NPASS Compound

Structure

CID141765 OpenBabel06191715502D 30 33 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 -5.0638 -1.0751 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 2.0000 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 -2.4277 -0.8494 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 -1.7321 -0.0000 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 -1.7321 -1.0000 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 -2.6368 -2.8384 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 -0.0000 -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 0 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 0.0000 -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 2 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 0.8660 0.5000 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 -4.1503 -0.6683 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 0.1609 -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 25 1 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 11 2 0 0 0 0 5 15 1 0 0 0 0 6 11 1 0 0 0 0 6 16 2 0 0 0 0 7 12 2 0 0 0 0 7 17 1 0 0 0 0 8 12 1 0 0 0 0 8 18 2 0 0 0 0 9 30 1 0 0 0 0 10 29 1 0 0 0 0 13 9 1 1 0 0 0 13 14 1 0 0 0 0 13 21 1 0 0 0 0 14 10 1 1 0 0 0 14 22 1 0 0 0 0 15 19 2 0 0 0 0 15 25 1 0 0 0 0 16 19 1 0 0 0 0 16 26 1 0 0 0 0 17 20 2 0 0 0 0 17 27 1 0 0 0 0 18 20 1 0 0 0 0 18 28 1 0 0 0 0 19 23 1 0 0 0 0 20 24 1 0 0 0 0 21 11 1 6 0 0 0 21 29 1 0 0 0 0 22 12 1 6 0 0 0 22 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	418.16
Volume:	409.345
LogP:	2.395
LogD:	2.567
LogS:	-4.333
# Rotatable Bonds:	6
TPSA:	95.84
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.738
Synthetic Accessibility Score:	3.758
Fsp3:	0.455
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.781
MDCK Permeability:	2.5596451450837776e-05
Pgp-inhibitor:	0.191
Pgp-substrate:	0.073
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.042

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.229
Plasma Protein Binding (PPB):	69.16068267822266%
Volume Distribution (VD):	0.408
Pgp-substrate:	27.592628479003906%

ADMET: Metabolism

CYP1A2-inhibitor:	0.022
CYP1A2-substrate:	0.947
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.876
CYP2C9-inhibitor:	0.146
CYP2C9-substrate:	0.576
CYP2D6-inhibitor:	0.092
CYP2D6-substrate:	0.774
CYP3A4-inhibitor:	0.204
CYP3A4-substrate:	0.845

ADMET: Excretion

Clearance (CL):	10.248
Half-life (T1/2):	0.684

ADMET: Toxicity

hERG Blockers:	0.409
Human Hepatotoxicity (H-HT):	0.182
Drug-inuced Liver Injury (DILI):	0.864
AMES Toxicity:	0.06
Rat Oral Acute Toxicity:	0.105
Maximum Recommended Daily Dose:	0.491
Skin Sensitization:	0.959
Carcinogencity:	0.039
Eye Corrosion:	0.004
Eye Irritation:	0.47
Respiratory Toxicity:	0.829

Download Data

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

Natural Product: NPC141765

Natural Product ID:	NPC141765
*Common Name:**	Syringaresinol
IUPAC Name:	4-[(3S,3aR,6S,6aR)-6-(4-hydroxy-3,5-dimethoxyphenyl)-1,3,3a,4,6,6a-hexahydrofuro[3,4-c]furan-3-yl]-2,6-dimethoxyphenol
Synonyms:	(+)-Syringaresinol; (+/-)-Syringaresinol
Standard InCHIKey:	KOWMJRJXZMEZLD-HCIHMXRSSA-N
Standard InCHI:	InChI=1S/C22H26O8/c1-25-15-5-11(6-16(26-2)19(15)23)21-13-9-30-22(14(13)10-29-21)12-7-17(27-3)20(24)18(8-12)28-4/h5-8,13-14,21-24H,9-10H2,1-4H3/t13-,14-,21+,22+/m0/s1
SMILES:	COc1cc(cc(c1O)OC)[C@H]1OC[C@H]2[C@@H]1CO[C@@H]2c1cc(OC)c(c(c1)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL361362
PubChem CID:	443023
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
NPO2073	Ancistrocladus korupensis	Species	Ancistrocladaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9873424]
NPO11164	Renealmia alpinia	Species	Zingiberaceae	Eukaryota	n.a.	Suriname rainforest	n.a.	PMID[9428162]
NPO2073	Ancistrocladus korupensis	Species	Ancistrocladaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9249970]
NPO659	Secale cereale	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9134744]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9051910]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	leaf	n.a.	PMID[8699184]
NPO29196	Cryptocarya kurzii	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8377019]
NPO28686	Syzygium claviflorum	Species	Myrtaceae	Eukaryota	n.a.	leaf	n.a.	PMID[8176401]
NPO1692	Aquilaria malaccensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7320738]
NPO7925	Asparagus officinalis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6821187]

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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
NPO16509	NPC141765	Dried Or Powder	n.a.	0.351999998	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO26343	NPC141765	Dried Or Powder	n.a.	0.247999996	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO8589	NPC141765	Dried Or Powder	n.a.	0.372000009	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO22132	NPC141765	Dried Or Powder	n.a.	0.169	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO659	NPC141765	Dried Or Powder	n.a.	0.97299999	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]

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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
ED50	7
IC50	24
Kd	2
MIC	1
Others	22

Activity Type	# Activity
Cell Line	33
Individual Protein	15
NON-MOLECULAR	4
Organism	5

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT91	Cell Line	KB	Homo sapiens	IC50	>	47800.0	nM	PMID[515456]
NPT189	Cell Line	Vero	Chlorocebus aethiops	IC50	>	47800.0	nM	PMID[515456]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	>	47800.0	nM	PMID[515456]
NPT461	Cell Line	PANC-1	Homo sapiens	IC50	=	61100.0	nM	PMID[515455]
NPT848	Cell Line	N9	Homo sapiens	IC50	=	2680.0	nM	PMID[515454]
NPT2219	Cell Line	C2C12	Mus musculus	Activity	=	18.0	%	PMID[515453]
NPT2219	Cell Line	C2C12	Mus musculus	Activity	=	14.0	%	PMID[515453]
NPT4633	Individual Protein	Peroxisome proliferator-activated receptor delta	Mus musculus	FC	=	2.0	n.a.	PMID[515453]
NPT4633	Individual Protein	Peroxisome proliferator-activated receptor delta	Mus musculus	FC	=	3.0	n.a.	PMID[515453]
NPT4633	Individual Protein	Peroxisome proliferator-activated receptor delta	Mus musculus	FC	=	4.0	n.a.	PMID[515453]

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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 NPC141765 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	423
0.1-0.2	1363
0.2-0.3	4042
0.3-0.4	11085
0.4-0.5	7946
0.5-0.6	5196
0.6-0.7	8729
0.7-0.8	2754
0.8-0.85	777
0.85-0.9	300
0.9-0.95	67
0.95-1	15

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC24490
1.0	High Similarity	NPC34103
1.0	High Similarity	NPC165155
0.9845	High Similarity	NPC126409
0.9845	High Similarity	NPC99572

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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 NPC141765 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	328
0.1-0.2	811
0.2-0.3	1899
0.3-0.4	2884
0.4-0.5	1696
0.5-0.6	1004
0.6-0.7	460
0.7-0.8	61
0.8-0.85	6
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
0.9231	High Similarity	NPD3027	Phase 3
0.8603	High Similarity	NPD1612	Clinical (unspecified phase)
0.8603	High Similarity	NPD1613	Approved
0.8533	High Similarity	NPD6234	Discontinued
0.8507	High Similarity	NPD1530	Clinical (unspecified phase)

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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