NPASS Compound

Structure

NPC217901 OpenBabel07101719512D 38 43 0 0 1 0 0 0 0 0999 V2000 -1.8369 8.0510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3586 1.7642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2942 0.3066 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6881 -0.7912 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0262 0.7639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1452 7.0997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4755 6.3571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7837 5.4058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1140 4.6632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4223 3.7119 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7526 2.9692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0609 2.0179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3911 1.2753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9280 -0.5124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7056 0.7380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6381 -3.6289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4056 0.7653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7370 -1.1002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1678 0.2510 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1190 -1.1002 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6757 -1.2618 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4280 -2.0513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5491 -0.7748 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8099 -2.2527 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8771 -2.8859 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5641 0.2251 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1189 -2.9755 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6994 0.3240 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4280 -2.0513 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1827 -0.7489 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4508 -4.6112 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0158 -2.8603 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3900 -3.7443 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6591 -2.6906 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0904 -3.2126 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3888 -0.0208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0823 -0.1577 0.0000 O 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 1 6 1 0 0 0 0 2 17 2 0 0 0 0 3 17 1 0 0 0 0 4 18 1 0 0 0 0 5 19 1 0 0 0 0 6 7 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 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 14 18 2 0 0 0 0 14 20 1 0 0 0 0 15 19 1 0 0 0 0 15 26 1 0 0 0 0 16 31 1 0 0 0 0 18 22 1 0 0 0 0 19 30 1 1 0 0 0 20 29 1 6 0 0 0 20 30 1 0 0 0 0 21 23 1 0 0 0 0 21 24 1 0 0 0 0 21 30 1 1 0 0 0 22 29 1 0 0 0 0 22 32 2 0 0 0 0 23 26 1 6 0 0 0 23 36 1 0 0 0 0 24 27 1 1 0 0 0 24 35 1 0 0 0 0 25 27 1 6 0 0 0 25 29 1 0 0 0 0 25 33 1 0 0 0 0 26 17 1 1 0 0 0 26 37 1 0 0 0 0 27 16 1 6 0 0 0 27 35 1 0 0 0 0 28 13 1 6 0 0 0 28 36 1 0 0 0 0 28 37 1 0 0 0 0 28 38 1 0 0 0 0 29 34 1 6 0 0 0 30 38 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	532.3
Volume:	538.51
LogP:	4.643
LogD:	3.781
LogS:	-4.206
# Rotatable Bonds:	10
TPSA:	117.98
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	6
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.223
Synthetic Accessibility Score:	6.456
Fsp3:	0.833
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:	-4.807
MDCK Permeability:	3.594782901927829e-05
Pgp-inhibitor:	0.338
Pgp-substrate:	0.281
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.84
30% Bioavailability (F30%):	0.077

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.646
Plasma Protein Binding (PPB):	92.9333267211914%
Volume Distribution (VD):	1.806
Pgp-substrate:	3.7227630615234375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.985
CYP2C19-inhibitor:	0.09
CYP2C19-substrate:	0.829
CYP2C9-inhibitor:	0.452
CYP2C9-substrate:	0.022
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.123
CYP3A4-inhibitor:	0.788
CYP3A4-substrate:	0.3

ADMET: Excretion

Clearance (CL):	10.348
Half-life (T1/2):	0.265

ADMET: Toxicity

hERG Blockers:	0.352
Human Hepatotoxicity (H-HT):	0.917
Drug-inuced Liver Injury (DILI):	0.204
AMES Toxicity:	0.297
Rat Oral Acute Toxicity:	0.855
Maximum Recommended Daily Dose:	0.95
Skin Sensitization:	0.812
Carcinogencity:	0.749
Eye Corrosion:	0.004
Eye Irritation:	0.02
Respiratory Toxicity:	0.986

Download Data

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

Natural Product: NPC217901

Natural Product ID:	NPC217901
*Common Name:**	Simplexin
IUPAC Name:	n.a.
Synonyms:	Simplexin
Standard InCHIKey:	JAQJQYMDHBSCKO-JDVVNZBPSA-N
Standard InCHI:	InChI=1S/C30H44O8/c1-6-7-8-9-10-11-12-13-28-36-23-21-24-27(16-31,35-24)25(33)29(34)20(14-18(4)22(29)32)30(21,38-28)19(5)15-26(23,37-28)17(2)3/h14,19-21,23-25,31,33-34H,2,6-13,15-16H2,1,3-5H3/t19-,20-,21-,23-,24+,25-,26-,27+,28-,29-,30+/m1/s1
SMILES:	CCCCCCCCC[C@@]12O[C@H]3[C@@](O1)(C[C@H]([C@@]1(O2)[C@H]3[C@@H]2O[C@@]2([C@H]([C@]2([C@H]1C=C(C2=O)C)O)O)CO)C)C(=C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL444290
PubChem CID:	119045
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003494] Rhamnofolane and daphnane diterpenoids

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32223193]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31860304]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31150241]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27228307]
NPO7067	Stellera chamaejasme	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26562066]
NPO7067	Stellera chamaejasme	Species	Thymelaeaceae	Eukaryota	roots	n.a.	n.a.	PMID[24931277]
NPO7067	Stellera chamaejasme	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23611151]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[23558238]
NPO7067	Stellera chamaejasme	Species	Thymelaeaceae	Eukaryota	n.a.	callus	n.a.	PMID[22368856]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	flower	n.a.	PMID[21916433]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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
EC50	1
ED50	1
IC50	11
Others	14

Activity Type	# Activity
Cell Line	12
NON-MOLECULAR	1
Organism	13
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT25	Cell Line	MT4	Homo sapiens	CC50	>=	18800.0	nM	PMID[452593]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	47.0	nM	PMID[452593]
NPT2	Others	Unspecified		Ratio CC50/EC50	>=	400.0	n.a.	PMID[452593]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	0.3	nM	PMID[452592]
NPT111	Cell Line	K562	Homo sapiens	IC50	>	50000.0	nM	PMID[452591]
NPT466	Cell Line	U-937	Homo sapiens	IC50	>	50000.0	nM	PMID[452591]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	50000.0	nM	PMID[452591]
NPT453	Cell Line	HT-1080	Homo sapiens	IC50	<	100.0	nM	PMID[452591]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	26960.0	nM	PMID[452591]
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	>	50000.0	nM	PMID[452591]

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☑ 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 NPC217901 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	274
0.1-0.2	1644
0.2-0.3	4862
0.3-0.4	7687
0.4-0.5	12827
0.5-0.6	8620
0.6-0.7	5410
0.7-0.8	1257
0.8-0.85	62
0.85-0.9	20
0.9-0.95	18
0.95-1	16

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Similarity Score	Similarity Level	Natural Product ID
0.9914	High Similarity	NPC475273
0.9914	High Similarity	NPC168849
0.9746	High Similarity	NPC162495
0.9664	High Similarity	NPC251564
0.9664	High Similarity	NPC477189

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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 NPC217901 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	243
0.1-0.2	1872
0.2-0.3	3935
0.3-0.4	2038
0.4-0.5	616
0.5-0.6	270
0.6-0.7	152
0.7-0.8	24
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7857	Intermediate Similarity	NPD6054	Approved
0.7734	Intermediate Similarity	NPD6370	Approved
0.7717	Intermediate Similarity	NPD6059	Approved
0.7656	Intermediate Similarity	NPD6015	Approved
0.7656	Intermediate Similarity	NPD6016	Approved

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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