NPASS Compound

Structure

NPC283747 OpenBabel06302215342D 31 35 0 0 1 0 0 0 0 0999 V2000 -1.7166 -1.1460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0181 -2.0747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9731 -2.2779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3646 -2.8001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6660 -3.7288 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4096 -2.5968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1081 -1.6681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8469 -1.4648 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5004 -2.1903 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8466 -0.4885 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6918 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6915 0.9773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9768 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0006 1.9768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8469 1.4652 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8472 2.4426 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6938 2.9311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5401 2.4421 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3861 2.9306 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3864 3.9306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2319 2.4417 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2316 1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3856 0.9758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5398 1.4648 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5396 0.4873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6932 0.9763 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6930 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8463 -0.4889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0003 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0981 2.9413 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 2 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 6 0 0 0 10 8 1 6 0 0 0 10 11 1 0 0 0 0 10 29 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 29 1 0 0 0 0 13 14 1 1 0 0 0 13 15 1 0 0 0 0 15 16 1 1 0 0 0 15 26 1 0 0 0 0 16 17 1 0 0 0 0 18 17 1 6 0 0 0 18 19 1 0 0 0 0 18 24 1 0 0 0 0 19 20 1 1 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 21 31 1 1 0 0 0 22 23 1 0 0 0 0 24 23 1 1 0 0 0 24 26 1 0 0 0 0 24 25 1 0 0 0 0 26 25 1 6 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	428.37
Volume:	482.302
LogP:	6.099
LogD:	5.165
LogS:	-5.757
# Rotatable Bonds:	5
TPSA:	37.3
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.51
Synthetic Accessibility Score:	5.491
Fsp3:	0.966
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.922
MDCK Permeability:	1.3903269973525312e-05
Pgp-inhibitor:	0.767
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.994
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.1
Plasma Protein Binding (PPB):	94.2878646850586%
Volume Distribution (VD):	1.435
Pgp-substrate:	1.3533602952957153%

ADMET: Metabolism

CYP1A2-inhibitor:	0.049
CYP1A2-substrate:	0.553
CYP2C19-inhibitor:	0.074
CYP2C19-substrate:	0.959
CYP2C9-inhibitor:	0.198
CYP2C9-substrate:	0.281
CYP2D6-inhibitor:	0.031
CYP2D6-substrate:	0.572
CYP3A4-inhibitor:	0.919
CYP3A4-substrate:	0.849

ADMET: Excretion

Clearance (CL):	8.765
Half-life (T1/2):	0.121

ADMET: Toxicity

hERG Blockers:	0.874
Human Hepatotoxicity (H-HT):	0.33
Drug-inuced Liver Injury (DILI):	0.799
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.183
Maximum Recommended Daily Dose:	0.037
Skin Sensitization:	0.916
Carcinogencity:	0.366
Eye Corrosion:	0.051
Eye Irritation:	0.046
Respiratory Toxicity:	0.953

Download Data

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

Natural Product: NPC283747

Natural Product ID:	NPC283747
*Common Name:**	ZRKCGAGDWUJBNN-JLPNRFMESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZRKCGAGDWUJBNN-JLPNRFMESA-N
Standard InCHI:	InChI=1S/C29H48O2/c1-18(2)23(30)9-7-19(3)21-11-13-27(6)25-10-8-22-20(4)24(31)12-14-28(22)17-29(25,28)16-15-26(21,27)5/h18-22,24-25,31H,7-17H2,1-6H3/t19-,20+,21-,22+,24-,25+,26-,27+,28-,29+/m1/s1
SMILES:	CC(C)C(=O)CC[C@@H](C)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@H]4[C@H](C)[C@@H](CC[C@]54C[C@@]35CC[C@]12C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002321] Cycloartanols and derivatives

*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
NPO18252	Cajanus cajan	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[136119]
NPO16746	Lendenfeldia frondosa	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[1402955]
NPO18252	Cajanus cajan	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO18252	Cajanus cajan	Species	Fabaceae	Eukaryota	n.a.	leaf	n.a.	PMID[24680612]
NPO18252	Cajanus cajan	Species	Fabaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO18252	Cajanus cajan	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO18252	Cajanus cajan	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO19073	Uncaria lancifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16040	Pristimera indica	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18659	Prunus japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18252	Cajanus cajan	Species	Fabaceae	Eukaryota	Seeds	n.a.		Database[Phenol-Explorer]
NPO16040	Pristimera indica	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18659	Prunus japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11777	Pluchea sericea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3022	Toxicopueraria peduncularis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19073	Uncaria lancifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18659	Prunus japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18659	Prunus japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16746	Lendenfeldia frondosa	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11777	Pluchea sericea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18659	Prunus japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28174	Poterium sanguisorba	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13673	Ipomoea muelleri	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18008	Viburnum rhytidophyllum	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3022	Toxicopueraria peduncularis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6425	Betula davurica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18497	Euphorbia aellenii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19229	Aniba parviflora	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15430	Abutilon grandiflorum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14953	Thapsia transtagana	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17440	Thryptomene kochii	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18830	Valeriana cardamines	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19753	Liabum bourgeaui	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14711.1	Arabidopsis lyrata subsp. lyrata	Subspecies	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16040	Pristimera indica	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19073	Uncaria lancifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23370	Sticta mougeotiana	Species	Lobariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29099	Sinocrassula indica	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19692	Quercus variabilis	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11042	Lecanora sordida	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18252	Cajanus cajan	Species	Fabaceae	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 NPC283747 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	326
0.1-0.2	3381
0.2-0.3	15072
0.3-0.4	9917
0.4-0.5	5463
0.5-0.6	5053
0.6-0.7	2567
0.7-0.8	740
0.8-0.85	108
0.85-0.9	48
0.9-0.95	20
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 NPC283747 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	371
0.1-0.2	3658
0.2-0.3	3634
0.3-0.4	906
0.4-0.5	213
0.5-0.6	199
0.6-0.7	131
0.7-0.8	16
0.8-0.85	4
0.85-0.9	14
0.9-0.95	4
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