NPASS Compound

Structure

NPC208120 OpenBabel07101718282D 26 29 0 0 1 0 0 0 0 0999 V2000 5.1369 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2321 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7321 0.0000 0.0000 C 0 0 0 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 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1369 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 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 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 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 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 2.5981 0.5000 0.0000 C 0 0 0 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 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 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 1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 19 1 0 0 0 0 3 19 1 0 0 0 0 5 6 1 0 0 0 0 5 10 1 0 0 0 0 6 20 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 8 1 1 6 0 0 0 8 26 1 0 0 0 0 9 13 2 0 0 0 0 9 17 1 0 0 0 0 10 19 1 0 0 0 0 10 21 2 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 11 14 1 0 0 0 0 12 15 1 0 0 0 0 12 20 1 0 0 0 0 13 22 1 0 0 0 0 14 16 1 0 0 0 0 14 23 2 0 0 0 0 15 17 2 0 0 0 0 15 24 1 0 0 0 0 16 18 2 0 0 0 0 16 25 1 0 0 0 0 17 26 1 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 20 4 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	434.14
Volume:	439.261
LogP:	4.026
LogD:	3.266
LogS:	-4.247
# Rotatable Bonds:	5
TPSA:	116.45
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.357
Synthetic Accessibility Score:	3.573
Fsp3:	0.16
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.314
MDCK Permeability:	6.943348125787452e-06
Pgp-inhibitor:	0.01
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.029
20% Bioavailability (F20%):	0.997
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.033
Plasma Protein Binding (PPB):	98.66993713378906%
Volume Distribution (VD):	0.629
Pgp-substrate:	1.2788970470428467%

ADMET: Metabolism

CYP1A2-inhibitor:	0.849
CYP1A2-substrate:	0.397
CYP2C19-inhibitor:	0.35
CYP2C19-substrate:	0.058
CYP2C9-inhibitor:	0.825
CYP2C9-substrate:	0.963
CYP2D6-inhibitor:	0.706
CYP2D6-substrate:	0.516
CYP3A4-inhibitor:	0.879
CYP3A4-substrate:	0.175

ADMET: Excretion

Clearance (CL):	10.597
Half-life (T1/2):	0.779

ADMET: Toxicity

hERG Blockers:	0.19
Human Hepatotoxicity (H-HT):	0.047
Drug-inuced Liver Injury (DILI):	0.32
AMES Toxicity:	0.133
Rat Oral Acute Toxicity:	0.142
Maximum Recommended Daily Dose:	0.871
Skin Sensitization:	0.948
Carcinogencity:	0.271
Eye Corrosion:	0.003
Eye Irritation:	0.799
Respiratory Toxicity:	0.179

Download Data

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

Natural Product: NPC208120

Natural Product ID:	NPC208120
*Common Name:**	Teuvincenone A
IUPAC Name:	(9S,11bR)-5,7,11-trihydroxy-4,4,9,11b-tetramethyl-1,2,8,9-tetrahydronaphtho[2,1-f][1]benzofuran-3,6-dione
Synonyms:
Standard InCHIKey:	GWRKJHSVPDIUPU-FFVOIRBGSA-N
Standard InCHI:	InChI=1S/C20H22O6/c1-8-7-9-13(22)11-12(15(24)17(9)26-8)20(4)6-5-10(21)19(2,3)18(20)16(25)14(11)23/h8,22,24-25H,5-7H2,1-4H3/t8-,20+/m0/s1
SMILES:	C[C@H]1Cc2c(O1)c(O)c1c(c2O)C(=O)C(=C2[C@]1(C)CCC(=O)C2(C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1287906
PubChem CID:	14467636
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] 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
NPO18676	Clerodendrum trichotomum	Species	Lamiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29924604]
NPO24239	Teucrium polium	Species	Lamiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[21084196]
NPO24239	Teucrium polium	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18676	Clerodendrum trichotomum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24239	Teucrium polium	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18676	Clerodendrum trichotomum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24239	Teucrium polium	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]

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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	7
Others	1

Activity Type	# Activity
Cell Line	6
NON-MOLECULAR	1
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	>	50000.0	nM	PMID[572043]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	30000.0	nM	PMID[572042]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	3500.0	nM	PMID[572042]
NPT793	Cell Line	MOLT-3	Homo sapiens	IC50	=	2700.0	nM	PMID[572042]
NPT466	Cell Line	U-937	Homo sapiens	IC50	=	1500.0	nM	PMID[572042]
NPT926	Cell Line	SK-MEL-1	Homo sapiens	IC50	>	30000.0	nM	PMID[572042]
NPT1	Others	Radical scavenging activity		IC50	=	63000.0	nM	PMID[572041]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	50.0	%	PMID[572041]

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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 NPC208120 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	434
0.1-0.2	1883
0.2-0.3	3871
0.3-0.4	9541
0.4-0.5	9243
0.5-0.6	4427
0.6-0.7	5810
0.7-0.8	5958
0.8-0.85	1282
0.85-0.9	212
0.9-0.95	21
0.95-1	15

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC173587
0.9935	High Similarity	NPC21016
0.9935	High Similarity	NPC146584
0.9809	High Similarity	NPC232936
0.9747	High Similarity	NPC213416

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 NPC208120 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	365
0.1-0.2	1130
0.2-0.3	2227
0.3-0.4	2606
0.4-0.5	1689
0.5-0.6	726
0.6-0.7	291
0.7-0.8	100
0.8-0.85	16
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
0.8415	Intermediate Similarity	NPD3882	Suspended
0.8405	Intermediate Similarity	NPD2801	Approved
0.8405	Intermediate Similarity	NPD2393	Clinical (unspecified phase)
0.8344	Intermediate Similarity	NPD1934	Approved
0.828	Intermediate Similarity	NPD2800	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