NPASS Compound

Structure

NPC50815 OpenBabel07101719122D 32 35 0 0 1 0 0 0 0 0999 V2000 -0.8660 -4.5000 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 -6.5683 2.9680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9234 2.4135 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 -5.2301 4.4543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9429 3.2953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -4.0000 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 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8690 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2812 0.1910 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 -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 -0.8660 0.5000 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 -5.5902 2.7601 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 -3.4641 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2812 1.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 1 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 0.0000 -1.0000 0.0000 C 0 0 2 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 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.9211 3.5032 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 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 1 8 1 0 0 0 0 2 17 1 0 0 0 0 6 30 1 0 0 0 0 7 30 1 0 0 0 0 8 17 2 0 0 0 0 9 10 1 0 0 0 0 9 19 1 0 0 0 0 11 12 1 0 0 0 0 11 21 1 0 0 0 0 12 22 1 0 0 0 0 13 14 1 0 0 0 0 13 23 1 0 0 0 0 14 27 1 0 0 0 0 15 19 2 0 0 0 0 15 24 1 0 0 0 0 16 25 1 0 0 0 0 16 28 1 0 0 0 0 17 26 1 0 0 0 0 18 3 1 6 0 0 0 18 21 1 0 0 0 0 18 30 1 0 0 0 0 19 28 1 0 0 0 0 20 10 1 1 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 21 27 1 6 0 0 0 22 27 1 6 0 0 0 23 28 1 6 0 0 0 24 25 1 0 0 0 0 24 29 1 6 0 0 0 25 31 1 6 0 0 0 26 29 2 3 0 0 0 26 32 1 0 0 0 0 27 4 1 6 0 0 0 28 5 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	442.36
Volume:	490.283
LogP:	4.58
LogD:	4.29
LogS:	-4.097
# Rotatable Bonds:	5
TPSA:	52.57
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.479
Synthetic Accessibility Score:	4.953
Fsp3:	0.821
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:	-4.937
MDCK Permeability:	1.2014856110909022e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.84
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.133
30% Bioavailability (F30%):	0.06

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.346
Plasma Protein Binding (PPB):	71.14022064208984%
Volume Distribution (VD):	1.548
Pgp-substrate:	14.75490951538086%

ADMET: Metabolism

CYP1A2-inhibitor:	0.068
CYP1A2-substrate:	0.643
CYP2C19-inhibitor:	0.17
CYP2C19-substrate:	0.941
CYP2C9-inhibitor:	0.296
CYP2C9-substrate:	0.05
CYP2D6-inhibitor:	0.695
CYP2D6-substrate:	0.87
CYP3A4-inhibitor:	0.912
CYP3A4-substrate:	0.678

ADMET: Excretion

Clearance (CL):	8.598
Half-life (T1/2):	0.089

ADMET: Toxicity

hERG Blockers:	0.188
Human Hepatotoxicity (H-HT):	0.33
Drug-inuced Liver Injury (DILI):	0.379
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.888
Maximum Recommended Daily Dose:	0.471
Skin Sensitization:	0.767
Carcinogencity:	0.565
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.97

Download Data

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

Natural Product: NPC50815

Natural Product ID:	NPC50815
*Common Name:**	(E)-N-[(2S,3R,8S,9S,10R,13S,14S,17S)-17-[(1S)-1-(Dimethylamino)Ethyl]-2-Hydroxy-10,13-Dimethyl-2,3,6,7,8,9,11,12,14,15,16,17-Dodecahydro-1H-Cyclopenta[A]Phenanthren-3-Yl]-2-Methylbut-2-Enamide
IUPAC Name:	(E)-N-[(2S,3R,8S,9S,10R,13S,14S,17S)-17-[(1S)-1-(dimethylamino)ethyl]-2-hydroxy-10,13-dimethyl-2,3,6,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]-2-methylbut-2-enamide
Synonyms:
Standard InCHIKey:	HPMZAZCMGAGHFS-SYDZCELUSA-N
Standard InCHI:	InChI=1S/C28H46N2O2/c1-8-17(2)26(32)29-24-15-19-9-10-20-22-12-11-21(18(3)30(6)7)27(22,4)14-13-23(20)28(19,5)16-25(24)31/h8,15,18,20-25,31H,9-14,16H2,1-7H3,(H,29,32)/b17-8+/t18-,20-,21+,22-,23-,24+,25-,27+,28-/m0/s1
SMILES:	C/C=C(C)/C(=N[C@@H]1C=C2CC[C@H]3[C@@H]4CC[C@H]([C@H](C)N(C)C)[C@@]4(C)CC[C@@H]3[C@@]2(C)C[C@@H]1O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL139424
PubChem CID:	11430659
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001295] Hydroxysteroids

*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	1

Activity Type	# Activity
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	IC50	=	15848.93	nM	PMID[559479]

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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 NPC50815 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	86
0.1-0.2	661
0.2-0.3	7368
0.3-0.4	17131
0.4-0.5	10581
0.5-0.6	5635
0.6-0.7	1067
0.7-0.8	153
0.8-0.85	12
0.85-0.9	0
0.9-0.95	2
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9789	High Similarity	NPC247060
0.9381	High Similarity	NPC471083
0.8725	High Similarity	NPC55462
0.8571	High Similarity	NPC472359
0.84	Intermediate Similarity	NPC240650

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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 NPC50815 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	89
0.1-0.2	325
0.2-0.3	2188
0.3-0.4	4456
0.4-0.5	1605
0.5-0.6	406
0.6-0.7	76
0.7-0.8	5
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
0.7745	Intermediate Similarity	NPD5771	Approved
0.734	Intermediate Similarity	NPD7339	Approved
0.734	Intermediate Similarity	NPD6942	Approved
0.7083	Intermediate Similarity	NPD3701	Clinical (unspecified phase)
0.699	Remote Similarity	NPD4751	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