NPASS Compound

Structure

NPC470236 OpenBabel07101719132D 37 39 0 0 1 0 0 0 0 0999 V2000 -0.8660 4.5000 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 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 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 3.5000 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 6.9282 6.0000 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 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 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 6.9282 5.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7942 4.5000 0.0000 C 0 0 1 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 7.7942 3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.9282 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 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 6.0622 3.5000 0.0000 C 0 0 1 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 7.7942 6.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 2.0000 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 -0.8660 3.5000 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 5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 4.5000 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 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 32 1 0 0 0 0 2 33 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 4 10 1 0 0 0 0 5 34 1 0 0 0 0 6 10 2 0 0 0 0 6 11 1 0 0 0 0 7 10 1 0 0 0 0 7 12 2 0 0 0 0 8 24 1 0 0 0 0 9 25 1 0 0 0 0 11 21 2 0 0 0 0 11 32 1 0 0 0 0 12 21 1 0 0 0 0 12 33 1 0 0 0 0 13 8 1 1 0 0 0 13 15 1 0 0 0 0 13 35 1 0 0 0 0 14 9 1 6 0 0 0 14 16 1 0 0 0 0 14 36 1 0 0 0 0 15 17 1 0 0 0 0 15 26 1 6 0 0 0 16 18 1 0 0 0 0 16 27 1 1 0 0 0 17 19 1 0 0 0 0 17 28 1 1 0 0 0 18 20 1 0 0 0 0 18 29 1 6 0 0 0 19 22 1 0 0 0 0 19 30 1 6 0 0 0 20 23 1 0 0 0 0 20 31 1 1 0 0 0 21 37 1 0 0 0 0 22 34 1 1 0 0 0 22 35 1 0 0 0 0 23 36 1 0 0 0 0 23 37 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	534.19
Volume:	493.212
LogP:	-1.226
LogD:	-1.349
LogS:	-1.554
# Rotatable Bonds:	10
TPSA:	217.22
# H-Bond Aceptor:	14
# H-Bond Donor:	8
# Rings:	3
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.148
Synthetic Accessibility Score:	4.493
Fsp3:	0.652
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.218
MDCK Permeability:	8.58226339914836e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.993
Human Intestinal Absorption (HIA):	0.911
20% Bioavailability (F20%):	0.013
30% Bioavailability (F30%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.208
Plasma Protein Binding (PPB):	30.61803436279297%
Volume Distribution (VD):	0.361
Pgp-substrate:	27.217992782592773%

ADMET: Metabolism

CYP1A2-inhibitor:	0.013
CYP1A2-substrate:	0.116
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.516
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.136
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.15
CYP3A4-inhibitor:	0.005
CYP3A4-substrate:	0.006

ADMET: Excretion

Clearance (CL):	1.016
Half-life (T1/2):	0.729

ADMET: Toxicity

hERG Blockers:	0.371
Human Hepatotoxicity (H-HT):	0.196
Drug-inuced Liver Injury (DILI):	0.165
AMES Toxicity:	0.126
Rat Oral Acute Toxicity:	0.023
Maximum Recommended Daily Dose:	0.001
Skin Sensitization:	0.562
Carcinogencity:	0.03
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.009

Download Data

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

Natural Product: NPC470236

Natural Product ID:	NPC470236
*Common Name:**	Isosyringinoside
IUPAC Name:	(2S,3S,4R,5R,6S)-2-[(E)-3-[3,5-dimethoxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]prop-2-enoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms:	Isosyringinoside
Standard InCHIKey:	RYVGCUJETSKZDU-NXJCARKOSA-N
Standard InCHI:	InChI=1S/C23H34O14/c1-32-11-6-10(4-3-5-34-22-19(30)17(28)15(26)13(8-24)35-22)7-12(33-2)21(11)37-23-20(31)18(29)16(27)14(9-25)36-23/h3-4,6-7,13-20,22-31H,5,8-9H2,1-2H3/b4-3+/t13-,14+,15-,16+,17+,18-,19-,20+,22-,23-/m0/s1
SMILES:	COC1=CC(=CC(=C1OC2C(C(C(C(O2)CO)O)O)O)OC)C=CCOC3C(C(C(C(O3)CO)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1911059
PubChem CID:	57399043
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic 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
NPO16259	Syringa reticulata	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21955940]
NPO16259	Syringa reticulata	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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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	2

Activity Type	# Activity
NON-MOLECULAR	1
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	EC50	=	14140.0	nM	PMID[491857]
NPT1	Others	Radical scavenging activity	""	EC50	>	100000.0	nM	PMID[491857]

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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 NPC470236 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	1594
0.2-0.3	4522
0.3-0.4	10754
0.4-0.5	7761
0.5-0.6	5515
0.6-0.7	7653
0.7-0.8	3740
0.8-0.85	522
0.85-0.9	170
0.9-0.95	67
0.95-1	5

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Similarity Score	Similarity Level	Natural Product ID
0.9922	High Similarity	NPC164857
0.9766	High Similarity	NPC162093
0.969	High Similarity	NPC49074
0.9538	High Similarity	NPC69513
0.9538	High Similarity	NPC215833

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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 NPC470236 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	316
0.1-0.2	860
0.2-0.3	2021
0.3-0.4	2871
0.4-0.5	1631
0.5-0.6	900
0.6-0.7	479
0.7-0.8	65
0.8-0.85	7
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8552	High Similarity	NPD1653	Approved
0.8382	Intermediate Similarity	NPD3027	Phase 3
0.8333	Intermediate Similarity	NPD1091	Approved
0.8333	Intermediate Similarity	NPD1613	Approved
0.8333	Intermediate Similarity	NPD1612	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