NPASS Compound

Structure

NPC471901 OpenBabel07101718302D 36 40 0 0 1 0 0 0 0 0999 V2000 4.7183 0.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1112 1.4666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5347 4.3902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1379 -2.3547 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 -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 -3.5103 1.4634 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 4.0360 -0.9756 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 -1.6898 2.9268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4626 -1.7649 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 -0.8449 -0.4878 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 -1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7640 0.7415 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3796 3.9024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4626 -0.1863 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6898 0.0000 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 -1.6898 0.9756 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 -0.4878 0.0000 C 0 0 2 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 2.5347 -1.4634 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8449 1.4634 0.0000 C 0 0 1 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 -2.5347 1.4634 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2245 4.3902 0.0000 O 0 0 0 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 -2.5347 -0.2264 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 19 2 0 0 0 0 2 19 1 0 0 0 0 3 20 1 0 0 0 0 6 30 1 0 0 0 0 9 10 1 0 0 0 0 9 22 1 0 0 0 0 10 23 1 0 0 0 0 11 14 1 0 0 0 0 11 21 1 0 0 0 0 12 16 1 0 0 0 0 12 24 1 0 0 0 0 13 15 1 0 0 0 0 13 25 1 0 0 0 0 14 28 1 0 0 0 0 15 29 1 0 0 0 0 16 31 1 0 0 0 0 17 18 1 0 0 0 0 17 28 1 0 0 0 0 18 30 1 0 0 0 0 20 33 2 0 0 0 0 20 36 1 0 0 0 0 21 19 1 6 0 0 0 21 26 1 0 0 0 0 22 26 1 0 0 0 0 22 30 1 6 0 0 0 23 29 1 1 0 0 0 23 31 1 0 0 0 0 24 29 1 1 0 0 0 24 32 1 0 0 0 0 25 32 1 1 0 0 0 25 36 1 0 0 0 0 26 28 1 1 0 0 0 27 32 1 0 0 0 0 27 34 2 0 0 0 0 27 35 1 0 0 0 0 28 4 1 1 0 0 0 29 5 1 1 0 0 0 30 31 1 1 0 0 0 31 7 1 1 0 0 0 32 8 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	498.37
Volume:	546.497
LogP:	5.341
LogD:	5.047
LogS:	-4.754
# Rotatable Bonds:	4
TPSA:	63.6
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.32
Synthetic Accessibility Score:	4.879
Fsp3:	0.875
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:	-5.248
MDCK Permeability:	8.249463280662894e-05
Pgp-inhibitor:	0.005
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.683

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	91.5213851928711%
Volume Distribution (VD):	0.886
Pgp-substrate:	2.343862771987915%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.466
CYP2C19-inhibitor:	0.022
CYP2C19-substrate:	0.947
CYP2C9-inhibitor:	0.133
CYP2C9-substrate:	0.759
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.354
CYP3A4-inhibitor:	0.218
CYP3A4-substrate:	0.284

ADMET: Excretion

Clearance (CL):	1.948
Half-life (T1/2):	0.337

ADMET: Toxicity

hERG Blockers:	0.121
Human Hepatotoxicity (H-HT):	0.163
Drug-inuced Liver Injury (DILI):	0.022
AMES Toxicity:	0.001
Rat Oral Acute Toxicity:	0.019
Maximum Recommended Daily Dose:	0.149
Skin Sensitization:	0.854
Carcinogencity:	0.007
Eye Corrosion:	0.988
Eye Irritation:	0.927
Respiratory Toxicity:	0.474

Download Data

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

Natural Product: NPC471901

Natural Product ID:	NPC471901
*Common Name:**	3-O-Acetyl-Lupeolic Acid
IUPAC Name:	(1R,3aR,5aR,5bR,7aR,8R,9S,11aR,11bR,13aR,13bR)-9-acetyloxy-3a,5a,5b,8,11a-pentamethyl-1-prop-1-en-2-yl-1,2,3,4,5,6,7,7a,9,10,11,11b,12,13,13a,13b-hexadecahydrocyclopenta[a]chrysene-8-carboxylic acid
Synonyms:
Standard InCHIKey:	DULLEXJVWYWBKQ-VDHVTXALSA-N
Standard InCHI:	InChI=1S/C32H50O4/c1-19(2)21-11-14-28(4)17-18-30(6)22(26(21)28)9-10-23-29(5)15-13-25(36-20(3)33)32(8,27(34)35)24(29)12-16-31(23,30)7/h21-26H,1,9-18H2,2-8H3,(H,34,35)/t21-,22+,23+,24+,25-,26+,28+,29+,30+,31+,32+/m0/s1
SMILES:	CC(=C)C1CCC2(C1C3CCC4C5(CCC(C(C5CCC4(C3(CC2)C)C)(C)C(=O)O)OC(=O)C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3289106
PubChem CID:	90644331
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
NPO33055	boswellia spp.	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24844534]

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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	6
Others	1

Activity Type	# Activity
Cell Line	1
Individual Protein	4
NON-MOLECULAR	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT136	Cell Line	SK-N-SH	Homo sapiens	IC50	=	4100.0	nM	PMID[465307]
NPT324	Individual Protein	Cyclooxygenase-1	Ovis aries	IC50	>	10000.0	nM	PMID[465307]
NPT31	Individual Protein	Cyclooxygenase-2	Homo sapiens	IC50	>	10000.0	nM	PMID[465307]
NPT956	Individual Protein	Prostaglandin E synthase	Homo sapiens	Activity	=	51.4	%	PMID[465307]
NPT956	Individual Protein	Prostaglandin E synthase	Homo sapiens	IC50	=	10000.0	nM	PMID[465307]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	4100.0	nM	PMID[465307]

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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 NPC471901 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	208
0.1-0.2	1687
0.2-0.3	6137
0.3-0.4	15109
0.4-0.5	6834
0.5-0.6	5037
0.6-0.7	4734
0.7-0.8	2582
0.8-0.85	284
0.85-0.9	57
0.9-0.95	20
0.95-1	8

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Similarity Score	Similarity Level	Natural Product ID
0.9884	High Similarity	NPC287118
0.9884	High Similarity	NPC471902
0.9884	High Similarity	NPC473690
0.9767	High Similarity	NPC475416
0.9647	High Similarity	NPC4309

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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 NPC471901 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	188
0.1-0.2	2027
0.2-0.3	4054
0.3-0.4	1948
0.4-0.5	478
0.5-0.6	191
0.6-0.7	183
0.7-0.8	78
0.8-0.85	1
0.85-0.9	0
0.9-0.95	2
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9318	High Similarity	NPD8035	Phase 2
0.9318	High Similarity	NPD8034	Phase 2
0.907	High Similarity	NPD7520	Clinical (unspecified phase)
0.8298	Intermediate Similarity	NPD7748	Approved
0.8041	Intermediate Similarity	NPD7902	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