NPASS Compound

Structure

NPC41586 OpenBabel06302215292D 57 64 0 0 1 0 0 0 0 0999 V2000 -5.8389 -1.5992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0957 -0.9301 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1446 -1.2391 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4015 -0.5700 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.6094 0.4081 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5605 0.7172 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.3036 0.0480 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7684 1.6953 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0252 2.3644 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0742 2.0554 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8663 1.0773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3310 2.7246 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5390 3.7027 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4900 4.0117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2332 3.3426 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1842 3.6516 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7958 4.3718 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8447 4.0628 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6368 3.0847 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3800 2.4155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3142 2.7756 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0574 3.4448 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8495 4.4229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1016 4.7319 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3095 5.7101 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0084 3.1358 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2163 2.1576 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4732 1.4885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6811 0.5103 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6322 0.2013 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8890 -0.4678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3753 0.8705 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3264 0.5614 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5343 -0.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7911 -1.0858 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.8401 -0.7768 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0969 -1.4460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3048 -2.4241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2559 -2.7331 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3048 -3.0421 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6626 -3.6467 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6571 -3.5421 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8651 -2.5640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9990 -2.0640 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4058 -1.1504 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8090 0.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6180 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3090 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8968 -1.7601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3090 -0.9511 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 3.1674 1.8486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4504 -0.8790 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2425 -1.8572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2915 -2.1662 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9857 -2.5263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9367 -2.2173 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 57 1 6 0 0 0 4 5 1 0 0 0 0 4 53 1 6 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 1 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 15 1 0 0 0 0 10 11 1 6 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 17 1 6 0 0 0 14 15 1 0 0 0 0 15 16 1 1 0 0 0 18 17 1 1 0 0 0 18 19 1 0 0 0 0 18 24 1 0 0 0 0 19 20 1 6 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 26 1 6 0 0 0 23 24 1 0 0 0 0 24 25 1 1 0 0 0 27 26 1 6 0 0 0 27 28 1 0 0 0 0 27 52 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 36 1 0 0 0 0 30 31 1 6 0 0 0 30 32 1 0 0 0 0 32 33 1 1 0 0 0 32 52 1 0 0 0 0 33 34 1 0 0 0 0 35 34 1 1 0 0 0 35 36 1 0 0 0 0 35 44 1 0 0 0 0 36 37 1 6 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 39 44 1 0 0 0 0 39 40 1 6 0 0 0 39 41 1 0 0 0 0 41 42 1 0 0 0 0 41 46 1 6 0 0 0 42 43 1 0 0 0 0 43 44 1 0 0 0 0 44 45 1 6 0 0 0 46 51 1 0 0 0 0 46 47 2 0 0 0 0 47 48 1 0 0 0 0 48 49 2 0 0 0 0 48 50 1 0 0 0 0 50 51 1 0 0 0 0 53 54 1 0 0 0 0 54 55 2 0 0 0 0 54 56 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	806.45
Volume:	798.986
LogP:	4.497
LogD:	3.722
LogS:	-4.687
# Rotatable Bonds:	9
TPSA:	195.97
# H-Bond Aceptor:	14
# H-Bond Donor:	5
# Rings:	8
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.178
Synthetic Accessibility Score:	6.144
Fsp3:	0.884
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:	-5.574
MDCK Permeability:	0.00016300793504342437
Pgp-inhibitor:	0.002
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.0
30% Bioavailability (F30%):	0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.029
Plasma Protein Binding (PPB):	92.82987213134766%
Volume Distribution (VD):	0.372
Pgp-substrate:	8.829874992370605%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.813
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.541
CYP2C9-inhibitor:	0.065
CYP2C9-substrate:	0.022
CYP2D6-inhibitor:	0.028
CYP2D6-substrate:	0.107
CYP3A4-inhibitor:	0.27
CYP3A4-substrate:	0.784

ADMET: Excretion

Clearance (CL):	1.937
Half-life (T1/2):	0.11

ADMET: Toxicity

hERG Blockers:	0.893
Human Hepatotoxicity (H-HT):	0.282
Drug-inuced Liver Injury (DILI):	0.464
AMES Toxicity:	0.638
Rat Oral Acute Toxicity:	0.954
Maximum Recommended Daily Dose:	0.989
Skin Sensitization:	0.852
Carcinogencity:	0.307
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC41586

Natural Product ID:	NPC41586
*Common Name:**	HPMZBILYSWLILX-UMDUKNJSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HPMZBILYSWLILX-UMDUKNJSSA-N
Standard InCHI:	InChI=1S/C43H66O14/c1-21-38(48)33(54-24(4)44)19-37(51-21)57-40-23(3)53-36(18-32(40)46)56-39-22(2)52-35(17-31(39)45)55-27-9-12-41(5)26(16-27)7-8-30-29(41)10-13-42(6)28(11-14-43(30,42)49)25-15-34(47)50-20-25/h15,21-23,26-33,35-40,45-46,48-49H,7-14,16-20H2,1-6H3/t21-,22-,23-,26-,27+,28-,29+,30-,31+,32+,33+,35+,36+,37+,38-,39-,40-,41+,42-,43+/m1/s1
SMILES:	C[C@@H]1[C@H]([C@H](C[C@@H](O1)O[C@@H]1[C@@H](C)O[C@H](C[C@@H]1O)O[C@@H]1[C@@H](C)O[C@H](C[C@@H]1O)O[C@H]1CC[C@@]2(C)[C@H](CC[C@@H]3[C@@H]2CC[C@]2(C)[C@H](CC[C@]32O)C2=CC(=O)OC2)C1)OC(=O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5284512
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
NPO17774	Hemerocallis fulva	Species	Xanthorrhoeaceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1016/j.lwt.2014.11.023]
NPO4443	Digitalis purpurea	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9834166]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO13401	Phoenix canariensis	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22245	Digitalis lanata	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4443	Digitalis purpurea	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17774	Hemerocallis fulva	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19015	Begonia glabra	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19015	Begonia glabra	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22245	Digitalis lanata	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4443	Digitalis purpurea	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17774	Hemerocallis fulva	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13401	Phoenix canariensis	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4443	Digitalis purpurea	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19015	Begonia glabra	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17774	Hemerocallis fulva	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22245	Digitalis lanata	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18930	Rubus coreanus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22245	Digitalis lanata	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[TM-MC]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17774	Hemerocallis fulva	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19015	Begonia glabra	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13401	Phoenix canariensis	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18930	Rubus coreanus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12474	Cordyline fruticosa	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19441	Strychnos splendens	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17774	Hemerocallis fulva	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19175	Iguana iguana	Species	Iguanidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17635	Aria arguta	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22245	Digitalis lanata	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18180	Erysimum repandum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19093	Streptomyces aburaviensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO27168	Atropa belladona	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4443	Digitalis purpurea	Species	Plantaginaceae	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

Activity Type	# Activity
Others	4

Activity Type	# Activity
Others	4

Target ID	Target Type	Target Name	Activity Type	Activity Relation	Value	Unit	Reference
NPT897	Others	Monoclonal antibody (mAb)	IC50 ratio	=	3.9	n.a.	PMID[516846]
NPT897	Others	Monoclonal antibody (mAb)	IC50 ratio	=	25.0	n.a.	PMID[516846]
NPT897	Others	Monoclonal antibody (mAb)	IC50 ratio	=	20.0	n.a.	PMID[516846]
NPT897	Others	Monoclonal antibody (mAb)	IC50 ratio	=	48.0	n.a.	PMID[516846]

☑ 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 NPC41586 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC41586 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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