NPASS Compound

Structure

CID298093 OpenBabel06191716102D 29 33 0 0 1 0 0 0 0 0999 V2000 -3.9049 -1.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9049 -2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 -1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 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 -3.4049 -2.0000 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 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 -2.0000 0.0000 C 0 0 2 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 4.3301 0.5000 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 0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 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 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 2.0000 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 -1.8171 -2.8090 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 11 2 0 0 0 0 2 11 1 0 0 0 0 3 25 1 0 0 0 0 4 26 1 0 0 0 0 5 6 2 0 0 0 0 5 12 1 0 0 0 0 6 15 1 0 0 0 0 7 13 2 0 0 0 0 7 18 1 0 0 0 0 8 14 1 0 0 0 0 8 16 1 0 0 0 0 9 17 2 0 0 0 0 9 19 1 0 0 0 0 10 27 1 0 0 0 0 12 22 1 0 0 0 0 12 23 2 0 0 0 0 13 17 1 0 0 0 0 14 15 2 0 0 0 0 14 23 1 0 0 0 0 15 28 1 0 0 0 0 16 11 1 1 0 0 0 16 28 1 0 0 0 0 17 27 1 0 0 0 0 18 19 2 0 0 0 0 18 25 1 0 0 0 0 19 26 1 0 0 0 0 20 10 1 6 0 0 0 20 21 1 0 0 0 0 20 29 1 0 0 0 0 21 13 1 6 0 0 0 21 22 1 0 0 0 0 22 24 2 0 0 0 0 23 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	394.14
Volume:	395.232
LogP:	4.401
LogD:	3.457
LogS:	-6.008
# Rotatable Bonds:	3
TPSA:	63.22
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.74
Synthetic Accessibility Score:	3.868
Fsp3:	0.348
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:	-4.828
MDCK Permeability:	3.43161154887639e-05
Pgp-inhibitor:	0.844
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.172
Plasma Protein Binding (PPB):	95.71747589111328%
Volume Distribution (VD):	0.861
Pgp-substrate:	5.91374397277832%

ADMET: Metabolism

CYP1A2-inhibitor:	0.104
CYP1A2-substrate:	0.901
CYP2C19-inhibitor:	0.911
CYP2C19-substrate:	0.843
CYP2C9-inhibitor:	0.859
CYP2C9-substrate:	0.911
CYP2D6-inhibitor:	0.518
CYP2D6-substrate:	0.903
CYP3A4-inhibitor:	0.902
CYP3A4-substrate:	0.632

ADMET: Excretion

Clearance (CL):	8.641
Half-life (T1/2):	0.089

ADMET: Toxicity

hERG Blockers:	0.079
Human Hepatotoxicity (H-HT):	0.402
Drug-inuced Liver Injury (DILI):	0.895
AMES Toxicity:	0.42
Rat Oral Acute Toxicity:	0.871
Maximum Recommended Daily Dose:	0.908
Skin Sensitization:	0.183
Carcinogencity:	0.22
Eye Corrosion:	0.003
Eye Irritation:	0.117
Respiratory Toxicity:	0.758

Download Data

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

Natural Product: NPC298093

Natural Product ID:	NPC298093
*Common Name:**	Rotenone
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JUVIOZPCNVVQFO-HBGVWJBISA-N
Standard InCHI:	InChI=1S/C23H22O6/c1-11(2)16-8-14-15(28-16)6-5-12-22(24)21-13-7-18(25-3)19(26-4)9-17(13)27-10-20(21)29-23(12)14/h5-7,9,16,20-21H,1,8,10H2,2-4H3/t16-,20-,21+/m1/s1
SMILES:	COc1cc2c(cc1OC)OC[C@@H]1[C@H]2C(=O)c2c(O1)c1C[C@@H](Oc1cc2)C(=C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL429023
PubChem CID:	6758
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0001607] Rotenoids [CHEMONTID:0003528] Rotenones

*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
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9917277]
NPO16519	Persea americana	Species	Lauraceae	Eukaryota	Unripe fruit	n.a.	n.a.	PMID[9644064]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9322367]
NPO29252	Moneses uniflora	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8984155]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8350086]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8326318]
NPO1201	Xylopia aromatica	Species	Annonaceae	Eukaryota	Barks	n.a.	n.a.	PMID[8021648]
NPO1201	Xylopia aromatica	Species	Annonaceae	Eukaryota	Barks	n.a.	n.a.	PMID[7714532]
NPO1201	Xylopia aromatica	Species	Annonaceae	Eukaryota	Barks	n.a.	n.a.	PMID[7623031]
NPO14197	Patrinia scabra	Species	Caprifoliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29799195]

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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
AC50	3
EC50	4
ED50	15
GI50	70
IC50	70
Ki	1
LD50	6
MIC	8
Others	1396
Potency	221

Activity Type	# Activity
Cell Line	138
Individual Protein	110
NON-MOLECULAR	14
Organism	1356
Others	172
Protein Complex	4
SINGLE PROTEIN	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	756.2	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	7.8	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	188.3	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	9.7	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	279.1	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	24.7	nM	PubChem BioAssay data set
NPT152	Individual Protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	7.7	nM	PubChem BioAssay data set
NPT152	Individual Protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	12358.6	nM	PubChem BioAssay data set
NPT152	Individual Protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	13332.2	nM	PubChem BioAssay data set
NPT106	Individual Protein	Peroxisome proliferator-activated receptor delta	Homo sapiens	Potency	n.a.	39419.3	nM	PubChem BioAssay data set

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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 NPC298093 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	491
0.1-0.2	1680
0.2-0.3	4049
0.3-0.4	9948
0.4-0.5	8307
0.5-0.6	3499
0.6-0.7	5230
0.7-0.8	5901
0.8-0.85	2625
0.85-0.9	853
0.9-0.95	105
0.95-1	9

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Similarity Score	Similarity Level	Natural Product ID
0.9679	High Similarity	NPC173292
0.9679	High Similarity	NPC128293
0.9675	High Similarity	NPC165549
0.9608	High Similarity	NPC19097
0.9551	High Similarity	NPC273959

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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 NPC298093 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	413
0.1-0.2	976
0.2-0.3	1715
0.3-0.4	2624
0.4-0.5	1834
0.5-0.6	961
0.6-0.7	432
0.7-0.8	157
0.8-0.85	31
0.85-0.9	6
0.9-0.95	0
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD5494	Approved
0.8797	High Similarity	NPD2393	Clinical (unspecified phase)
0.8734	High Similarity	NPD1934	Approved
0.8704	High Similarity	NPD1247	Approved
0.8679	High Similarity	NPD2801	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