NPASS Compound

Structure

NPC139037 OpenBabel06302216212D 34 36 0 0 1 0 0 0 0 0999 V2000 -6.0622 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9282 -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 1 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 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 -3.4641 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 2 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 -1.7321 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 1 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 -2.5981 -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 -0.0000 -1.0000 0.0000 C 0 0 2 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 1.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 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 -0.0000 -0.0000 0.0000 C 0 0 1 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 0.8660 1.5000 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 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 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 -3.4641 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 34 1 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 33 1 1 0 0 0 4 5 1 0 0 0 0 4 32 1 6 0 0 0 5 6 1 0 0 0 0 5 31 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 10 29 1 1 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 17 1 0 0 0 0 13 14 1 0 0 0 0 13 16 1 6 0 0 0 14 15 1 1 0 0 0 18 17 1 1 0 0 0 18 19 1 0 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 19 27 1 6 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 26 1 1 0 0 0 22 23 1 0 0 0 0 22 25 1 1 0 0 0 23 24 1 6 0 0 0 27 28 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	504.17
Volume:	434.858
LogP:	-3.156
LogD:	-3.801
LogS:	-0.215
# Rotatable Bonds:	7
TPSA:	268.68
# H-Bond Aceptor:	16
# H-Bond Donor:	11
# Rings:	3
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.154
Synthetic Accessibility Score:	4.74
Fsp3:	1.0
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:	-6.473
MDCK Permeability:	0.0002856104401871562
Pgp-inhibitor:	0.001
Pgp-substrate:	0.979
Human Intestinal Absorption (HIA):	0.999
20% Bioavailability (F20%):	0.973
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.319
Plasma Protein Binding (PPB):	15.990131378173828%
Volume Distribution (VD):	0.252
Pgp-substrate:	57.22710037231445%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.006
CYP2C19-inhibitor:	0.006
CYP2C19-substrate:	0.053
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.018
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.056
CYP3A4-inhibitor:	0.002
CYP3A4-substrate:	0.0

ADMET: Excretion

Clearance (CL):	0.787
Half-life (T1/2):	0.902

ADMET: Toxicity

hERG Blockers:	0.338
Human Hepatotoxicity (H-HT):	0.049
Drug-inuced Liver Injury (DILI):	0.1
AMES Toxicity:	0.098
Rat Oral Acute Toxicity:	0.024
Maximum Recommended Daily Dose:	0.0
Skin Sensitization:	0.182
Carcinogencity:	0.015
Eye Corrosion:	0.003
Eye Irritation:	0.016
Respiratory Toxicity:	0.02

Download Data

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

Natural Product: NPC139037

Natural Product ID:	NPC139037
*Common Name:**	FYGDTMLNYKFZSV-MRCIVHHJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FYGDTMLNYKFZSV-MRCIVHHJSA-N
Standard InCHI:	InChI=1S/C18H32O16/c19-1-4-7(22)8(23)12(27)17(31-4)34-15-6(3-21)32-18(13(28)10(15)25)33-14-5(2-20)30-16(29)11(26)9(14)24/h4-29H,1-3H2/t4-,5-,6-,7-,8+,9-,10-,11-,12-,13-,14-,15-,16+,17?,18?/m1/s1
SMILES:	C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O[C@@H]1[C@@H](CO)OC([C@@H]([C@H]1O)O)O[C@@H]1[C@@H](CO)O[C@@H]([C@@H]([C@H]1O)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	62698
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000198] Oligosaccharides

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15516765]
NPO2746	Apis cerana	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16377847]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18270436]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20973550]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23700450]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23793896]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	leaf	n.a.	PMID[23849114]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24310066]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[24967651]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[25433632]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[26860358]
NPO27364	Gallus gallus	Species	Phasianidae	Eukaryota	n.a.	n.a.	n.a.	PMID[27439360]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		PMID[31861466]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Petiole	n.a.	n.a.	Database[FooDB]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Protoplast	n.a.	n.a.	Database[FooDB]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO9788	Coffea arabica	Species	Rubiaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO9788	Coffea arabica	Species	Rubiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO9788	Coffea arabica	Species	Rubiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2746	Apis cerana	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9788	Coffea arabica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27364	Gallus gallus	Species	Phasianidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2746	Apis cerana	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	Database[MetaboLights]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO27364	Gallus gallus	Species	Phasianidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5264	Dens draconis preparata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2746	Apis cerana	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8319	Massa fermentata hordei germinatus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO9788	Coffea arabica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2746	Apis cerana	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27364	Gallus gallus	Species	Phasianidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27364	Gallus gallus	Species	Phasianidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9788	Coffea arabica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2746	Apis cerana	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22132	Hordeum vulgare	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
NPO9788	NPC139037	Other	Seed	870	870	870	mg/100g	Database [DUKE]
NPO8541	NPC139037	Other	Seed	1805	1560	2050	mg/100g	Database [DUKE]

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC139037 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	1207
0.1-0.2	9377
0.2-0.3	16633
0.3-0.4	9703
0.4-0.5	3901
0.5-0.6	1553
0.6-0.7	191
0.7-0.8	100
0.8-0.85	14
0.85-0.9	17
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID

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 NPC139037 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1182
0.1-0.2	5440
0.2-0.3	1753
0.3-0.4	483
0.4-0.5	161
0.5-0.6	78
0.6-0.7	29
0.7-0.8	14
0.8-0.85	3
0.85-0.9	6
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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