NPASS Compound

Structure

NPC175230 OpenBabel07101719252D 46 49 0 0 1 0 0 0 0 0999 V2000 3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 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 -3.4641 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 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 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 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 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 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 -2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 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 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 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 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 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 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 16 1 0 0 0 0 2 7 1 0 0 0 0 2 17 2 0 0 0 0 3 8 2 0 0 0 0 3 17 1 0 0 0 0 4 10 2 0 0 0 0 4 18 1 0 0 0 0 5 11 2 0 0 0 0 5 18 1 0 0 0 0 6 13 2 0 0 0 0 6 17 1 0 0 0 0 7 19 2 0 0 0 0 8 19 1 0 0 0 0 9 12 2 0 0 0 0 9 20 1 0 0 0 0 10 21 1 0 0 0 0 11 22 1 0 0 0 0 12 24 1 0 0 0 0 13 26 1 0 0 0 0 14 18 2 0 0 0 0 14 23 1 0 0 0 0 15 43 1 0 0 0 0 16 33 2 0 0 0 0 16 44 1 0 0 0 0 19 34 1 0 0 0 0 20 21 1 0 0 0 0 20 27 2 0 0 0 0 21 35 2 0 0 0 0 22 23 2 0 0 0 0 22 36 1 0 0 0 0 23 37 1 0 0 0 0 24 28 2 0 0 0 0 24 45 1 0 0 0 0 25 15 1 6 0 0 0 25 31 1 0 0 0 0 25 46 1 0 0 0 0 26 38 2 0 0 0 0 26 43 1 0 0 0 0 27 28 1 0 0 0 0 27 39 1 0 0 0 0 28 40 1 0 0 0 0 29 30 1 0 0 0 0 29 31 1 0 0 0 0 29 41 1 6 0 0 0 30 32 1 0 0 0 0 30 42 1 1 0 0 0 31 44 1 1 0 0 0 32 45 1 6 0 0 0 32 46 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	638.16
Volume:	613.955
LogP:	2.823
LogD:	1.427
LogS:	-3.237
# Rotatable Bonds:	12
TPSA:	229.74
# H-Bond Aceptor:	14
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.073
Synthetic Accessibility Score:	4.294
Fsp3:	0.219
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.482
MDCK Permeability:	2.2268284737947397e-05
Pgp-inhibitor:	0.041
Pgp-substrate:	0.509
Human Intestinal Absorption (HIA):	0.684
20% Bioavailability (F20%):	0.99
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.022
Plasma Protein Binding (PPB):	100.96942901611328%
Volume Distribution (VD):	0.466
Pgp-substrate:	1.1603902578353882%

ADMET: Metabolism

CYP1A2-inhibitor:	0.487
CYP1A2-substrate:	0.017
CYP2C19-inhibitor:	0.2
CYP2C19-substrate:	0.047
CYP2C9-inhibitor:	0.624
CYP2C9-substrate:	0.475
CYP2D6-inhibitor:	0.57
CYP2D6-substrate:	0.183
CYP3A4-inhibitor:	0.182
CYP3A4-substrate:	0.102

ADMET: Excretion

Clearance (CL):	4.85
Half-life (T1/2):	0.945

ADMET: Toxicity

hERG Blockers:	0.099
Human Hepatotoxicity (H-HT):	0.203
Drug-inuced Liver Injury (DILI):	0.953
AMES Toxicity:	0.813
Rat Oral Acute Toxicity:	0.253
Maximum Recommended Daily Dose:	0.071
Skin Sensitization:	0.967
Carcinogencity:	0.26
Eye Corrosion:	0.003
Eye Irritation:	0.47
Respiratory Toxicity:	0.043

Download Data

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

Natural Product: NPC175230

Natural Product ID:	NPC175230
*Common Name:**	[(2R,3S,4R,5R,6S)-3-Acetyloxy-6-[4-[(E)-3-(3,4-Dihydroxyphenyl)Prop-2-Enoyl]-2,3-Dihydroxyphenoxy]-4,5-Dihydroxyoxan-2-Yl]Methyl (E)-3-(4-Hydroxyphenyl)Prop-2-Enoate
IUPAC Name:	[(2R,3S,4R,5R,6S)-3-acetyloxy-6-[4-[(E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-2,3-dihydroxyphenoxy]-4,5-dihydroxyoxan-2-yl]methyl (E)-3-(4-hydroxyphenyl)prop-2-enoate
Synonyms:
Standard InCHIKey:	WKVRKYAYLUKIBW-KNSAYTCFSA-N
Standard InCHI:	InChI=1S/C32H30O14/c1-16(33)44-31-25(15-43-26(38)13-6-17-2-7-19(34)8-3-17)46-32(30(42)29(31)41)45-24-12-9-20(27(39)28(24)40)21(35)10-4-18-5-11-22(36)23(37)14-18/h2-14,25,29-32,34,36-37,39-42H,15H2,1H3/b10-4+,13-6+/t25-,29-,30-,31-,32-/m1/s1
SMILES:	CC(=O)O[C@@H]1[C@@H](COC(=O)/C=C/c2ccc(cc2)O)O[C@H]([C@@H]([C@H]1O)O)Oc1ccc(C(=O)/C=C/c2ccc(c(c2)O)O)c(c1O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL454529
PubChem CID:	10371911
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides

*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
NPO19496	Bidens leucantha	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9090869]
NPO19496	Bidens leucantha	Species	Asteraceae	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
EC50	1
Others	2

Activity Type	# Activity
Cell Line	1
Organism	1
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1452	Cell Line	C8166	Homo sapiens	TC50	=	100.0	ug ml-1	PMID[538444]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	10.0	ug.mL-1	PMID[538444]
NPT2	Others	Unspecified		Selectivity Index	>	10.0	n.a.	PMID[538444]

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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 NPC175230 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	380
0.1-0.2	1663
0.2-0.3	3929
0.3-0.4	8551
0.4-0.5	9291
0.5-0.6	4334
0.6-0.7	4942
0.7-0.8	5710
0.8-0.85	2335
0.85-0.9	1071
0.9-0.95	463
0.95-1	28

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC172033
1.0	High Similarity	NPC88560
0.9876	High Similarity	NPC204937
0.9876	High Similarity	NPC149011
0.9755	High Similarity	NPC472993

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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 NPC175230 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	342
0.1-0.2	914
0.2-0.3	1922
0.3-0.4	2604
0.4-0.5	1850
0.5-0.6	944
0.6-0.7	375
0.7-0.8	144
0.8-0.85	34
0.85-0.9	14
0.9-0.95	7
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9341	High Similarity	NPD4338	Clinical (unspecified phase)
0.9333	High Similarity	NPD7054	Approved
0.9277	High Similarity	NPD7472	Approved
0.9277	High Similarity	NPD7074	Phase 3
0.9273	High Similarity	NPD3818	Discontinued

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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