NPASS Compound

Structure

NPC157479 OpenBabel07101718222D 34 37 0 0 1 0 0 0 0 0999 V2000 6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 4.0000 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 -4.8363 -2.9680 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 -2.1913 -2.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4980 -4.4543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2109 -3.2953 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 -0.8660 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 -4.1369 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 -0.1910 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 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 3.4641 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 5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8581 -2.7601 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 1.0000 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 -1.7321 -0.0000 0.0000 C 0 0 1 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 -2.5981 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1890 -3.5032 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 N 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 1 20 1 0 0 0 0 2 20 1 0 0 0 0 3 21 1 0 0 0 0 7 32 1 0 0 0 0 8 32 1 0 0 0 0 9 33 1 0 0 0 0 10 11 1 0 0 0 0 10 23 1 0 0 0 0 12 13 1 0 0 0 0 12 26 2 0 0 0 0 13 27 1 0 0 0 0 14 16 1 0 0 0 0 14 24 1 0 0 0 0 15 17 1 0 0 0 0 15 28 1 0 0 0 0 16 30 1 0 0 0 0 17 31 1 0 0 0 0 18 21 2 0 0 0 0 18 29 1 0 0 0 0 19 23 1 0 0 0 0 19 24 1 0 0 0 0 20 21 1 0 0 0 0 22 4 1 1 0 0 0 22 26 1 0 0 0 0 22 32 1 0 0 0 0 23 30 1 1 0 0 0 24 33 1 1 0 0 0 25 11 1 6 0 0 0 25 27 1 0 0 0 0 25 28 1 0 0 0 0 26 31 1 0 0 0 0 27 31 1 1 0 0 0 28 30 1 1 0 0 0 29 33 1 0 0 0 0 29 34 2 0 0 0 0 30 5 1 1 0 0 0 31 6 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	468.41
Volume:	533.381
LogP:	6.807
LogD:	4.887
LogS:	-5.023
# Rotatable Bonds:	6
TPSA:	23.55
# H-Bond Aceptor:	3
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.322
Synthetic Accessibility Score:	4.85
Fsp3:	0.839
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:	-4.715
MDCK Permeability:	1.329784299741732e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.374
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.455
30% Bioavailability (F30%):	0.381

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.156
Plasma Protein Binding (PPB):	81.36363983154297%
Volume Distribution (VD):	0.951
Pgp-substrate:	6.789710521697998%

ADMET: Metabolism

CYP1A2-inhibitor:	0.061
CYP1A2-substrate:	0.418
CYP2C19-inhibitor:	0.227
CYP2C19-substrate:	0.972
CYP2C9-inhibitor:	0.439
CYP2C9-substrate:	0.052
CYP2D6-inhibitor:	0.862
CYP2D6-substrate:	0.859
CYP3A4-inhibitor:	0.953
CYP3A4-substrate:	0.911

ADMET: Excretion

Clearance (CL):	13.217
Half-life (T1/2):	0.043

ADMET: Toxicity

hERG Blockers:	0.216
Human Hepatotoxicity (H-HT):	0.432
Drug-inuced Liver Injury (DILI):	0.548
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.95
Maximum Recommended Daily Dose:	0.927
Skin Sensitization:	0.949
Carcinogencity:	0.799
Eye Corrosion:	0.957
Eye Irritation:	0.11
Respiratory Toxicity:	0.982

Download Data

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

Natural Product: NPC157479

Natural Product ID:	NPC157479
*Common Name:**	1N-[14-(1-Dimethylaminoethyl)-2,15-Dimethyl-(1S,7S,10R,11S)-Tetracyclo[8.7.0.02,7.011,15]Heptadec-13-En-5-Yl]-1N,3,4-Trimethyl-(E)-2-Pentenamide
IUPAC Name:	(E)-N-[(3S,5S,8R,9S,10S,13S,14S)-17-[(1S)-1-(dimethylamino)ethyl]-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,14,15-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]-N,3,4-trimethylpent-2-enamide
Synonyms:
Standard InCHIKey:	BWTGOLYEGGOWMU-KFDGPNQLSA-N
Standard InCHI:	InChI=1S/C31H52N2O/c1-20(2)21(3)18-29(34)33(9)24-14-16-30(5)23(19-24)10-11-25-27-13-12-26(22(4)32(7)8)31(27,6)17-15-28(25)30/h12,18,20,22-25,27-28H,10-11,13-17,19H2,1-9H3/b21-18+/t22-,23-,24-,25-,27-,28-,30-,31+/m0/s1
SMILES:	CC(/C(=C/C(=O)N([C@H]1CC[C@]2([C@H](C1)CC[C@@H]1[C@@H]2CC[C@]2([C@H]1CC=C2[C@@H](N(C)C)C)C)C)C)/C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL424100
PubChem CID:	10961666
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002340] Azasteroids and derivatives

*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
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9548847]
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14643329]
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14584959]
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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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	3
Ki	2

Activity Type	# Activity
Individual Protein	5

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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	IC50	=	6165.95	nM	PMID[529361]
NPT2668	Individual Protein	Acetylcholinesterase	Torpedo californica	IC50	=	6200.0	nM	PMID[529360]
NPT2668	Individual Protein	Acetylcholinesterase	Torpedo californica	Ki	=	10700.0	nM	PMID[529360]
NPT439	Individual Protein	Butyrylcholinesterase	Homo sapiens	IC50	=	3650.0	nM	PMID[529360]
NPT439	Individual Protein	Butyrylcholinesterase	Homo sapiens	Ki	=	9100.0	nM	PMID[529360]

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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 NPC157479 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	123
0.1-0.2	1627
0.2-0.3	20342
0.3-0.4	13955
0.4-0.5	5760
0.5-0.6	747
0.6-0.7	109
0.7-0.8	29
0.8-0.85	2
0.85-0.9	1
0.9-0.95	1
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.963	High Similarity	NPC147513
0.9136	High Similarity	NPC90150
0.9024	High Similarity	NPC215474
0.8295	Intermediate Similarity	NPC43308
0.8025	Intermediate Similarity	NPC265789

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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 NPC157479 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	103
0.1-0.2	760
0.2-0.3	4140
0.3-0.4	3166
0.4-0.5	891
0.5-0.6	84
0.6-0.7	6
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
0.6813	Remote Similarity	NPD7155	Clinical (unspecified phase)
0.6591	Remote Similarity	NPD5365	Phase 2
0.6239	Remote Similarity	NPD7333	Discontinued
0.6238	Remote Similarity	NPD6934	Discontinued
0.6214	Remote Similarity	NPD5769	Clinical (unspecified phase)

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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