NPASS Compound

Structure

NPC18064 OpenBabel07101718182D 33 37 0 0 1 0 0 0 0 0999 V2000 2.5297 4.3816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8432 3.4079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0165 -2.3038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0429 -2.3038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6865 0.9737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8432 -1.4605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8432 -0.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.9474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8432 1.4605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3729 2.9211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8432 -1.4605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3729 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5297 0.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3729 1.9474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6865 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5297 0.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5297 3.4079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6865 2.9211 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8432 1.4605 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6865 -0.9737 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8432 0.4868 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3729 -0.9737 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6865 1.9474 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3729 0.9737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5297 -1.4605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6865 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8432 0.4868 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 2.5297 1.4605 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2162 -1.4605 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3729 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2162 1.4605 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 18 1 0 0 0 0 3 26 1 0 0 0 0 4 26 1 0 0 0 0 6 28 1 0 0 0 0 8 9 1 0 0 0 0 8 20 1 0 0 0 0 9 22 1 0 0 0 0 10 15 1 0 0 0 0 10 18 2 0 0 0 0 11 14 1 0 0 0 0 11 21 1 0 0 0 0 12 13 1 0 0 0 0 12 23 1 0 0 0 0 13 27 1 0 0 0 0 14 29 1 0 0 0 0 15 30 1 0 0 0 0 16 17 1 0 0 0 0 16 28 1 0 0 0 0 17 30 1 0 0 0 0 18 19 1 0 0 0 0 19 2 1 6 0 0 0 19 24 1 0 0 0 0 20 24 1 0 0 0 0 20 28 1 6 0 0 0 21 26 1 0 0 0 0 21 27 1 1 0 0 0 22 27 1 1 0 0 0 22 29 1 0 0 0 0 23 26 1 0 0 0 0 23 31 1 1 0 0 0 24 30 1 1 0 0 0 25 32 2 0 0 0 0 25 33 1 0 0 0 0 27 5 1 1 0 0 0 28 29 1 1 0 0 0 29 7 1 1 0 0 0 30 25 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	456.36
Volume:	505.751
LogP:	5.944
LogD:	5.282
LogS:	-4.44
# Rotatable Bonds:	1
TPSA:	57.53
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.414
Synthetic Accessibility Score:	4.858
Fsp3:	0.9
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.389
MDCK Permeability:	4.051754513056949e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.825
30% Bioavailability (F30%):	0.894

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.019
Plasma Protein Binding (PPB):	94.44322967529297%
Volume Distribution (VD):	0.734
Pgp-substrate:	2.4050018787384033%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.495
CYP2C19-inhibitor:	0.021
CYP2C19-substrate:	0.912
CYP2C9-inhibitor:	0.174
CYP2C9-substrate:	0.892
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.444
CYP3A4-inhibitor:	0.155
CYP3A4-substrate:	0.166

ADMET: Excretion

Clearance (CL):	2.327
Half-life (T1/2):	0.258

ADMET: Toxicity

hERG Blockers:	0.037
Human Hepatotoxicity (H-HT):	0.207
Drug-inuced Liver Injury (DILI):	0.007
AMES Toxicity:	0.001
Rat Oral Acute Toxicity:	0.266
Maximum Recommended Daily Dose:	0.917
Skin Sensitization:	0.811
Carcinogencity:	0.01
Eye Corrosion:	0.837
Eye Irritation:	0.76
Respiratory Toxicity:	0.964

Download Data

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

Natural Product: NPC18064

Natural Product ID:	NPC18064
*Common Name:**	3Beta-Hydroxy-18Alpha,19Alpha-Urs-20-En-28-Oic Acid
IUPAC Name:	(1S,4aR,6aR,6aR,6bR,8aR,10S,12aR,14aR,14bR)-10-hydroxy-1,2,6a,6b,9,9,12a-heptamethyl-4,5,6,6a,7,8,8a,10,11,12,13,14,14a,14b-tetradecahydro-1H-picene-4a-carboxylic acid
Synonyms:
Standard InCHIKey:	HNJKFVJZKCXLRL-SILQXMKOSA-N
Standard InCHI:	InChI=1S/C30H48O3/c1-18-10-15-30(25(32)33)17-16-28(6)20(24(30)19(18)2)8-9-22-27(5)13-12-23(31)26(3,4)21(27)11-14-29(22,28)7/h10,19-24,31H,8-9,11-17H2,1-7H3,(H,32,33)/t19-,20-,21+,22-,23+,24-,27+,28-,29-,30+/m1/s1
SMILES:	CC1=CC[C@]2([C@H]([C@@H]1C)[C@H]1CC[C@H]3[C@@]([C@@]1(CC2)C)(C)CC[C@@H]1[C@]3(C)CC[C@@H](C1(C)C)O)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL517086
PubChem CID:	44575399
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
NPO4734	Syzygium nervosum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27797185]
NPO24313	Calyptranthes pallens	Species	Myrtaceae	Eukaryota	leaves and twigs	Southern Florida	n.a.	PMID[15844953]
NPO4734	Syzygium nervosum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24313	Calyptranthes pallens	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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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
ED50	5
IC50	3

Activity Type	# Activity
Cell Line	8

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	1900.0	nM	PMID[447732]
NPT465	Cell Line	NCI-N87	Homo sapiens	IC50	=	2400.0	nM	PMID[447732]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	4300.0	nM	PMID[447732]
NPT1034	Cell Line	Lu1	Homo sapiens	ED50	=	12.9	ug ml-1	PMID[447731]
NPT858	Cell Line	LNCaP	Homo sapiens	ED50	=	7.3	ug ml-1	PMID[447731]
NPT83	Cell Line	MCF7	Homo sapiens	ED50	=	9.7	ug ml-1	PMID[447731]
NPT91	Cell Line	KB	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[447731]
NPT737	Cell Line	HUVEC	Homo sapiens	ED50	=	10.4	ug ml-1	PMID[447731]

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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 NPC18064 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	201
0.1-0.2	1291
0.2-0.3	5131
0.3-0.4	15242
0.4-0.5	8188
0.5-0.6	5273
0.6-0.7	4701
0.7-0.8	2067
0.8-0.85	212
0.85-0.9	136
0.9-0.95	158
0.95-1	97

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC98442
1.0	High Similarity	NPC307426
1.0	High Similarity	NPC130577
1.0	High Similarity	NPC293564
1.0	High Similarity	NPC102683

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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 NPC18064 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	181
0.1-0.2	1681
0.2-0.3	3917
0.3-0.4	2260
0.4-0.5	655
0.5-0.6	193
0.6-0.7	200
0.7-0.8	56
0.8-0.85	1
0.85-0.9	4
0.9-0.95	1
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9529	High Similarity	NPD7515	Phase 2
0.9091	High Similarity	NPD7748	Approved
0.8824	High Similarity	NPD7520	Clinical (unspecified phase)
0.8791	High Similarity	NPD7902	Approved
0.8554	High Similarity	NPD7645	Phase 2

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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