NPASS Compound

Structure

CID161557 OpenBabel06191715532D 26 29 0 0 1 0 0 0 0 0999 V2000 -1.9323 -4.4207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4277 -0.8494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3413 -1.2561 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 -1.7232 -2.4317 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 -0.9040 0.8613 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9040 -0.8613 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6187 -1.4371 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 -0.4973 -0.0523 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4973 0.0523 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4458 -2.2506 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 -2.6368 -2.8384 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 -0.7052 -1.0304 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7052 1.0304 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3594 -2.6574 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 -2.7413 -3.8329 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1609 -1.5304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1609 1.5304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 23 1 0 0 0 0 2 24 1 0 0 0 0 3 5 2 0 0 0 0 3 11 1 0 0 0 0 4 6 2 0 0 0 0 4 12 1 0 0 0 0 5 15 1 0 0 0 0 6 16 1 0 0 0 0 7 11 2 0 0 0 0 7 17 1 0 0 0 0 8 12 2 0 0 0 0 8 18 1 0 0 0 0 9 26 1 0 0 0 0 10 25 1 0 0 0 0 13 9 1 1 0 0 0 13 14 1 0 0 0 0 13 19 1 0 0 0 0 14 10 1 1 0 0 0 14 20 1 0 0 0 0 15 17 2 0 0 0 0 15 21 1 0 0 0 0 16 18 2 0 0 0 0 16 22 1 0 0 0 0 17 23 1 0 0 0 0 18 24 1 0 0 0 0 19 11 1 1 0 0 0 19 25 1 0 0 0 0 20 12 1 6 0 0 0 20 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	358.14
Volume:	357.173
LogP:	2.474
LogD:	2.754
LogS:	-4.082
# Rotatable Bonds:	4
TPSA:	77.38
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.874
Synthetic Accessibility Score:	3.679
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.755
MDCK Permeability:	1.6237649106187746e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.513
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.012
30% Bioavailability (F30%):	0.025

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.054
Plasma Protein Binding (PPB):	93.69544219970703%
Volume Distribution (VD):	0.552
Pgp-substrate:	9.500166893005371%

ADMET: Metabolism

CYP1A2-inhibitor:	0.059
CYP1A2-substrate:	0.85
CYP2C19-inhibitor:	0.093
CYP2C19-substrate:	0.648
CYP2C9-inhibitor:	0.425
CYP2C9-substrate:	0.704
CYP2D6-inhibitor:	0.359
CYP2D6-substrate:	0.867
CYP3A4-inhibitor:	0.31
CYP3A4-substrate:	0.606

ADMET: Excretion

Clearance (CL):	8.585
Half-life (T1/2):	0.635

ADMET: Toxicity

hERG Blockers:	0.358
Human Hepatotoxicity (H-HT):	0.223
Drug-inuced Liver Injury (DILI):	0.842
AMES Toxicity:	0.17
Rat Oral Acute Toxicity:	0.109
Maximum Recommended Daily Dose:	0.845
Skin Sensitization:	0.945
Carcinogencity:	0.193
Eye Corrosion:	0.005
Eye Irritation:	0.924
Respiratory Toxicity:	0.893

Download Data

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

Natural Product: NPC161557

Natural Product ID:	NPC161557
*Common Name:**	Pinoresinol
IUPAC Name:	4-[(3R,3aR,6S,6aR)-6-(4-hydroxy-3-methoxyphenyl)-1,3,3a,4,6,6a-hexahydrofuro[3,4-c]furan-3-yl]-2-methoxyphenol
Synonyms:	Epipinoresinol; Pinoresinol
Standard InCHIKey:	HGXBRUKMWQGOIE-WZBLMQSHSA-N
Standard InCHI:	InChI=1S/C20H22O6/c1-23-17-7-11(3-5-15(17)21)19-13-9-26-20(14(13)10-25-19)12-4-6-16(22)18(8-12)24-2/h3-8,13-14,19-22H,9-10H2,1-2H3/t13-,14-,19-,20+/m0/s1
SMILES:	COc1cc(ccc1O)[C@@H]1OC[C@H]2[C@@H]1CO[C@@H]2c1ccc(c(c1)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL487611
PubChem CID:	637584
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans

*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
NPO211	Aplysina cauliformis	Species	Aplysinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[8350091]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561896]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6481366]
NPO40011	Allamanda schottii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3379414]
NPO14126	Garcinia oligantha	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33296199]
NPO9740	Dacrycarpus imbricatus	Species	Podocarpaceae	Eukaryota	Twigs	n.a.	n.a.	PMID[32786878]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32223193]
NPO4554	Isatis tinctoria	Species	Brassicaceae	Eukaryota	Roots	n.a.	n.a.	PMID[32004936]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31860304]
NPO6329	Abies chensiensis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31557016]

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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	4
ED50	1
IC50	6
Others	2
Potency	1

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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2740	Cell Line	Neutrophils		IC50	=	3.4	ug.mL-1	PMID[495011]
NPT2740	Cell Line	Neutrophils		IC50	>	10.0	ug.mL-1	PMID[495011]
NPT2740	Cell Line	Neutrophils		Inhibition	>	50.0	%	PMID[495011]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	39500.0	nM	PMID[495008]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	>	50000.0	nM	PMID[495008]
NPT106	Individual Protein	Peroxisome proliferator-activated receptor delta	Homo sapiens	EC50	=	49500.0	nM	PMID[495007]
NPT2	Others	Unspecified		EC50	=	10300.0	nM	PMID[495007]
NPT866	Individual Protein	Peroxisome proliferator-activated receptor alpha	Homo sapiens	EC50	>	60000.0	nM	PMID[495007]
NPT99	Individual Protein	Peroxisome proliferator-activated receptor gamma	Homo sapiens	EC50	=	58600.0	nM	PMID[495007]
NPT64	Individual Protein	ATPase family AAA domain-containing protein 5	Homo sapiens	Potency	n.a.	11577.4	nM	PMID[495006]

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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 NPC161557 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	387
0.1-0.2	1267
0.2-0.3	3617
0.3-0.4	10295
0.4-0.5	8894
0.5-0.6	5384
0.6-0.7	9155
0.7-0.8	2710
0.8-0.85	673
0.85-0.9	218
0.9-0.95	79
0.95-1	18

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC27843
1.0	High Similarity	NPC158079
1.0	High Similarity	NPC40432
1.0	High Similarity	NPC115207
1.0	High Similarity	NPC228346

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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 NPC161557 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	309
0.1-0.2	769
0.2-0.3	1728
0.3-0.4	2767
0.4-0.5	1869
0.5-0.6	1060
0.6-0.7	560
0.7-0.8	82
0.8-0.85	5
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.907	High Similarity	NPD3027	Phase 3
0.8468	Intermediate Similarity	NPD5283	Phase 1
0.8444	Intermediate Similarity	NPD1613	Approved
0.8444	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.8306	Intermediate Similarity	NPD228	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