NPASS Compound

Structure

NPC469706 OpenBabel07101719512D 41 44 0 0 1 0 0 0 0 0999 V2000 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -2.5000 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 -4.3301 -1.5000 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 -3.4641 2.0000 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 -2.5981 -1.5000 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 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 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 -3.4641 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 2 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 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -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 1 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 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 0.8660 1.5000 0.0000 C 0 0 2 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 -0.0000 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 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 -0.8660 0.5000 0.0000 C 0 0 1 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 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 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 36 1 0 0 0 0 2 37 1 0 0 0 0 3 38 1 0 0 0 0 4 39 1 0 0 0 0 5 12 1 0 0 0 0 5 14 1 0 0 0 0 6 12 2 0 0 0 0 6 18 1 0 0 0 0 7 13 2 0 0 0 0 7 16 1 0 0 0 0 8 13 1 0 0 0 0 8 17 2 0 0 0 0 9 29 1 0 0 0 0 10 30 1 0 0 0 0 11 40 1 0 0 0 0 12 21 1 0 0 0 0 14 9 1 1 0 0 0 14 15 1 0 0 0 0 15 11 1 6 0 0 0 15 20 1 0 0 0 0 16 22 2 0 0 0 0 16 36 1 0 0 0 0 17 22 1 0 0 0 0 17 37 1 0 0 0 0 18 24 2 0 0 0 0 18 38 1 0 0 0 0 19 10 1 6 0 0 0 19 23 1 0 0 0 0 19 41 1 0 0 0 0 20 13 1 1 0 0 0 20 21 1 0 0 0 0 21 27 2 0 0 0 0 22 31 1 0 0 0 0 23 25 1 0 0 0 0 23 32 1 6 0 0 0 24 27 1 0 0 0 0 24 33 1 0 0 0 0 25 26 1 0 0 0 0 25 34 1 1 0 0 0 26 28 1 0 0 0 0 26 35 1 1 0 0 0 27 39 1 0 0 0 0 28 40 1 6 0 0 0 28 41 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	582.23
Volume:	557.072
LogP:	0.085
LogD:	1.024
LogS:	-2.999
# Rotatable Bonds:	10
TPSA:	196.99
# H-Bond Aceptor:	13
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.196
Synthetic Accessibility Score:	4.6
Fsp3:	0.571
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:	-6.316
MDCK Permeability:	2.221424256276805e-05
Pgp-inhibitor:	0.112
Pgp-substrate:	0.978
Human Intestinal Absorption (HIA):	0.79
20% Bioavailability (F20%):	0.016
30% Bioavailability (F30%):	0.217

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.165
Plasma Protein Binding (PPB):	77.14723205566406%
Volume Distribution (VD):	0.421
Pgp-substrate:	36.17792510986328%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.908
CYP2C19-inhibitor:	0.004
CYP2C19-substrate:	0.858
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.409
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.221
CYP3A4-inhibitor:	0.062
CYP3A4-substrate:	0.537

ADMET: Excretion

Clearance (CL):	5.165
Half-life (T1/2):	0.894

ADMET: Toxicity

hERG Blockers:	0.366
Human Hepatotoxicity (H-HT):	0.251
Drug-inuced Liver Injury (DILI):	0.043
AMES Toxicity:	0.063
Rat Oral Acute Toxicity:	0.01
Maximum Recommended Daily Dose:	0.018
Skin Sensitization:	0.72
Carcinogencity:	0.015
Eye Corrosion:	0.003
Eye Irritation:	0.027
Respiratory Toxicity:	0.028

Download Data

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

Natural Product: NPC469706

Natural Product ID:	NPC469706
*Common Name:**	2-[(1R,2S,3S)-7-Hydroxy-1-(4-Hydroxy-3,5-Dimethoxy-Phenyl)-3-Hydroxymethyl-6,8-Dimethoxy-1,2,3,4-Tetrahydro-Naphthalen-2-Ylmethoxy]-6-Hydroxymethyl-Tetrahydro-Pyran-3,4,5-Triol
IUPAC Name:	(2S,3S,4S,5S,6S)-2-[[(1R,2S,3S)-7-hydroxy-1-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-6,8-dimethoxy-1,2,3,4-tetrahydronaphthalen-2-yl]methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms:
Standard InCHIKey:	PQQRNPDHSJDAGV-MAYNYCRRSA-N
Standard InCHI:	InChI=1S/C28H38O13/c1-36-16-7-13(8-17(37-2)22(16)31)20-15(11-40-28-26(35)25(34)23(32)19(10-30)41-28)14(9-29)5-12-6-18(38-3)24(33)27(39-4)21(12)20/h6-8,14-15,19-20,23,25-26,28-35H,5,9-11H2,1-4H3/t14-,15-,19+,20+,23-,25+,26+,28+/m1/s1
SMILES:	COC1=CC(=CC(=C1O)OC)C2C(C(CC3=CC(=C(C(=C23)OC)O)OC)CO)COC4C(C(C(C(O4)CO)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1159486
PubChem CID:	46905140
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001511] Lignan 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
NPO4138.1	Betula platyphylla var. japonica	Varieties	Betulaceae	Eukaryota	bark	n.a.	n.a.	PMID[9873651]
NPO4138.1	Betula platyphylla var. japonica	Varieties	Betulaceae	Eukaryota	floral spikes	n.a.	n.a.	PMID[17346076]
NPO4138.1	Betula platyphylla var. japonica	Varieties	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4138.1	Betula platyphylla var. japonica	Varieties	Betulaceae	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
Others	6

Activity Type	# Activity
Organism	6

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	8.3	%	PMID[504340]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	7.6	%	PMID[504340]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	10.5	%	PMID[504340]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	28.9	%	PMID[504340]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	58.8	%	PMID[504340]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	87.2	%	PMID[504340]

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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 NPC469706 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	465
0.1-0.2	1573
0.2-0.3	3854
0.3-0.4	8825
0.4-0.5	9112
0.5-0.6	4991
0.6-0.7	7507
0.7-0.8	4956
0.8-0.85	986
0.85-0.9	371
0.9-0.95	43
0.95-1	14

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC225815
1.0	High Similarity	NPC214326
1.0	High Similarity	NPC185955
1.0	High Similarity	NPC260781
1.0	High Similarity	NPC145979

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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 NPC469706 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	378
0.1-0.2	866
0.2-0.3	1914
0.3-0.4	2838
0.4-0.5	1629
0.5-0.6	933
0.6-0.7	473
0.7-0.8	107
0.8-0.85	10
0.85-0.9	2
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8924	High Similarity	NPD7228	Approved
0.8836	High Similarity	NPD6674	Discontinued
0.8718	High Similarity	NPD6234	Discontinued
0.8636	High Similarity	NPD37	Approved
0.859	High Similarity	NPD4967	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