NPASS Compound

Structure

NPC62725 OpenBabel07101718302D 71 78 0 0 1 0 0 0 0 0999 V2000 -1.7101 1.9747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0589 4.3108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0715 4.3108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0589 -2.3361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0715 -2.3361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7101 0.9873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8551 -1.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8551 -0.4937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5652 1.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4203 1.9747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.9747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8551 1.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8551 -1.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4203 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5652 0.4937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4203 2.9620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7101 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4203 1.9747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5652 0.4937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2753 1.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7101 2.9620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4057 1.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5652 -2.4684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8551 1.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7101 1.9747 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.4057 0.4937 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4203 -2.9620 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7101 -0.9873 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8551 0.4937 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4203 -0.9873 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.2608 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4203 -3.9494 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.2608 -0.9873 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2753 -4.4430 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.4057 -1.4810 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1304 -3.9494 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8405 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.8405 -0.9873 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9854 0.4937 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9854 -1.4810 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9854 1.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5506 -0.9873 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1304 -2.9620 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1304 -0.9873 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4203 0.9873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5652 3.4557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5652 -1.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7101 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8551 0.4937 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 2.5652 1.4810 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.2608 1.9747 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7101 -2.9620 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.1158 0.4937 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5652 -4.4430 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.1158 -1.4810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2753 -5.4304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.4057 -2.4684 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9854 -4.4430 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6956 0.4937 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8405 1.9747 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4203 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2753 1.4810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1304 1.9747 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5506 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2753 -2.4684 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2753 -1.4810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6956 -1.4810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1304 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9854 -2.4684 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 9 1 0 0 0 0 2 47 1 0 0 0 0 3 47 1 0 0 0 0 4 48 1 0 0 0 0 5 48 1 0 0 0 0 7 50 1 0 0 0 0 9 10 1 0 0 0 0 10 21 1 0 0 0 0 11 12 1 0 0 0 0 11 25 2 0 0 0 0 12 30 1 0 0 0 0 13 16 1 0 0 0 0 13 29 1 0 0 0 0 14 15 1 0 0 0 0 14 31 1 0 0 0 0 15 49 1 0 0 0 0 16 51 1 0 0 0 0 17 19 1 0 0 0 0 17 47 1 0 0 0 0 18 20 1 0 0 0 0 18 50 1 0 0 0 0 19 52 1 0 0 0 0 20 52 1 0 0 0 0 21 65 1 0 0 0 0 22 26 1 0 0 0 0 22 47 1 0 0 0 0 23 53 1 0 0 0 0 24 54 1 0 0 0 0 25 26 1 0 0 0 0 25 50 1 0 0 0 0 26 52 1 6 0 0 0 27 23 1 1 0 0 0 27 32 1 0 0 0 0 27 66 1 0 0 0 0 28 24 1 6 0 0 0 28 33 1 0 0 0 0 28 67 1 0 0 0 0 29 48 1 0 0 0 0 29 49 1 1 0 0 0 30 49 1 1 0 0 0 30 51 1 0 0 0 0 31 48 1 0 0 0 0 31 68 1 1 0 0 0 32 34 1 0 0 0 0 32 55 1 1 0 0 0 33 35 1 0 0 0 0 33 56 1 1 0 0 0 34 36 1 0 0 0 0 34 57 1 1 0 0 0 35 37 1 0 0 0 0 35 58 1 6 0 0 0 36 43 1 0 0 0 0 36 59 1 6 0 0 0 37 44 1 0 0 0 0 37 60 1 1 0 0 0 38 39 1 0 0 0 0 38 40 1 0 0 0 0 38 61 1 6 0 0 0 39 41 1 0 0 0 0 39 69 1 1 0 0 0 40 42 1 1 0 0 0 40 70 1 0 0 0 0 41 45 1 0 0 0 0 41 71 1 6 0 0 0 42 62 2 0 0 0 0 42 65 1 0 0 0 0 43 66 1 0 0 0 0 43 69 1 1 0 0 0 44 67 1 0 0 0 0 44 71 1 6 0 0 0 45 68 1 1 0 0 0 45 70 1 0 0 0 0 46 63 2 0 0 0 0 46 64 1 0 0 0 0 49 6 1 1 0 0 0 50 51 1 1 0 0 0 51 8 1 1 0 0 0 52 46 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1012.56
Volume:	998.601
LogP:	3.778
LogD:	3.395
LogS:	-3.458
# Rotatable Bonds:	14
TPSA:	301.05
# H-Bond Aceptor:	19
# H-Bond Donor:	10
# Rings:	8
# Heavy Atoms:	19

MedChem Properties

QED Drug-Likeness Score:	0.055
Synthetic Accessibility Score:	6.402
Fsp3:	0.923
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.993
MDCK Permeability:	5.855594281456433e-05
Pgp-inhibitor:	0.982
Pgp-substrate:	0.013
Human Intestinal Absorption (HIA):	0.94
20% Bioavailability (F20%):	0.141
30% Bioavailability (F30%):	0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.038
Plasma Protein Binding (PPB):	85.0993881225586%
Volume Distribution (VD):	0.267
Pgp-substrate:	8.472020149230957%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.117
CYP2C19-inhibitor:	0.001
CYP2C19-substrate:	0.225
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.017
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.053
CYP3A4-inhibitor:	0.068
CYP3A4-substrate:	0.015

