NPASS Compound

Structure

NPC44220 OpenBabel06302215512D 41 45 0 0 1 0 0 0 0 0999 V2000 3.4641 -2.0000 0.0000 C 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 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 1 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 0.8660 1.5000 0.0000 C 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 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 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 1.0000 0.0000 C 0 0 0 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 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 1 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 7.7942 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7942 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.9282 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.9282 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -3.5000 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 8.6603 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 O 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 0.0000 4.0000 0.0000 O 0 0 0 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 0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 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 -1.7321 -0.0000 0.0000 C 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 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 15 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 13 1 0 0 0 0 4 3 1 6 0 0 0 4 5 1 0 0 0 0 4 31 1 0 0 0 0 5 10 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 29 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 9 28 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 16 1 0 0 0 0 17 16 1 1 0 0 0 17 18 1 0 0 0 0 17 24 1 0 0 0 0 18 19 1 0 0 0 0 18 27 1 6 0 0 0 19 20 1 0 0 0 0 19 26 1 1 0 0 0 20 21 1 0 0 0 0 20 25 1 6 0 0 0 21 22 1 1 0 0 0 21 24 1 0 0 0 0 22 23 1 0 0 0 0 29 30 1 0 0 0 0 31 32 1 0 0 0 0 31 38 1 1 0 0 0 32 33 1 0 0 0 0 32 41 1 6 0 0 0 33 34 1 0 0 0 0 33 40 1 1 0 0 0 34 35 1 0 0 0 0 34 39 1 6 0 0 0 35 36 1 1 0 0 0 35 38 1 0 0 0 0 36 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	580.18
Volume:	537.374
LogP:	-0.523
LogD:	-0.336
LogS:	-2.286
# Rotatable Bonds:	6
TPSA:	250.22
# H-Bond Aceptor:	14
# H-Bond Donor:	11
# Rings:	5
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.136
Synthetic Accessibility Score:	4.804
Fsp3:	0.481
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:	-6.447
MDCK Permeability:	1.3590008165920153e-05
Pgp-inhibitor:	0.005
Pgp-substrate:	0.955
Human Intestinal Absorption (HIA):	0.997
20% Bioavailability (F20%):	0.366
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.202
Plasma Protein Binding (PPB):	76.4113540649414%
Volume Distribution (VD):	0.423
Pgp-substrate:	19.449081420898438%

ADMET: Metabolism

CYP1A2-inhibitor:	0.068
CYP1A2-substrate:	0.009
CYP2C19-inhibitor:	0.007
CYP2C19-substrate:	0.081
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.081
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.127
CYP3A4-inhibitor:	0.004
CYP3A4-substrate:	0.002

ADMET: Excretion

Clearance (CL):	1.023
Half-life (T1/2):	0.771

ADMET: Toxicity

hERG Blockers:	0.234
Human Hepatotoxicity (H-HT):	0.05
Drug-inuced Liver Injury (DILI):	0.886
AMES Toxicity:	0.33
Rat Oral Acute Toxicity:	0.008
Maximum Recommended Daily Dose:	0.001
Skin Sensitization:	0.824
Carcinogencity:	0.027
Eye Corrosion:	0.003
Eye Irritation:	0.026
Respiratory Toxicity:	0.011

Download Data

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

Natural Product: NPC44220

Natural Product ID:	NPC44220
*Common Name:**	MNAYRSRTNMVAPR-ZHVWOXMGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MNAYRSRTNMVAPR-ZHVWOXMGSA-N
Standard InCHI:	InChI=1S/C27H32O14/c28-6-9-4-11-16(26-24(37)22(35)19(32)14(7-29)39-26)10-2-1-3-13(18(10)21(34)17(11)12(31)5-9)40-27-25(38)23(36)20(33)15(8-30)41-27/h1-5,14-16,19-20,22-33,35-38H,6-8H2/t14-,15-,16+,19-,20-,22+,23+,24-,25-,26+,27-/m1/s1
SMILES:	c1cc2[C@@H](c3cc(cc(c3C(=O)c2c(c1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)CO)[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	442727
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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO27239	Maclura tinctoria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11087602]
NPO27239	Maclura tinctoria	Species	Moraceae	Eukaryota	n.a.	stem	n.a.	PMID[12932124]
NPO27239	Maclura tinctoria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12932124]
NPO27164	Aspergillus alliaceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29517220]
NPO27164	Aspergillus alliaceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3417561]
NPO3980	Frangula purshiana	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19050	Garcinia polyantha	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27140	Amanita phalloides	Species	Amanitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27454	Turbo cornutus	Species	Turbinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27239	Maclura tinctoria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27164	Aspergillus alliaceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26972	Baccharis potosina	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27873	Ravenia spectabilis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17822	Fridericia triplinervia	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27564	Stevia berlandieri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10239	Magnolia figo	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27140	Amanita phalloides	Species	Amanitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24629	Achromobacter denitrificans	Species	Alcaligenaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO3980	Frangula purshiana	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27790	Delia arenicola	Species	Anthomyiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19050	Garcinia polyantha	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4132	Cranfillia fluviatilis	Species	Blechnaceae	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

☑ 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 NPC44220 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	425
0.1-0.2	1564
0.2-0.3	3221
0.3-0.4	7810
0.4-0.5	9635
0.5-0.6	5712
0.6-0.7	6233
0.7-0.8	6847
0.8-0.85	1016
0.85-0.9	198
0.9-0.95	34
0.95-1	2

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 NPC44220 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	367
0.1-0.2	876
0.2-0.3	1665
0.3-0.4	2632
0.4-0.5	2021
0.5-0.6	1032
0.6-0.7	404
0.7-0.8	125
0.8-0.85	25
0.85-0.9	1
0.9-0.95	2
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