NPASS Compound

Structure

NPC121036 OpenBabel07101718232D 37 39 0 0 1 0 0 0 0 0999 V2000 3.0640 -5.0653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4638 -5.7281 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9252 -4.3152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2101 -4.5571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3365 3.5591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7203 2.5174 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2140 1.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8613 0.8815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6253 -1.5206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6899 -4.0109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2987 -3.2175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8582 -2.9509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1262 1.8398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0692 -2.5767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5174 0.9195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5741 -1.8955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9160 -2.2936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1619 -1.0865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0726 -4.9347 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9978 -3.9411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7276 2.6388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8832 0.6736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1619 -1.0865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9160 -2.2936 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5741 -0.2775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6231 -0.5865 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9160 0.1206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2089 -0.5865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3536 -0.8536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6231 -1.5865 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2089 -1.5865 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9160 0.1206 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.6619 -0.2205 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2987 1.0445 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7150 -0.2038 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3450 -0.9841 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 19 1 0 0 0 0 2 19 1 0 0 0 0 3 20 1 0 0 0 0 4 20 1 0 0 0 0 5 21 1 0 0 0 0 6 21 1 0 0 0 0 7 22 1 0 0 0 0 8 22 1 0 0 0 0 10 11 1 0 0 0 0 10 19 2 0 0 0 0 11 24 1 0 0 0 0 12 14 1 0 0 0 0 12 20 2 0 0 0 0 13 15 1 0 0 0 0 13 21 2 0 0 0 0 16 23 1 0 0 0 0 16 30 1 0 0 0 0 17 24 1 0 0 0 0 17 31 1 0 0 0 0 18 23 1 0 0 0 0 18 33 2 0 0 0 0 22 25 1 0 0 0 0 23 25 2 0 0 0 0 24 30 1 1 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 26 30 1 1 0 0 0 27 32 1 0 0 0 0 27 34 2 0 0 0 0 28 31 1 0 0 0 0 28 32 1 0 0 0 0 28 35 2 0 0 0 0 29 31 1 0 0 0 0 29 36 2 0 0 0 0 29 37 1 0 0 0 0 30 9 1 1 0 0 0 31 14 1 6 0 0 0 32 15 1 6 0 0 0 32 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	508.32
Volume:	559.218
LogP:	6.807
LogD:	4.937
LogS:	-5.21
# Rotatable Bonds:	8
TPSA:	77.51
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.158
Synthetic Accessibility Score:	6.064
Fsp3:	0.625
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.814
MDCK Permeability:	1.8663260561879724e-05
Pgp-inhibitor:	0.263
Pgp-substrate:	0.973
Human Intestinal Absorption (HIA):	0.029
20% Bioavailability (F20%):	0.876
30% Bioavailability (F30%):	0.887

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.954
Plasma Protein Binding (PPB):	77.99561309814453%
Volume Distribution (VD):	3.2
Pgp-substrate:	8.638736724853516%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.282
CYP2C19-inhibitor:	0.31
CYP2C19-substrate:	0.787
CYP2C9-inhibitor:	0.105
CYP2C9-substrate:	0.019
CYP2D6-inhibitor:	0.124
CYP2D6-substrate:	0.007
CYP3A4-inhibitor:	0.881
CYP3A4-substrate:	0.89

ADMET: Excretion

Clearance (CL):	13.774
Half-life (T1/2):	0.009

ADMET: Toxicity

hERG Blockers:	0.003
Human Hepatotoxicity (H-HT):	0.955
Drug-inuced Liver Injury (DILI):	0.905
AMES Toxicity:	0.407
Rat Oral Acute Toxicity:	0.273
Maximum Recommended Daily Dose:	0.083
Skin Sensitization:	0.848
Carcinogencity:	0.862
Eye Corrosion:	0.027
Eye Irritation:	0.05
Respiratory Toxicity:	0.963

Download Data

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

Natural Product: NPC121036

Natural Product ID:	NPC121036
*Common Name:**	AEVDRGYEHJFKLT-UXSGCWECSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	AEVDRGYEHJFKLT-UXSGCWECSA-N
Standard InCHI:	InChI=1S/C32H44O5/c1-19(2)10-11-24-17-31(14-12-20(3)4)28(35)32(37-29(31)36,15-13-21(5)6)27(34)26-25(22(7)8)23(18-33)16-30(24,26)9/h10,12-13,18,22,24,26H,11,14-17H2,1-9H3/t24-,26+,30+,31+,32-/m0/s1
SMILES:	CC(=CC[C@H]1C[C@]2(CC=C(C)C)C(=O)[C@](CC=C(C)C)(C(=O)[C@H]3C(=C(C[C@]13C)C=O)C(C)C)OC2=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3581582
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones

*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
NPO19915	Hypericum henryi	Species	Hypericaceae	Eukaryota	aerial parts	Yunnan, China	n.a.	PMID[25871261]
NPO19915	Hypericum henryi	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19915	Hypericum henryi	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

Showing 1 to 3 of 3 entries

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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
IC50	5
Others	1

Activity Type	# Activity
Cell Line	5
Individual Protein	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT204	Individual Protein	Acetylcholinesterase	Homo sapiens	Inhibition	=	-100.0	%	PMID[501649]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	40000.0	nM	PMID[501649]
NPT659	Cell Line	SMMC-7721	Homo sapiens	IC50	>	40000.0	nM	PMID[501649]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	40000.0	nM	PMID[501649]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	40000.0	nM	PMID[501649]
NPT660	Cell Line	SW480	Homo sapiens	IC50	>	40000.0	nM	PMID[501649]

Showing 1 to 6 of 6 entries

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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 NPC121036 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	252
0.1-0.2	1951
0.2-0.3	8461
0.3-0.4	15126
0.4-0.5	8825
0.5-0.6	6346
0.6-0.7	1650
0.7-0.8	77
0.8-0.85	5
0.85-0.9	0
0.9-0.95	2
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC472674
0.8876	High Similarity	NPC472686
0.8876	High Similarity	NPC290329
0.7822	Intermediate Similarity	NPC54843
0.77	Intermediate Similarity	NPC31021

Showing 1 to 5 of 200 entries

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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 NPC121036 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	234
0.1-0.2	2604
0.2-0.3	4034
0.3-0.4	1590
0.4-0.5	407
0.5-0.6	219
0.6-0.7	62
0.7-0.8	0
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
0.7273	Intermediate Similarity	NPD6672	Approved
0.7273	Intermediate Similarity	NPD5737	Approved
0.7143	Intermediate Similarity	NPD5696	Approved
0.7087	Intermediate Similarity	NPD5282	Discontinued
0.703	Intermediate Similarity	NPD6673	Approved

Showing 1 to 5 of 200 entries

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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