NPASS Compound

Structure

NPC294972 OpenBabel07101718282D 31 32 0 0 1 0 0 0 0 0999 V2000 -3.4641 0.0000 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 -6.9282 3.0000 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 1.7321 1.0000 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 -8.6603 0.0000 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 -9.5263 -0.5000 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 -6.9282 1.0000 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 -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 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 -1.7321 1.0000 0.0000 C 0 0 0 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 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 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 0.0000 0.0000 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 -10.3923 0.0000 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 -4.3301 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 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 0.8660 1.5000 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 26 1 0 0 0 0 3 27 1 0 0 0 0 4 28 1 0 0 0 0 5 29 1 0 0 0 0 6 30 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 8 15 1 0 0 0 0 9 24 1 0 0 0 0 10 15 2 0 0 0 0 10 17 1 0 0 0 0 11 15 1 0 0 0 0 11 18 2 0 0 0 0 12 16 2 0 0 0 0 12 19 1 0 0 0 0 13 16 1 0 0 0 0 13 20 2 0 0 0 0 14 1 1 1 0 0 0 14 21 1 0 0 0 0 14 31 1 0 0 0 0 16 21 1 0 0 0 0 17 23 2 0 0 0 0 17 26 1 0 0 0 0 18 23 1 0 0 0 0 18 27 1 0 0 0 0 19 22 2 0 0 0 0 19 28 1 0 0 0 0 20 22 1 0 0 0 0 20 29 1 0 0 0 0 21 25 2 0 0 0 0 22 30 1 0 0 0 0 23 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	432.18
Volume:	438.481
LogP:	2.386
LogD:	2.346
LogS:	-3.982
# Rotatable Bonds:	11
TPSA:	92.68
# H-Bond Aceptor:	8
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.54
Synthetic Accessibility Score:	2.897
Fsp3:	0.348
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.592
MDCK Permeability:	3.2647592888679355e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.491
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.049

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.599
Plasma Protein Binding (PPB):	68.12670135498047%
Volume Distribution (VD):	0.466
Pgp-substrate:	24.318838119506836%

ADMET: Metabolism

CYP1A2-inhibitor:	0.142
CYP1A2-substrate:	0.96
CYP2C19-inhibitor:	0.082
CYP2C19-substrate:	0.899
CYP2C9-inhibitor:	0.064
CYP2C9-substrate:	0.756
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.89
CYP3A4-inhibitor:	0.492
CYP3A4-substrate:	0.908

ADMET: Excretion

Clearance (CL):	6.572
Half-life (T1/2):	0.878

ADMET: Toxicity

hERG Blockers:	0.098
Human Hepatotoxicity (H-HT):	0.125
Drug-inuced Liver Injury (DILI):	0.455
AMES Toxicity:	0.045
Rat Oral Acute Toxicity:	0.101
Maximum Recommended Daily Dose:	0.034
Skin Sensitization:	0.639
Carcinogencity:	0.039
Eye Corrosion:	0.003
Eye Irritation:	0.043
Respiratory Toxicity:	0.091

Download Data

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

Natural Product: NPC294972

Natural Product ID:	NPC294972
*Common Name:**	(+)-(8R)-3,4,5,3',5'-Pentamethoxy-Delta-7',8'-9'-Hydroxy-7-Oxo-8-O-4'-Neolignan
IUPAC Name:	(2R)-2-[4-[(E)-3-hydroxyprop-1-enyl]-2,6-dimethoxyphenoxy]-1-(3,4,5-trimethoxyphenyl)propan-1-one
Synonyms:
Standard InCHIKey:	SECJGGUDGJJKDQ-HSBSLETESA-N
Standard InCHI:	InChI=1S/C23H28O8/c1-14(21(25)16-12-19(28-4)22(30-6)20(13-16)29-5)31-23-17(26-2)10-15(8-7-9-24)11-18(23)27-3/h7-8,10-14,24H,9H2,1-6H3/b8-7+/t14-/m1/s1
SMILES:	OC/C=C/c1cc(OC)c(c(c1)OC)O[C@@H](C(=O)c1cc(OC)c(c(c1)OC)OC)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3105550
PubChem CID:	76324798
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0001831] Carbonyl compounds [CHEMONTID:0000118] Ketones [CHEMONTID:0003670] Aryl ketones [CHEMONTID:0004296] Phenylketones [CHEMONTID:0004298] Alkyl-phenylketones

*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
NPO20323	Saururus chinensis	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31642320]
NPO20323	Saururus chinensis	Species	Saururaceae	Eukaryota	Aerial Parts	n.a.	n.a.	PMID[24387347]
NPO20323	Saururus chinensis	Species	Saururaceae	Eukaryota	Roots	n.a.	n.a.	PMID[24359277]
NPO20323	Saururus chinensis	Species	Saururaceae	Eukaryota	roots	n.a.	n.a.	PMID[18841903]
NPO20323	Saururus chinensis	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15482936]
NPO20323	Saururus chinensis	Species	Saururaceae	Eukaryota	n.a.	root	n.a.	PMID[14750033]
NPO20323	Saururus chinensis	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11754613]
NPO20323	Saururus chinensis	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10924192]
NPO20323	Saururus chinensis	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20323	Saururus chinensis	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

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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
Organism	1
Others	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	""	Ratio CC50/EC50	=	2.5	n.a.	PMID[506511]
NPT27	Others	Unspecified	""	CC50	>	200000.0	nM	PMID[506511]
NPT164	Organism	Human herpesvirus 4	Human herpesvirus 4	EC50	=	80100.0	nM	PMID[506511]

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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 NPC294972 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	394
0.1-0.2	1492
0.2-0.3	4295
0.3-0.4	10226
0.4-0.5	7786
0.5-0.6	3622
0.6-0.7	5536
0.7-0.8	6982
0.8-0.85	2068
0.85-0.9	290
0.9-0.95	2
0.95-1	4

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Similarity Score	Similarity Level	Natural Product ID
0.9643	High Similarity	NPC28326
0.9315	High Similarity	NPC473091
0.9189	High Similarity	NPC75695
0.8993	High Similarity	NPC62354
0.8947	High Similarity	NPC178854

Showing 1 to 5 of 200 entries

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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 NPC294972 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	337
0.1-0.2	918
0.2-0.3	1743
0.3-0.4	2595
0.4-0.5	1845
0.5-0.6	1036
0.6-0.7	506
0.7-0.8	138
0.8-0.85	25
0.85-0.9	6
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9073	High Similarity	NPD3882	Suspended
0.8882	High Similarity	NPD3817	Phase 2
0.8671	High Similarity	NPD6167	Clinical (unspecified phase)
0.8671	High Similarity	NPD6168	Clinical (unspecified phase)
0.8671	High Similarity	NPD6166	Phase 2

Showing 1 to 5 of 200 entries

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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