NPASS Compound

Structure

NPC485395 OpenBabel06302216202D 55 59 0 0 1 0 0 0 0 0999 V2000 0.5000 6.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 6.0622 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 4.3301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 3.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 3.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5000 4.3301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5000 6.0622 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5000 2.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5000 0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6691 2.4752 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4612 3.4533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2044 4.1225 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5827 2.0685 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4487 2.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4487 3.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3147 4.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1808 3.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1808 2.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3147 2.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0468 2.0685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0468 1.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0468 4.0685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9128 3.5685 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9128 2.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7788 2.0685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7788 4.0685 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.6449 3.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5109 4.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3769 3.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3769 2.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5109 2.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6449 2.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5109 1.0685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6449 0.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2429 2.0685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7788 5.0685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3147 5.0685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1808 5.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4781 1.0739 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 10 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 53 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 51 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 6 0 0 0 21 24 1 0 0 0 0 22 23 1 0 0 0 0 24 25 1 1 0 0 0 24 50 1 0 0 0 0 25 30 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 27 28 1 0 0 0 0 27 48 1 0 0 0 0 28 29 2 0 0 0 0 28 33 1 0 0 0 0 29 30 1 0 0 0 0 29 31 1 0 0 0 0 31 32 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 6 0 0 0 34 37 1 0 0 0 0 35 36 1 0 0 0 0 37 38 1 0 0 0 0 37 47 1 1 0 0 0 38 43 2 0 0 0 0 38 39 1 0 0 0 0 39 40 2 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 41 46 1 0 0 0 0 42 43 1 0 0 0 0 42 44 1 0 0 0 0 44 45 1 0 0 0 0 48 49 1 0 0 0 0 50 51 1 0 0 0 0 51 52 2 0 0 0 0 52 53 1 0 0 0 0 52 54 1 0 0 0 0 54 55 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	762.29
Volume:	761.062
LogP:	3.918
LogD:	3.011
LogS:	-4.367
# Rotatable Bonds:	19
TPSA:	192.06
# H-Bond Aceptor:	14
# H-Bond Donor:	5
# Rings:	5
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.052
Synthetic Accessibility Score:	4.461
Fsp3:	0.341
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.787
MDCK Permeability:	3.124980503343977e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.861
Human Intestinal Absorption (HIA):	0.034
20% Bioavailability (F20%):	0.06
30% Bioavailability (F30%):	0.066

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.015
Plasma Protein Binding (PPB):	86.5487289428711%
Volume Distribution (VD):	0.386
Pgp-substrate:	25.727149963378906%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.85
CYP2C19-inhibitor:	0.169
CYP2C19-substrate:	0.79
CYP2C9-inhibitor:	0.817
CYP2C9-substrate:	0.865
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.884
CYP3A4-inhibitor:	0.783
CYP3A4-substrate:	0.933

ADMET: Excretion

Clearance (CL):	6.927
Half-life (T1/2):	0.713

ADMET: Toxicity

hERG Blockers:	0.482
Human Hepatotoxicity (H-HT):	0.157
Drug-inuced Liver Injury (DILI):	0.087
AMES Toxicity:	0.061
Rat Oral Acute Toxicity:	0.136
Maximum Recommended Daily Dose:	0.911
Skin Sensitization:	0.94
Carcinogencity:	0.026
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.035

Download Data

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

Natural Product: NPC485395

Natural Product ID:	NPC485395
*Common Name:**	TXCVWSBILJVFSH-XWRZMSEUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	TXCVWSBILJVFSH-XWRZMSEUSA-N
Standard InCHI:	InChI=1S/C41H46O14/c1-48-31-16-23(8-11-29(31)44)9-13-37(46)53-14-6-7-24-15-27-28(21-42)39(55-40(27)33(17-24)50-3)26-19-34(51-4)41(35(20-26)52-5)54-36(22-43)38(47)25-10-12-30(45)32(18-25)49-2/h8-13,15-20,28,36,38-39,42-45,47H,6-7,14,21-22H2,1-5H3/b13-9+/t28-,36-,38-,39+/m1/s1
SMILES:	COc1cc(ccc1O)/C=C/C(=O)OCCCc1cc2[C@@H](CO)[C@H](c3cc(c(c(c3)OC)O[C@H](CO)[C@@H](c3ccc(c(c3)OC)O)O)OC)Oc2c(c1)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	127033420
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003405] 2-arylbenzofuran flavonoids

*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
NPO17434	Sambucus williamsii	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26988298]
NPO17434	Sambucus williamsii	Species	Adoxaceae	Eukaryota	n.a.	stem	n.a.	PMID[16651764]
NPO17434	Sambucus williamsii	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17434	Sambucus williamsii	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17434	Sambucus williamsii	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17434	Sambucus williamsii	Species	Adoxaceae	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
IC50	5
Others	3

Activity Type	# Activity
Cell Line	5
NON-MOLECULAR	2
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	=	16370.0	nM	PMID[26988298]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	IC50	=	14080.0	nM	PMID[26988298]
NPT574	Cell Line	XF498	Homo sapiens	IC50	=	18390.0	nM	PMID[26988298]
NPT76	Cell Line	C6	Rattus norvegicus	Activity	=	153.99	%	PMID[26988298]
NPT76	Cell Line	C6	Rattus norvegicus	Activity	=	82.7	%	PMID[26988298]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	17460.0	nM	PMID[26988298]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	7040.0	nM	PMID[26988298]
NPT27	Others	Unspecified		Activity	=	146.18	%	PMID[26988298]

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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 NPC485395 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	361
0.1-0.2	1445
0.2-0.3	3514
0.3-0.4	8523
0.4-0.5	10104
0.5-0.6	3762
0.6-0.7	5857
0.7-0.8	7583
0.8-0.85	1189
0.85-0.9	302
0.9-0.95	50
0.95-1	7

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Similarity Score	Similarity Level	Natural Product ID
No data available in table

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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 NPC485395 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	296
0.1-0.2	907
0.2-0.3	1737
0.3-0.4	2691
0.4-0.5	1843
0.5-0.6	959
0.6-0.7	569
0.7-0.8	136
0.8-0.85	12
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
No data available in table

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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