 0 0 0 25 26 1 0 0 0 0 29 28 1 1 0 0 0 29 30 1 0 0 0 0 29 36 1 0 0 0 0 30 31 1 0 0 0 0 30 49 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 37 1 0 0 0 0 33 34 1 0 0 0 0 33 36 1 0 0 0 0 34 35 1 0 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 38 44 1 0 0 0 0 39 40 1 0 0 0 0 39 47 1 0 0 0 0 40 41 1 0 0 0 0 40 46 1 0 0 0 0 41 42 1 0 0 0 0 41 45 1 0 0 0 0 42 43 1 0 0 0 0 42 44 1 0 0 0 0 51 52 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	754.41
Volume:	735.075
LogP:	2.237
LogD:	1.899
LogS:	-3.405
# Rotatable Bonds:	5
TPSA:	217.22
# H-Bond Aceptor:	14
# H-Bond Donor:	8
# Rings:	8
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.178
Synthetic Accessibility Score:	6.53
Fsp3:	0.949
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:	-6.097
MDCK Permeability:	0.00017302006017416716
Pgp-inhibitor:	0.033
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.903
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.053
Plasma Protein Binding (PPB):	60.16564178466797%
Volume Distribution (VD):	0.252
Pgp-substrate:	17.662052154541016%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.3
CYP2C19-inhibitor:	0.005
CYP2C19-substrate:	0.181
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.007
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.07
CYP3A4-inhibitor:	0.013
CYP3A4-substrate:	0.032

ADMET: Excretion

Clearance (CL):	0.999
Half-life (T1/2):	0.727

ADMET: Toxicity

hERG Blockers:	0.601
Human Hepatotoxicity (H-HT):	0.273
Drug-inuced Liver Injury (DILI):	0.04
AMES Toxicity:	0.139
Rat Oral Acute Toxicity:	0.352
Maximum Recommended Daily Dose:	0.723
Skin Sensitization:	0.684
Carcinogencity:	0.114
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.985

Download Data

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

Natural Product: NPC143251

Natural Product ID:	NPC143251
*Common Name:**	GLANCWZQIQVJID-FEDSMYBDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GLANCWZQIQVJID-FEDSMYBDSA-N
Standard InCHI:	InChI=1S/C39H62O14/c1-16-10-27(42)39(48-15-16)17(2)28-24(53-39)12-23-21-7-6-19-11-20(8-9-37(19,4)22(21)13-26(41)38(23,28)5)50-36-33(47)31(45)34(25(14-40)51-36)52-35-32(46)30(44)29(43)18(3)49-35/h6,16-18,20-36,40-47H,7-15H2,1-5H3/t16-,17-,18-,20-,21+,22-,23-,24-,25+,26+,27-,28-,29-,30+,31+,32+,33+,34+,35-,36+,37-,38+,39-/m0/s1
SMILES:	C[C@H]1C[C@@H]([C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC=C6C[C@H](CC[C@]6(C)[C@H]5C[C@H]([C@]34C)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O[C@H]3[C@@H]([C@@H]([C@H]([C@H](C)O3)O)O)O)O)O)O2)OC1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides [CHEMONTID:0002364] Steroidal 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
NPO12418	Myroxylon peruiferum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/0031-9422(79)80020-5]
NPO12418	Myroxylon peruiferum	Species	Fabaceae	Eukaryota	n.a.	Brazilian	n.a.	PMID[10328294]
NPO7006	Garcinia subelliptica	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15568764]
NPO7006	Garcinia subelliptica	Species	Clusiaceae	Eukaryota	pericarp	n.a.	n.a.	PMID[16038565]
NPO12653	Diacarnus levii	Species	Podospongiidae	Eukaryota	n.a.	at a depth of -10 M off the coast of Papua New Guinea	1998-JUN	PMID[17253866]
NPO7006	Garcinia subelliptica	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18166016]
NPO7006	Garcinia subelliptica	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20232858]
NPO7006	Garcinia subelliptica	Species	Clusiaceae	Eukaryota	n.a.	xylem	n.a.	Database[Article]
NPO2289	Vicia hirsuta	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3671	Rhodiola coccinea	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2289	Vicia hirsuta	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3671	Rhodiola coccinea	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7006	Garcinia subelliptica	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12418	Myroxylon peruiferum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7006	Garcinia subelliptica	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5311	Isertia haenkeana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3671	Rhodiola coccinea	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12047	Solanum unguiculatum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4923	Ononis hircina	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12762	Elattostachys apetala	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2289	Vicia hirsuta	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10102	Pithecellobium albicans	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5173	Antidesma pentandrum	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7648	Geigeria plumosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1455	Aspergillus caelatus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12653	Diacarnus levii	Species	Podospongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11397	Cladophora rupestris	Species	Cladophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12526	Veronica turrilliana	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9561	Preussia australis	Species	Sporormiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7323	Lindera pipericarpa	Species	Tineidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13096	Lecidea kochiana	Species	Lecideaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10553	Heterophyllaea pustulata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11674	Viburnum lantanoides	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9254	Scutellaria racemosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2576	Eusideroxylon zwageri	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO396	Ventilago goughii	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14776	Petrosia weinbergi	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26737	Solanum mauritianum	Species	Solanaceae	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 NPC143251 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	307
0.1-0.2	2098
0.2-0.3	6917
0.3-0.4	13978
0.4-0.5	8494
0.5-0.6	5349
0.6-0.7	3123
0.7-0.8	1339
0.8-0.85	585
0.85-0.9	311
0.9-0.95	119
0.95-1	77

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 NPC143251 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	245
0.1-0.2	2265
0.2-0.3	4363
0.3-0.4	1495
0.4-0.5	408
0.5-0.6	243
0.6-0.7	99
0.7-0.8	18
0.8-0.85	5
0.85-0.9	9
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