NPASS Compound

Structure

CID247139 OpenBabel06191716052D 36 40 0 0 1 0 0 0 0 0999 V2000 5.0694 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5103 1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8449 -1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9756 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8674 0.8449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6898 0.9756 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8449 1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2245 -1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6898 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8449 -0.4878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3796 -1.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8449 -1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6898 -1.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8449 2.4390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0225 0.6185 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2245 -0.4878 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6898 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6898 2.9268 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6898 0.9756 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 0.9756 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5347 -0.4878 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5347 2.4390 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5347 -2.4390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8449 1.4634 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5347 1.4634 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8449 -0.4878 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 3.3796 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5347 -1.4634 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.9981 0.6185 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6898 3.9024 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3796 2.9268 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6898 -2.9268 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3796 -2.9268 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8918 0.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 17 1 0 0 0 0 4 27 1 0 0 0 0 7 8 1 0 0 0 0 7 18 2 0 0 0 0 8 21 1 0 0 0 0 9 12 1 0 0 0 0 9 17 1 0 0 0 0 10 11 1 0 0 0 0 10 20 1 0 0 0 0 11 28 1 0 0 0 0 12 30 1 0 0 0 0 13 14 1 0 0 0 0 13 27 1 0 0 0 0 14 30 1 0 0 0 0 15 19 1 0 0 0 0 15 25 1 0 0 0 0 16 26 1 0 0 0 0 16 31 1 0 0 0 0 17 29 1 6 0 0 0 18 22 1 0 0 0 0 18 27 1 0 0 0 0 19 23 1 0 0 0 0 19 32 1 6 0 0 0 20 25 1 1 0 0 0 20 26 1 0 0 0 0 21 25 1 1 0 0 0 21 28 1 0 0 0 0 22 29 1 6 0 0 0 22 30 1 0 0 0 0 23 26 1 1 0 0 0 23 33 1 0 0 0 0 24 34 2 0 0 0 0 24 35 1 0 0 0 0 25 2 1 1 0 0 0 26 3 1 1 0 0 0 27 28 1 1 0 0 0 28 5 1 1 0 0 0 29 6 1 1 0 0 0 29 36 1 0 0 0 0 30 24 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	504.35
Volume:	532.122
LogP:	3.452
LogD:	2.762
LogS:	-3.575
# Rotatable Bonds:	2
TPSA:	118.22
# H-Bond Aceptor:	6
# H-Bond Donor:	5
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.361
Synthetic Accessibility Score:	5.17
Fsp3:	0.9
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.64
MDCK Permeability:	7.4646295615821145e-06
Pgp-inhibitor:	0.005
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.017
20% Bioavailability (F20%):	0.164
30% Bioavailability (F30%):	0.65

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.212
Plasma Protein Binding (PPB):	90.43804168701172%
Volume Distribution (VD):	0.522
Pgp-substrate:	5.430739879608154%

ADMET: Metabolism

CYP1A2-inhibitor:	0.007
CYP1A2-substrate:	0.627
CYP2C19-inhibitor:	0.004
CYP2C19-substrate:	0.787
CYP2C9-inhibitor:	0.031
CYP2C9-substrate:	0.131
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.092
CYP3A4-inhibitor:	0.246
CYP3A4-substrate:	0.146

ADMET: Excretion

Clearance (CL):	1.632
Half-life (T1/2):	0.493

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.201
Drug-inuced Liver Injury (DILI):	0.021
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.659
Maximum Recommended Daily Dose:	0.894
Skin Sensitization:	0.207
Carcinogencity:	0.019
Eye Corrosion:	0.06
Eye Irritation:	0.146
Respiratory Toxicity:	0.982

