NPASS Compound

Structure

NPC239860 OpenBabel06302215382D 39 44 0 0 1 0 0 0 0 0999 V2000 2.4062 3.3280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7100 2.3943 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.6705 2.1906 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.9743 1.2570 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.3176 0.5270 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.3572 0.7308 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0534 1.6644 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7005 0.0008 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8500 0.4914 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8497 1.4737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0006 1.9646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8506 1.4732 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8509 2.4770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8503 0.4909 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7009 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5518 0.4904 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5520 1.4727 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.7014 1.9641 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.7017 2.9458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5526 3.4368 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4032 2.9454 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4035 3.9491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2541 3.4363 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2544 4.4176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6538 5.3139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9247 5.9708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0275 6.9467 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0747 5.4804 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2785 4.5204 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1035 2.9449 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.1032 1.9632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4029 1.9636 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4026 0.9636 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9698 3.4444 0.0000 O 0 0 0 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 3.6214 -0.4066 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9347 1.0532 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5914 1.7832 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3271 2.9205 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 7 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 3 39 1 6 0 0 0 4 5 1 0 0 0 0 4 37 1 0 0 0 0 5 6 1 0 0 0 0 5 36 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 6 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 35 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 18 1 0 0 0 0 12 13 1 6 0 0 0 12 14 1 0 0 0 0 14 15 1 1 0 0 0 14 35 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 32 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 20 21 1 0 0 0 0 21 32 1 0 0 0 0 21 22 1 6 0 0 0 21 23 1 0 0 0 0 23 24 1 6 0 0 0 23 30 1 0 0 0 0 24 29 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 30 31 1 0 0 0 0 30 34 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 6 0 0 0 37 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	550.31
Volume:	549.936
LogP:	2.319
LogD:	2.773
LogS:	-3.527
# Rotatable Bonds:	4
TPSA:	141.98
# H-Bond Aceptor:	9
# H-Bond Donor:	5
# Rings:	6
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.358
Synthetic Accessibility Score:	5.389
Fsp3:	0.867
Lipinski Rule-of-5:	Accepted
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:	-5.679
MDCK Permeability:	2.676348594832234e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.59
Human Intestinal Absorption (HIA):	0.933
20% Bioavailability (F20%):	0.333
30% Bioavailability (F30%):	0.96

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.1
Plasma Protein Binding (PPB):	94.1916732788086%
Volume Distribution (VD):	0.975
Pgp-substrate:	6.231554985046387%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.693
CYP2C19-inhibitor:	0.004
CYP2C19-substrate:	0.618
CYP2C9-inhibitor:	0.03
CYP2C9-substrate:	0.089
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.145
CYP3A4-inhibitor:	0.113
CYP3A4-substrate:	0.341

ADMET: Excretion

Clearance (CL):	7.222
Half-life (T1/2):	0.144

ADMET: Toxicity

hERG Blockers:	0.335
Human Hepatotoxicity (H-HT):	0.299
Drug-inuced Liver Injury (DILI):	0.035
AMES Toxicity:	0.036
Rat Oral Acute Toxicity:	0.932
Maximum Recommended Daily Dose:	0.931
Skin Sensitization:	0.125
Carcinogencity:	0.063
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.96

Download Data

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

Natural Product: NPC239860

Natural Product ID:	NPC239860
*Common Name:**	CPFNIKYEDJFRAT-SWTABQFUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CPFNIKYEDJFRAT-SWTABQFUSA-N
Standard InCHI:	InChI=1S/C30H46O9/c1-15-24(33)26(36-4)25(34)27(38-15)39-18-7-9-28(2)17(12-18)5-6-20-19(28)8-10-29(3)23(16-11-22(32)37-14-16)21(31)13-30(20,29)35/h11,15,17-21,23-27,31,33-35H,5-10,12-14H2,1-4H3/t15?,17-,18-,19?,20?,21?,23+,24+,25?,26?,27+,28+,29-,30+/m1/s1
SMILES:	CC1[C@@H](C(C([C@@H](O1)O[C@@H]1CC[C@@]2(C)[C@H](CCC3C2CC[C@]2(C)[C@@H](C4=CC(=O)OC4)C(C[C@]32O)O)C1)O)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11967808
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001555] Cardenolides and derivatives [CHEMONTID:0001559] Cardenolide glycosides and derivatives

*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
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	leaves	Niigata City, Niigata Province, Japan	2000-Nov	PMID[15730243]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	leaves	n.a.	n.a.	PMID[16933868]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17253842]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	stems and twigs	Niigata City, Niigata Province, Japan	2001-NOV	PMID[17595134]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	stems and twigs	n.a.	n.a.	PMID[17595134]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29693393]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	Leaves; Stems	n.a.	n.a.	PMID[9214727]
NPO4443	Digitalis purpurea	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9834166]
NPO9481	Strophanthus divaricatus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31396	Nerium indicum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11771	Strophanthus kombe	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4443	Digitalis purpurea	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9481	Strophanthus divaricatus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4443	Digitalis purpurea	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11771	Strophanthus kombe	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4443	Digitalis purpurea	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11771	Strophanthus kombe	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9481	Strophanthus divaricatus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31396	Nerium indicum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4443	Digitalis purpurea	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4443	Digitalis purpurea	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11771	Strophanthus kombe	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10021	Nerium oleander	Species	Apocynaceae	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 NPC239860 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	251
0.1-0.2	1705
0.2-0.3	4954
0.3-0.4	10756
0.4-0.5	10382
0.5-0.6	6600
0.6-0.7	4694
0.7-0.8	2615
0.8-0.85	450
0.85-0.9	151
0.9-0.95	67
0.95-1	72

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 NPC239860 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	217
0.1-0.2	1813
0.2-0.3	4020
0.3-0.4	2061
0.4-0.5	558
0.5-0.6	291
0.6-0.7	151
0.7-0.8	25
0.8-0.85	1
0.85-0.9	1
0.9-0.95	8
0.95-1	4

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