NPASS Compound

Structure

CID34103 OpenBabel06191715362D 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 2 0 0 0 0 0 0 0 0 0 0.4973 0.0523 0.0000 C 0 0 2 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 1 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 -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 6 0 0 0 13 14 1 0 0 0 0 13 21 1 0 0 0 0 14 10 1 6 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 1 0 0 0 21 29 1 0 0 0 0 22 12 1 1 0 0 0 22 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	418.16
Volume:	409.345
LogP:	2.14
LogD:	2.582
LogS:	-3.773
# 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:	-5.027
MDCK Permeability:	2.0694003978860565e-05
Pgp-inhibitor:	0.496
Pgp-substrate:	0.04
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.042

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.153
Plasma Protein Binding (PPB):	76.3994369506836%
Volume Distribution (VD):	0.593
Pgp-substrate:	21.32622718811035%

ADMET: Metabolism

CYP1A2-inhibitor:	0.033
CYP1A2-substrate:	0.967
CYP2C19-inhibitor:	0.03
CYP2C19-substrate:	0.827
CYP2C9-inhibitor:	0.238
CYP2C9-substrate:	0.734
CYP2D6-inhibitor:	0.103
CYP2D6-substrate:	0.516
CYP3A4-inhibitor:	0.386
CYP3A4-substrate:	0.602

ADMET: Excretion

Clearance (CL):	8.071
Half-life (T1/2):	0.737

ADMET: Toxicity

hERG Blockers:	0.206
Human Hepatotoxicity (H-HT):	0.141
Drug-inuced Liver Injury (DILI):	0.749
AMES Toxicity:	0.101
Rat Oral Acute Toxicity:	0.064
Maximum Recommended Daily Dose:	0.133
Skin Sensitization:	0.945
Carcinogencity:	0.069
Eye Corrosion:	0.004
Eye Irritation:	0.516
Respiratory Toxicity:	0.458

Download Data

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

Natural Product: NPC34103

Natural Product ID:	NPC34103
*Common Name:**	(-)-Syringaresinol
IUPAC Name:	4-[(3R,3aS,6R,6aS)-6-(4-hydroxy-3,5-dimethoxyphenyl)-1,3,3a,4,6,6a-hexahydrofuro[3,4-c]furan-3-yl]-2,6-dimethoxyphenol
Synonyms:	(-)-Syringaresinol
Standard InCHIKey:	KOWMJRJXZMEZLD-WRMVBYCNSA-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+/m1/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:	CHEMBL402653
PubChem CID:	11604108
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
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]
NPO26298	Zanthoxylum simulans	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7798955]
NPO12773	Stephania tetrandra	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3728032]
NPO25825	Saussurea lappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3572418]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	Fruit juice	n.a.	n.a.	PMID[3404148]
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]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31291099]

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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	14
Others	2

Activity Type	# Activity
Cell Line	8
NON-MOLECULAR	5
Organism	1
Others	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT34	Cell Line	BV-2	Mus musculus	IC50	>	100000.0	nM	PMID[543593]
NPT27	Others	Unspecified		Activity	=	110.1	%	PMID[543592]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	27530.0	nM	PMID[543592]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	45600.0	nM	PMID[543591]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	>	50000.0	nM	PMID[543591]
NPT34	Cell Line	BV-2	Mus musculus	IC50	=	13480.0	nM	PMID[543589]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	30000.0	nM	PMID[543589]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	IC50	=	14470.0	nM	PMID[543589]
NPT574	Cell Line	XF498	Homo sapiens	IC50	=	8820.0	nM	PMID[543589]
NPT146	Cell Line	SK-OV-3	Homo sapiens	IC50	>	30000.0	nM	PMID[543589]

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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 NPC34103 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	NPC141765
1.0	High Similarity	NPC165155
0.9845	High Similarity	NPC126409
0.9845	High Similarity	NPC99572

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 NPC34103 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