NPASS Compound

Structure

NPC274533 OpenBabel06302216122D 24 26 0 0 1 0 0 0 0 0999 V2000 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 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 -4.3301 1.5000 0.0000 O 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 -2.5981 1.5000 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 0.0000 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 -3.4641 0.0000 0.0000 C 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 -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 1.7321 -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 1 11 1 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 5 6 1 0 0 0 0 6 11 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 13 1 0 0 0 0 9 10 2 0 0 0 0 9 12 1 0 0 0 0 10 11 1 0 0 0 0 14 13 1 1 0 0 0 14 15 1 0 0 0 0 14 21 1 0 0 0 0 15 16 1 0 0 0 0 15 24 1 6 0 0 0 16 17 1 0 0 0 0 16 23 1 1 0 0 0 17 18 1 0 0 0 0 17 22 1 6 0 0 0 18 19 1 1 0 0 0 18 21 1 0 0 0 0 19 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	382.21
Volume:	408.776
LogP:	4.871
LogD:	4.096
LogS:	-5.758
# Rotatable Bonds:	4
TPSA:	55.76
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.48
Synthetic Accessibility Score:	4.388
Fsp3:	0.542
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.694
MDCK Permeability:	2.65903818217339e-05
Pgp-inhibitor:	0.918
Pgp-substrate:	0.712
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.04
30% Bioavailability (F30%):	0.15

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.316
Plasma Protein Binding (PPB):	93.6227035522461%
Volume Distribution (VD):	1.743
Pgp-substrate:	3.90867280960083%

ADMET: Metabolism

CYP1A2-inhibitor:	0.139
CYP1A2-substrate:	0.141
CYP2C19-inhibitor:	0.334
CYP2C19-substrate:	0.151
CYP2C9-inhibitor:	0.527
CYP2C9-substrate:	0.177
CYP2D6-inhibitor:	0.279
CYP2D6-substrate:	0.278
CYP3A4-inhibitor:	0.69
CYP3A4-substrate:	0.269

ADMET: Excretion

Clearance (CL):	6.212
Half-life (T1/2):	0.063

ADMET: Toxicity

hERG Blockers:	0.008
Human Hepatotoxicity (H-HT):	0.091
Drug-inuced Liver Injury (DILI):	0.766
AMES Toxicity:	0.048
Rat Oral Acute Toxicity:	0.442
Maximum Recommended Daily Dose:	0.309
Skin Sensitization:	0.289
Carcinogencity:	0.151
Eye Corrosion:	0.004
Eye Irritation:	0.073
Respiratory Toxicity:	0.936

Download Data

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

Natural Product: NPC274533

Natural Product ID:	NPC274533
*Common Name:**	WNBCMONIPIJTSB-TVKJYDDYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WNBCMONIPIJTSB-TVKJYDDYSA-N
Standard InCHI:	InChI=1S/C15H16O9/c16-5-10-12(19)13(20)14(21)15(24-10)23-9-4-8-6(3-7(9)17)1-2-11(18)22-8/h1-4,10,12-17,19-21H,5H2/t10-,12-,13+,14-,15-/m1/s1
SMILES:	c1cc(=O)oc2cc(c(cc12)O)O[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:	442101
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
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18341288]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18460139]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	Roots	n.a.		Database[FooDB]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	Flower	n.a.	n.a.	Database[FooDB]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO15057	Isodon gesneroides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO581	Conyza bonariensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21924	Althaea officinalis	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2161	Strychnos ledermannii	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11478	Aniba duckei	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO245	Euphorbia biglandulosa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15057	Isodon gesneroides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO513	Agathosma scaberula	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21924	Althaea officinalis	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9865	Cichorium intybus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11117	Xerula melanotricha	Species	Physalacriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12034	Dictamnus gymnostylis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29531	Lupinus cosentinii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13123	Balanophora harlandii	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO581	Conyza bonariensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1584	Tolypothrix tjipanasensis	Species	Tolypothrichaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO28881	Virola sebifera	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17549	Polemonium caeruleum	Species	Polemoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16888	Sophora davidii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4892	Viburnum davidii	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11895	Nama johnstonii	Species	Namaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17117	Diaporthe amygdali	Species	Diaporthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7201	Rhodopila globiformis	Species	Acetobacteraceae	Bacteria	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 NPC274533 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	1942
0.2-0.3	4799
0.3-0.4	10075
0.4-0.5	7833
0.5-0.6	4121
0.6-0.7	5248
0.7-0.8	5322
0.8-0.85	1976
0.85-0.9	770
0.9-0.95	182
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 NPC274533 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	392
0.1-0.2	967
0.2-0.3	2164
0.3-0.4	2624
0.4-0.5	1728
0.5-0.6	854
0.6-0.7	268
0.7-0.8	119
0.8-0.85	22
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