NPASS Compound

Structure

NPC101785 OpenBabel06302215392D 31 36 0 0 1 0 0 0 0 0999 V2000 -1.5068 0.8699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5023 0.8699 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 1.7399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0045 1.7399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5068 0.8699 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0760 1.6533 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7655 2.6087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9969 1.3541 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9969 0.3858 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8356 -0.0991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6753 1.3534 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.5151 1.8376 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.3542 1.3525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1940 1.8367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1946 2.8060 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.0341 3.2897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0344 4.2586 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.1952 4.7437 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.3557 4.2600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3554 3.2912 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.4897 3.7917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5157 2.8070 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.6770 3.2919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8372 2.8077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8367 1.8383 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.9709 2.3388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1959 5.7437 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.9006 4.7582 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0760 0.0865 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0045 0.0000 0.0000 O 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 31 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 29 1 0 0 0 0 5 6 1 0 0 0 0 5 30 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 25 1 0 0 0 0 9 10 1 0 0 0 0 9 29 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 25 1 0 0 0 0 12 13 1 0 0 0 0 12 22 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 20 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 28 1 0 0 0 0 18 19 1 0 0 0 0 18 27 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 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 25 26 1 0 0 0 0 30 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	432.32
Volume:	459.37
LogP:	5.541
LogD:	4.718
LogS:	-5.446
# Rotatable Bonds:	0
TPSA:	58.92
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.579
Synthetic Accessibility Score:	5.384
Fsp3:	1.0
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:	-4.76
MDCK Permeability:	1.7036016288329847e-05
Pgp-inhibitor:	0.995
Pgp-substrate:	0.981
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.591
30% Bioavailability (F30%):	0.3

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.141
Plasma Protein Binding (PPB):	76.7775650024414%
Volume Distribution (VD):	1.755
Pgp-substrate:	6.750737190246582%

ADMET: Metabolism

CYP1A2-inhibitor:	0.033
CYP1A2-substrate:	0.434
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.613
CYP2C9-inhibitor:	0.049
CYP2C9-substrate:	0.043
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.177
CYP3A4-inhibitor:	0.406
CYP3A4-substrate:	0.187

ADMET: Excretion

Clearance (CL):	17.305
Half-life (T1/2):	0.219

ADMET: Toxicity

hERG Blockers:	0.995
Human Hepatotoxicity (H-HT):	0.207
Drug-inuced Liver Injury (DILI):	0.913
AMES Toxicity:	0.097
Rat Oral Acute Toxicity:	0.114
Maximum Recommended Daily Dose:	0.126
Skin Sensitization:	0.975
Carcinogencity:	0.469
Eye Corrosion:	0.943
Eye Irritation:	0.542
Respiratory Toxicity:	0.96

Download Data

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

Natural Product: NPC101785

Natural Product ID:	NPC101785
*Common Name:**	FWCXELAAYFYCSR-HJXRQQMRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FWCXELAAYFYCSR-HJXRQQMRSA-N
Standard InCHI:	InChI=1S/C27H44O4/c1-15-7-10-27(30-14-15)16(2)24-23(31-27)12-20-18-6-5-17-11-21(28)22(29)13-26(17,4)19(18)8-9-25(20,24)3/h15-24,28-29H,5-14H2,1-4H3/t15-,16-,17-,18+,19-,20-,21+,22+,23-,24-,25-,26-,27+/m0/s1
SMILES:	C[C@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC[C@H]6C[C@H]([C@@H](C[C@]6(C)[C@H]5CC[C@]34C)O)O)O2)OC1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	12304409
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11599360]
NPO24670	Casearia lucida	Species	Salicaceae	Eukaryota	Barks	n.a.	n.a.	PMID[11858738]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[19757853]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21370894]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	seed	n.a.	PMID[21381697]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[8482946]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO24267	Paeonia veitchii	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO14127	Veratrum eschscholtzii	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4857	Veratrum fimbriatum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24267	Paeonia veitchii	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24267	Paeonia veitchii	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17037	Dichapetalum toxicarium	Species	Dichapetalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24764	Amphius huxleyi	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO22909	Echinogorgia flora	Species	Paramuriceidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24579	Rhamnus procumbens	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4857	Veratrum fimbriatum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14127	Veratrum eschscholtzii	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24961	Teucrium lucidum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24670	Casearia lucida	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24267	Paeonia veitchii	Species	Paeoniaceae	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 NPC101785 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	473
0.1-0.2	4588
0.2-0.3	14210
0.3-0.4	10570
0.4-0.5	5239
0.5-0.6	4326
0.6-0.7	2255
0.7-0.8	798
0.8-0.85	93
0.85-0.9	130
0.9-0.95	7
0.95-1	8

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 NPC101785 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	467
0.1-0.2	4385
0.2-0.3	3062
0.3-0.4	660
0.4-0.5	298
0.5-0.6	208
0.6-0.7	63
0.7-0.8	3
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
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