NPASS Compound

Structure

NPC472359 OpenBabel07101719132D 33 36 0 0 1 0 0 0 0 0999 V2000 -5.1962 -0.0000 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 5.7023 4.4680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0574 3.9135 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 4.3641 5.9543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0769 4.7953 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 2.5981 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 5.0029 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 1.6910 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 2.5981 3.5000 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 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7242 4.2601 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 4.4152 3.3090 0.0000 C 0 0 2 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 1.7321 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 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 -0.0000 -0.0000 0.0000 C 0 0 2 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 3.4641 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.0550 5.0032 0.0000 N 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 -0.0000 -1.0000 0.0000 O 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 1 8 1 0 0 0 0 2 16 1 0 0 0 0 6 30 1 0 0 0 0 7 30 1 0 0 0 0 8 16 2 0 0 0 0 9 10 1 0 0 0 0 10 22 1 0 0 0 0 11 12 1 0 0 0 0 11 19 1 0 0 0 0 12 20 2 0 0 0 0 13 14 1 0 0 0 0 13 21 1 0 0 0 0 14 27 1 0 0 0 0 15 23 1 0 0 0 0 15 28 1 0 0 0 0 16 26 1 0 0 0 0 17 3 1 1 0 0 0 17 19 1 0 0 0 0 17 30 1 0 0 0 0 18 9 1 6 0 0 0 18 20 1 0 0 0 0 18 21 1 0 0 0 0 19 27 1 1 0 0 0 20 27 1 0 0 0 0 21 28 1 1 0 0 0 22 25 1 0 0 0 0 22 28 1 0 0 0 0 23 24 1 0 0 0 0 23 31 1 1 0 0 0 24 25 1 0 0 0 0 24 29 1 1 0 0 0 25 32 1 1 0 0 0 26 29 2 3 0 0 0 26 33 1 0 0 0 0 27 4 1 1 0 0 0 28 5 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	458.35
Volume:	499.073
LogP:	3.315
LogD:	3.358
LogS:	-4.084
# Rotatable Bonds:	5
TPSA:	72.8
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.441
Synthetic Accessibility Score:	5.111
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:	-4.864
MDCK Permeability:	1.31665074150078e-05
Pgp-inhibitor:	0.995
Pgp-substrate:	0.587
Human Intestinal Absorption (HIA):	0.781
20% Bioavailability (F20%):	0.674
30% Bioavailability (F30%):	0.071

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.142
Plasma Protein Binding (PPB):	77.64432525634766%
Volume Distribution (VD):	0.938
Pgp-substrate:	13.268540382385254%

ADMET: Metabolism

CYP1A2-inhibitor:	0.029
CYP1A2-substrate:	0.756
CYP2C19-inhibitor:	0.072
CYP2C19-substrate:	0.954
CYP2C9-inhibitor:	0.139
CYP2C9-substrate:	0.095
CYP2D6-inhibitor:	0.626
CYP2D6-substrate:	0.905
CYP3A4-inhibitor:	0.777
CYP3A4-substrate:	0.645

ADMET: Excretion

Clearance (CL):	7.304
Half-life (T1/2):	0.308

ADMET: Toxicity

hERG Blockers:	0.105
Human Hepatotoxicity (H-HT):	0.276
Drug-inuced Liver Injury (DILI):	0.097
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.81
Maximum Recommended Daily Dose:	0.431
Skin Sensitization:	0.259
Carcinogencity:	0.238
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.972

Download Data

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

Natural Product: NPC472359

Natural Product ID:	NPC472359
*Common Name:**	(E)-N-[(2S,3S,4R,8R,9S,10R,13R,17S)-17-[(1S)-1-(Dimethylamino)Ethyl]-2,4-Dihydroxy-10,13-Dimethyl-2,3,4,5,6,7,8,9,11,12,16,17-Dodecahydro-1H-Cyclopenta[A]Phenanthren-3-Yl]-2-Methylbut-2-Enamide
IUPAC Name:	(E)-N-[(2S,3S,4R,8R,9S,10R,13R,17S)-17-[(1S)-1-(dimethylamino)ethyl]-2,4-dihydroxy-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]-2-methylbut-2-enamide
Synonyms:
Standard InCHIKey:	QVNOTNUGUHMPDI-AIWDQZKNSA-N
Standard InCHI:	InChI=1S/C28H46N2O3/c1-8-16(2)26(33)29-24-23(31)15-28(5)21-13-14-27(4)19(17(3)30(6)7)11-12-20(27)18(21)9-10-22(28)25(24)32/h8,12,17-19,21-25,31-32H,9-11,13-15H2,1-7H3,(H,29,33)/b16-8+/t17-,18-,19+,21-,22?,23-,24-,25+,27+,28+/m0/s1
SMILES:	CC=C(C)C(=O)NC1C(CC2(C(C1O)CCC3C2CCC4(C3=CCC4C(C)N(C)C)C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL337494
PubChem CID:	44358199
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	=	33113.11	nM	PMID[542319]

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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 NPC472359 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	99
0.1-0.2	843
0.2-0.3	4904
0.3-0.4	20464
0.4-0.5	10109
0.5-0.6	5494
0.6-0.7	747
0.7-0.8	27
0.8-0.85	6
0.85-0.9	1
0.9-0.95	2
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9223	High Similarity	NPC55462
0.9099	High Similarity	NPC242692
0.8932	High Similarity	NPC471083
0.885	High Similarity	NPC472458
0.875	High Similarity	NPC247060

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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 NPC472359 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	98
0.1-0.2	422
0.2-0.3	2835
0.3-0.4	4120
0.4-0.5	1353
0.5-0.6	302
0.6-0.7	20
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
0.7407	Intermediate Similarity	NPD5771	Approved
0.6667	Remote Similarity	NPD7525	Registered
0.6639	Remote Similarity	NPD7333	Discontinued
0.6639	Remote Similarity	NPD6640	Phase 3
0.6571	Remote Similarity	NPD6929	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