NPASS Compound

Structure

NPC470523 OpenBabel07101719152D 34 38 0 0 1 0 0 0 0 0999 V2000 -3.0872 1.8625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3801 1.1554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5708 -0.3282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3120 0.6378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8637 -1.0353 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 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 -0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2247 -1.2247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6730 0.4483 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 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1305 0.9914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3461 0.8966 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9659 -0.2588 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 -2.8978 -0.7765 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 -2.1907 -1.4836 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 -2.6390 0.1895 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 1 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 3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6628 1.6002 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4495 -2.4495 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 18 1 0 0 0 0 2 19 1 0 0 0 0 5 7 1 0 0 0 0 5 9 1 0 0 0 0 6 8 1 0 0 0 0 6 10 1 0 0 0 0 7 18 1 0 0 0 0 8 19 1 0 0 0 0 9 23 2 0 0 0 0 10 24 2 0 0 0 0 11 12 1 0 0 0 0 11 20 1 0 0 0 0 12 30 1 0 0 0 0 13 21 2 0 0 0 0 13 25 1 0 0 0 0 14 21 1 0 0 0 0 14 28 1 0 0 0 0 15 22 1 0 0 0 0 15 29 1 0 0 0 0 16 31 1 0 0 0 0 17 32 1 0 0 0 0 18 28 1 6 0 0 0 19 29 1 6 0 0 0 20 16 1 6 0 0 0 20 22 1 0 0 0 0 21 30 1 0 0 0 0 22 26 2 0 0 0 0 23 25 1 0 0 0 0 23 28 1 0 0 0 0 24 27 1 0 0 0 0 24 29 1 0 0 0 0 25 33 2 0 0 0 0 26 27 1 0 0 0 0 26 30 1 0 0 0 0 27 34 2 0 0 0 0 28 3 1 6 0 0 0 29 4 1 6 0 0 0 30 17 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	464.29
Volume:	503.996
LogP:	3.999
LogD:	2.055
LogS:	-4.132
# Rotatable Bonds:	3
TPSA:	74.6
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.578
Synthetic Accessibility Score:	5.671
Fsp3:	0.667
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.673
MDCK Permeability:	1.7971815395867452e-05
Pgp-inhibitor:	0.954
Pgp-substrate:	0.154
Human Intestinal Absorption (HIA):	0.017
20% Bioavailability (F20%):	0.102
30% Bioavailability (F30%):	0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.901
Plasma Protein Binding (PPB):	94.21915435791016%
Volume Distribution (VD):	1.728
Pgp-substrate:	3.1205711364746094%

ADMET: Metabolism

CYP1A2-inhibitor:	0.036
CYP1A2-substrate:	0.375
CYP2C19-inhibitor:	0.082
CYP2C19-substrate:	0.803
CYP2C9-inhibitor:	0.065
CYP2C9-substrate:	0.064
CYP2D6-inhibitor:	0.096
CYP2D6-substrate:	0.091
CYP3A4-inhibitor:	0.953
CYP3A4-substrate:	0.462

ADMET: Excretion

Clearance (CL):	11.402
Half-life (T1/2):	0.028

ADMET: Toxicity

hERG Blockers:	0.004
Human Hepatotoxicity (H-HT):	0.146
Drug-inuced Liver Injury (DILI):	0.039
AMES Toxicity:	0.016
Rat Oral Acute Toxicity:	0.888
Maximum Recommended Daily Dose:	0.877
Skin Sensitization:	0.058
Carcinogencity:	0.7
Eye Corrosion:	0.027
Eye Irritation:	0.015
Respiratory Toxicity:	0.989

Download Data

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

Natural Product: NPC470523

Natural Product ID:	NPC470523
*Common Name:**	Diincarvilone C
IUPAC Name:	(1R,4R,5S,10aR)-1-[(8S,8aR)-8,8a-dimethyl-4-oxo-1,6,7,8-tetrahydronaphthalen-2-yl]-1,4-bis(hydroxymethyl)-5,10a-dimethyl-3,4,5,6,7,10-hexahydro-2H-anthracen-9-one
Synonyms:	Diincarvilone C
Standard InCHIKey:	NEXXXJDVSHXFRB-GFHXGSRDSA-N
Standard InCHI:	InChI=1S/C30H40O4/c1-18-7-5-9-23-25(33)13-21(14-28(18,23)3)30(17-32)12-11-20(16-31)22-15-29(4)19(2)8-6-10-24(29)27(34)26(22)30/h9-10,13,18-20,31-32H,5-8,11-12,14-17H2,1-4H3/t18-,19-,20-,28+,29+,30+/m0/s1
SMILES:	CC1CCC=C2C1(CC(=CC2=O)C3(CCC(C4=C3C(=O)C5=CCCC(C5(C4)C)C)CO)CO)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2062968
PubChem CID:	70696899
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids [CHEMONTID:0003655] Eremophilane, 8,9-secoeremophilane and furoeremophilane sesquiterpenoids

*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
NPO21937	Incarvillea arguta	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22620677]
NPO21937	Incarvillea arguta	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21937	Incarvillea arguta	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21937	Incarvillea arguta	Species	Bignoniaceae	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	4

Activity Type	# Activity
Cell Line	4

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	40000.0	nM	PMID[545896]
NPT659	Cell Line	SMMC-7721	Homo sapiens	IC50	>	40000.0	nM	PMID[545896]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	40000.0	nM	PMID[545896]
NPT660	Cell Line	SW480	Homo sapiens	IC50	>	40000.0	nM	PMID[545896]

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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 NPC470523 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	199
0.1-0.2	1253
0.2-0.3	5794
0.3-0.4	15861
0.4-0.5	9302
0.5-0.6	6891
0.6-0.7	3020
0.7-0.8	365
0.8-0.85	7
0.85-0.9	1
0.9-0.95	2
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
0.9878	High Similarity	NPC470524
0.9	High Similarity	NPC470522
0.9	High Similarity	NPC135685
0.8675	High Similarity	NPC2482
0.8642	High Similarity	NPC470525

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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 NPC470523 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	189
0.1-0.2	1847
0.2-0.3	3989
0.3-0.4	2271
0.4-0.5	467
0.5-0.6	249
0.6-0.7	126
0.7-0.8	12
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
0.8043	Intermediate Similarity	NPD7515	Phase 2
0.8023	Intermediate Similarity	NPD4695	Discontinued
0.7889	Intermediate Similarity	NPD3618	Phase 1
0.7865	Intermediate Similarity	NPD3133	Approved
0.7865	Intermediate Similarity	NPD3666	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