Download Data

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

Natural Product: NPC247139

Natural Product ID:	NPC247139
*Common Name:**	19Alpha-Hydroxyasiatic Acid
IUPAC Name:	(1R,2R,4aS,6aR,6aS,6bR,8aR,9R,10R,11R,12aR,14bS)-1,10,11-trihydroxy-9-(hydroxymethyl)-1,2,6a,6b,9,12a-hexamethyl-2,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylic acid
Synonyms:	19Alpha-Hydroxyasiatic Acid
Standard InCHIKey:	YCOKATFNRPZIIU-NIZSJLHKSA-N
Standard InCHI:	InChI=1S/C30H48O6/c1-17-9-12-30(24(34)35)14-13-27(4)18(22(30)29(17,6)36)7-8-21-25(2)15-19(32)23(33)26(3,16-31)20(25)10-11-28(21,27)5/h7,17,19-23,31-33,36H,8-16H2,1-6H3,(H,34,35)/t17-,19-,20-,21-,22-,23+,25+,26+,27-,28-,29-,30+/m1/s1
SMILES:	C[C@@H]1CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)C[C@H]([C@@H]([C@@](C)(CO)[C@@H]5CC[C@@]34C)O)O)[C@@H]2[C@]1(C)O)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL515920
PubChem CID:	490367
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO30384	Combretum quadrangulare	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9934464]
NPO13106	Rhodomyrtus tomentosa	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28245113]
NPO13106	Rhodomyrtus tomentosa	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25466012]
NPO7372	Rosa laevigata	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23632365]
NPO7372	Rosa laevigata	Species	Rosaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21384845]
NPO7372	Rosa laevigata	Species	Rosaceae	Eukaryota	Leaves	Huangshan, Anhui Province, China	2008-NOV	PMID[21384845]
NPO30384	Combretum quadrangulare	Species	Combretaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21265555]
NPO30384	Combretum quadrangulare	Species	Combretaceae	Eukaryota	leaves	Khon Kaen, Thailand	2006-AUG	PMID[21265555]
NPO23655.1	Rubus ellipticus	Under-species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[19795885]
NPO41024	Eriobotrya japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1279126]

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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	2
Others	7

Activity Type	# Activity
Cell Line	1
Organism	4
Others	4

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		IC50	=	78960.0	nM	PMID[452701]
NPT2	Others	Unspecified		IC50	=	1370000.0	nM	PMID[452699]
NPT1452	Cell Line	C8166	Homo sapiens	TC50	=	20.0	ug ml-1	PMID[452698]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	Activity	=	0.0	%	PMID[452698]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	Activity	=	1.0	%	PMID[452698]
NPT27	Others	Unspecified		Activity	=	50.0	ug ml-1	PMID[452698]
NPT2517	Organism	Human rhinovirus 1B	Human rhinovirus 1B	Activity	=	100.0	%	PMID[452698]
NPT338	Organism	Sindbis virus	Sindbis virus	Activity	=	100.0	%	PMID[452698]

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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 NPC247139 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	227
0.1-0.2	1383
0.2-0.3	4591
0.3-0.4	12068
0.4-0.5	10616
0.5-0.6	5873
0.6-0.7	4990
0.7-0.8	2251
0.8-0.85	402
0.85-0.9	125
0.9-0.95	129
0.95-1	42

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC9613
0.9889	High Similarity	NPC73004
0.9889	High Similarity	NPC158371
0.9889	High Similarity	NPC259733
0.9889	High Similarity	NPC207922

Showing 1 to 5 of 200 entries

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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 NPC247139 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	199
0.1-0.2	1738
0.2-0.3	3735
0.3-0.4	2286
0.4-0.5	727
0.5-0.6	233
0.6-0.7	189
0.7-0.8	37
0.8-0.85	3
0.85-0.9	3
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8817	High Similarity	NPD7515	Phase 2
0.8557	High Similarity	NPD7902	Approved
0.8438	Intermediate Similarity	NPD7748	Approved
0.8247	Intermediate Similarity	NPD7900	Approved
0.8247	Intermediate Similarity	NPD7901	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