NPASS Compound

Structure

NPC47474 OpenBabel06302215582D 26 28 0 0 1 0 0 0 0 0999 V2000 -3.4641 -3.0000 0.0000 C 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 -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 -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 -3.4641 2.0000 0.0000 C 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 -2.5981 1.5000 0.0000 O 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 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 -0.8660 -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 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 1.7321 -1.0000 0.0000 C 0 0 2 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 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 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 2.5981 0.5000 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 0.8660 -2.5000 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 13 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 11 1 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 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 12 26 1 0 0 0 0 13 14 1 0 0 0 0 15 14 1 6 0 0 0 15 16 1 0 0 0 0 15 22 1 0 0 0 0 16 17 1 0 0 0 0 16 25 1 1 0 0 0 17 18 1 0 0 0 0 17 24 1 6 0 0 0 18 19 1 0 0 0 0 18 23 1 1 0 0 0 19 20 1 6 0 0 0 19 22 1 0 0 0 0 20 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	370.09
Volume:	334.343
LogP:	-0.569
LogD:	-0.585
LogS:	-1.636
# Rotatable Bonds:	4
TPSA:	159.05
# H-Bond Aceptor:	10
# H-Bond Donor:	5
# Rings:	3
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.409
Synthetic Accessibility Score:	3.893
Fsp3:	0.438
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.908
MDCK Permeability:	3.427014235057868e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.294
Human Intestinal Absorption (HIA):	0.515
20% Bioavailability (F20%):	0.018
30% Bioavailability (F30%):	0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.264
Plasma Protein Binding (PPB):	54.14319610595703%
Volume Distribution (VD):	0.804
Pgp-substrate:	31.022140502929688%

ADMET: Metabolism

CYP1A2-inhibitor:	0.066
CYP1A2-substrate:	0.541
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.123
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.206
CYP2D6-inhibitor:	0.015
CYP2D6-substrate:	0.194
CYP3A4-inhibitor:	0.009
CYP3A4-substrate:	0.024

ADMET: Excretion

Clearance (CL):	3.717
Half-life (T1/2):	0.826

ADMET: Toxicity

hERG Blockers:	0.144
Human Hepatotoxicity (H-HT):	0.701
Drug-inuced Liver Injury (DILI):	0.958
AMES Toxicity:	0.308
Rat Oral Acute Toxicity:	0.043
Maximum Recommended Daily Dose:	0.009
Skin Sensitization:	0.335
Carcinogencity:	0.366
Eye Corrosion:	0.003
Eye Irritation:	0.017
Respiratory Toxicity:	0.028

Download Data

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

Natural Product: NPC47474

Natural Product ID:	NPC47474
*Common Name:**	RVWWDDKOKZXKCJ-ZOLYHUHESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RVWWDDKOKZXKCJ-ZOLYHUHESA-N
Standard InCHI:	InChI=1S/C16H18O10/c1-23-7-4-6-2-3-9(18)25-14(6)13(22)15(7)26-16-12(21)11(20)10(19)8(5-17)24-16/h2-4,8,10-12,16-17,19-22H,5H2,1H3/t8-,10-,11+,12-,16+/m1/s1
SMILES:	COc1cc2ccc(=O)oc2c(c1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11508953
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives [CHEMONTID:0001743] Coumarin 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
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[17637068]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18302336]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22432912]
NPO2330	Alchornea cordifolia	Species	Euphorbiaceae	Eukaryota	n.a.	stem	n.a.	PMID[26724423]
NPO2330	Alchornea cordifolia	Species	Euphorbiaceae	Eukaryota	n.a.	root	n.a.	PMID[26724423]
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12487	Juniperus horizontalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23772	Tetradium glabrifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10098	Glycosmis pseudoracemosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13848	Amomum daniellii	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12487	Juniperus horizontalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5398	Peucedanum oroselinum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16801	Cota tinctoria	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7521	Hygrophorus eburneus	Species	Hygrophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10098	Glycosmis pseudoracemosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11430	Inula grantioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15329	Rhizoplaca baranowii	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1759	Alexandrium excavatum	Species	Gonyaulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13647	Calcarisporium thermophilum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2330	Alchornea cordifolia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1109	Corydalis persica	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14947	Lathyrus tingitanus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6906	Atalantia wightii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3761	Plectosphaerella cucumerina	Species	Plectosphaerellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18873.2	Salmonella enterica subsp. enterica serovar bovismorbificans	Subspecies	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO23772	Tetradium glabrifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15145	Rauvolfia salicifolia	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3965	Corynanthe pachyceras	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14526	Plectranthus caninus	Species	Lamiaceae	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 NPC47474 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	409
0.1-0.2	1890
0.2-0.3	4702
0.3-0.4	9891
0.4-0.5	8045
0.5-0.6	4181
0.6-0.7	5314
0.7-0.8	5235
0.8-0.85	1957
0.85-0.9	823
0.9-0.95	244
0.95-1	6

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 NPC47474 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	378
0.1-0.2	973
0.2-0.3	2130
0.3-0.4	2648
0.4-0.5	1728
0.5-0.6	861
0.6-0.7	280
0.7-0.8	115
0.8-0.85	25
0.85-0.9	10
0.9-0.95	1
0.95-1	1

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