NPASS Compound

Structure

NPC312904 OpenBabel06302215242D 28 31 0 0 1 0 0 0 0 0999 V2000 -1.6969 -0.9459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8612 -1.4431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0128 -0.9681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8192 -1.4632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6640 -0.9902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4948 -1.4855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3499 -1.0125 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3627 -0.0444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2122 0.4399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0425 -0.0665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0298 -1.0346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1865 -1.5078 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.1738 -2.4747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3301 -2.9470 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0047 -2.9691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8484 -2.4968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2251 1.4138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3769 1.9035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5334 1.4361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5205 0.4623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6768 -0.0221 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8448 0.4730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8356 0.4973 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6841 0.0222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7058 1.9311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9426 1.3415 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3854 2.8739 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 23 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 21 1 0 0 0 0 5 6 1 0 0 0 0 7 6 1 1 0 0 0 7 8 1 0 0 0 0 7 12 1 0 0 0 0 8 20 2 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 17 2 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 28 1 0 0 0 0 19 20 1 0 0 0 0 19 26 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	385.15
Volume:	382.829
LogP:	2.928
LogD:	3.169
LogS:	-3.791
# Rotatable Bonds:	5
TPSA:	77.46
# H-Bond Aceptor:	7
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.874
Synthetic Accessibility Score:	3.123
Fsp3:	0.381
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:	-4.777
MDCK Permeability:	2.5498640752630308e-05
Pgp-inhibitor:	0.439
Pgp-substrate:	0.929
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.012
30% Bioavailability (F30%):	0.343

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.142
Plasma Protein Binding (PPB):	86.97538757324219%
Volume Distribution (VD):	0.682
Pgp-substrate:	12.426279067993164%

ADMET: Metabolism

CYP1A2-inhibitor:	0.114
CYP1A2-substrate:	0.938
CYP2C19-inhibitor:	0.292
CYP2C19-substrate:	0.891
CYP2C9-inhibitor:	0.084
CYP2C9-substrate:	0.84
CYP2D6-inhibitor:	0.121
CYP2D6-substrate:	0.776
CYP3A4-inhibitor:	0.43
CYP3A4-substrate:	0.906

ADMET: Excretion

Clearance (CL):	5.514
Half-life (T1/2):	0.627

ADMET: Toxicity

hERG Blockers:	0.017
Human Hepatotoxicity (H-HT):	0.523
Drug-inuced Liver Injury (DILI):	0.79
AMES Toxicity:	0.344
Rat Oral Acute Toxicity:	0.264
Maximum Recommended Daily Dose:	0.962
Skin Sensitization:	0.053
Carcinogencity:	0.015
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.951

Download Data

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

Natural Product: NPC312904

Natural Product ID:	NPC312904
*Common Name:**	HUNDOXNVOAEPPU-AWEZNQCLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HUNDOXNVOAEPPU-AWEZNQCLSA-N
Standard InCHI:	InChI=1S/C21H23NO6/c1-25-16-9-12-7-14-18-11(5-6-22(14)21(24)28-4)8-15(23)20(27-3)19(18)13(12)10-17(16)26-2/h8-10,14,23H,5-7H2,1-4H3/t14-/m0/s1
SMILES:	COc1cc2C[C@H]3c4c(CCN3C(=O)OC)cc(c(c4-c2cc1OC)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0000381] Aporphines

*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
NPO27883	Bursera simaruba	Species	Burseraceae	Eukaryota	Resin	n.a.	n.a.	PMID[1294696]
NPO28935	Ericameria laricifolia	Species	Asteraceae	Eukaryota	n.a.	Sonoran Desert	n.a.	PMID[15043404]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	n.a.	aerial part	n.a.	PMID[18991207]
NPO27883	Bursera simaruba	Species	Burseraceae	Eukaryota	n.a.	bark	n.a.	PMID[19329133]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	essential oil	Tibet	n.a.	PMID[20944522]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	Twigs	n.a.	n.a.	PMID[28541690]
NPO27903	Delphinium denudatum	Species	Ranunculaceae	Eukaryota	n.a.	root	n.a.	PMID[9170290]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26851	Eupatorium rebaudianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27903	Delphinium denudatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27724	Polygala senega	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1079	Vachellia karroo	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18780	Diplacus aurantiacus	Species	Phrymaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26851	Eupatorium rebaudianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27724	Polygala senega	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27903	Delphinium denudatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27724	Polygala senega	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27724	Polygala senega	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29307	Loranthus longiflorus	Species	Loranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27724	Polygala senega	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27883	Bursera simaruba	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16079	Cephalaria leucantha	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29411	Streptomyces nigrescens	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO26851	Eupatorium rebaudianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26549	Polanisia trachysperma	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28959	Cissus quadrangularis	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1079	Vachellia karroo	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29377	Callistemon speciosus	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18780	Diplacus aurantiacus	Species	Phrymaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29218	Ramalina farinacea	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28549	Mentha incana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29144	Ormosia fordiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27256	Solanum boerhaavii	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28935	Ericameria laricifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27562	Coleus wulfenioides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27903	Delphinium denudatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO862	Podocarpus elatus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29110	Litsea cubeba	Species	Lauraceae	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 NPC312904 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	276
0.1-0.2	1442
0.2-0.3	6480
0.3-0.4	11708
0.4-0.5	5306
0.5-0.6	11547
0.6-0.7	4885
0.7-0.8	690
0.8-0.85	216
0.85-0.9	103
0.9-0.95	34
0.95-1	10

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 NPC312904 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	185
0.1-0.2	716
0.2-0.3	1091
0.3-0.4	2009
0.4-0.5	2607
0.5-0.6	1766
0.6-0.7	612
0.7-0.8	145
0.8-0.85	19
0.85-0.9	0
0.9-0.95	0
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