ADMET: Excretion

Clearance (CL):	0.722
Half-life (T1/2):	0.556

ADMET: Toxicity

hERG Blockers:	0.04
Human Hepatotoxicity (H-HT):	0.181
Drug-inuced Liver Injury (DILI):	0.016
AMES Toxicity:	0.101
Rat Oral Acute Toxicity:	0.07
Maximum Recommended Daily Dose:	0.633
Skin Sensitization:	0.024
Carcinogencity:	0.025
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.796

Download Data

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

Natural Product: NPC62725

Natural Product ID:	NPC62725
*Common Name:**	{Oleanolic Acid 3-O-Beta-D-Glucopyranosyl(1->2)-[Beta-D-Galactopyranosyl(1->3)]-Beta-D-Glucuronopyranoside-6-O-N-Butyl Ester}
IUPAC Name:	(4aS,6aR,6aS,6bR,8aR,10S,12aR,14bS)-10-[(2R,3R,4S,5S,6S)-6-butoxycarbonyl-5-hydroxy-4-[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-2,2,6a,6b,9,9,12a-heptamethyl-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylic acid
Synonyms:
Standard InCHIKey:	ZVBYEOQPQROTOB-NPGFZERMSA-N
Standard InCHI:	InChI=1S/C52H84O19/c1-9-10-21-65-42(62)40-38(61)39(69-43-36(59)34(57)32(55)27(23-53)66-43)41(71-44-37(60)35(58)33(56)28(24-54)67-44)45(70-40)68-31-14-15-49(6)29(48(31,4)5)13-16-51(8)30(49)12-11-25-26-22-47(2,3)17-19-52(26,46(63)64)20-18-50(25,51)7/h11,26-41,43-45,53-61H,9-10,12-24H2,1-8H3,(H,63,64)/t26-,27+,28+,29-,30+,31-,32-,33+,34-,35-,36+,37+,38-,39-,40-,41+,43-,44-,45+,49-,50+,51+,52-/m0/s1
SMILES:	CCCCOC(=O)[C@@H]1[C@H]([C@@H]([C@H]([C@H](O[C@H]2CC[C@@]3(C)[C@@H](CC[C@]4(C)[C@@H]3CC=C3[C@@H]5CC(C)(C)CC[C@@]5(CC[C@@]43C)C(=O)O)C2(C)C)O1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](CO)O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL510256
PubChem CID:	16099399
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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
NPO28919	Calendula officinalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23327299]
NPO28919	Calendula officinalis	Species	Asteraceae	Eukaryota	flowers	n.a.	n.a.	PMID[17190444]
NPO28919	Calendula officinalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28919	Calendula officinalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28919	Calendula officinalis	Species	Asteraceae	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
GI50	48
IC50	1
Others	9

Activity Type	# Activity
Cell Line	49
NON-MOLECULAR	3
Organism	1
Others	5

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT80	Cell Line	Raji	Homo sapiens	Activity	=	70.0	%	PMID[569788]
NPT80	Cell Line	Raji	Homo sapiens	Activity	>	80.0	%	PMID[569788]
NPT116	Cell Line	HL-60	Homo sapiens	GI50	=	22300.0	nM	PMID[569788]
NPT111	Cell Line	K562	Homo sapiens	GI50	=	23200.0	nM	PMID[569788]
NPT112	Cell Line	MOLT-4	Homo sapiens	GI50	=	7770.0	nM	PMID[569788]
NPT81	Cell Line	A549	Homo sapiens	GI50	=	34100.0	nM	PMID[569788]
NPT394	Cell Line	EKVX	Homo sapiens	GI50	=	24400.0	nM	PMID[569788]
NPT379	Cell Line	HOP-62	Homo sapiens	GI50	=	19400.0	nM	PMID[569788]
NPT372	Cell Line	HOP-92	Homo sapiens	GI50	=	33200.0	nM	PMID[569788]
NPT405	Cell Line	NCI-H226	Homo sapiens	GI50	=	29200.0	nM	PMID[569788]

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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 NPC62725 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	286
0.1-0.2	1994
0.2-0.3	5428
0.3-0.4	10455
0.4-0.5	11085
0.5-0.6	6855
0.6-0.7	3698
0.7-0.8	1941
0.8-0.85	359
0.85-0.9	122
0.9-0.95	347
0.95-1	127

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC64715
1.0	High Similarity	NPC86222
1.0	High Similarity	NPC31838
1.0	High Similarity	NPC114484
1.0	High Similarity	NPC297263

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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 NPC62725 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	269
0.1-0.2	2289
0.2-0.3	3839
0.3-0.4	1762
0.4-0.5	569
0.5-0.6	254
0.6-0.7	126
0.7-0.8	38
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	2

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9649	High Similarity	NPD8328	Phase 3
0.9464	High Similarity	NPD8295	Clinical (unspecified phase)
0.8348	Intermediate Similarity	NPD8132	Clinical (unspecified phase)
0.8095	Intermediate Similarity	NPD7736	Approved
0.8067	Intermediate Similarity	NPD8133	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