NPASS Compound

Structure

NPC242385 OpenBabel06302215132D 31 36 0 0 1 0 0 0 0 0999 V2000 -0.8431 1.5076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8429 0.4865 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6857 -0.0002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6856 -0.9735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8427 -1.4600 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8426 -2.4333 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8637 -2.4334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0004 -2.9198 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0004 -3.8937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8433 -4.3803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6866 -3.8936 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6865 -2.9197 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5294 -2.4330 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3727 -2.9196 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3728 -3.8935 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2162 -4.3801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0590 -3.8934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9251 -4.3933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0589 -2.9195 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9018 -2.4329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9018 -1.4596 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0589 -0.9730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2161 -1.4596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2161 -2.4329 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3500 -1.9329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7861 -0.9490 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8432 -2.4331 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8431 -1.4598 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0001 -0.9733 0.0000 N 0 3 3 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 -1.3530 -3.3176 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 30 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 29 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 6 31 1 0 0 0 0 8 9 1 6 0 0 0 8 27 1 0 0 0 0 9 10 1 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 15 1 0 0 0 0 12 13 1 6 0 0 0 12 27 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 24 1 0 0 0 0 15 16 1 1 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 6 0 0 0 19 24 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 26 1 6 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 6 0 0 0 27 28 1 1 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 M CHG 1 29 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	429.32
Volume:	458.94
LogP:	4.423
LogD:	4.401
LogS:	-4.144
# Rotatable Bonds:	0
TPSA:	60.77
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.613
Synthetic Accessibility Score:	5.011
Fsp3:	0.963
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:	-4.733
MDCK Permeability:	1.9673296264954843e-05
Pgp-inhibitor:	0.647
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.023
20% Bioavailability (F20%):	0.099
30% Bioavailability (F30%):	0.082

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.842
Plasma Protein Binding (PPB):	66.84464263916016%
Volume Distribution (VD):	3.67
Pgp-substrate:	13.200961112976074%

ADMET: Metabolism

CYP1A2-inhibitor:	0.048
CYP1A2-substrate:	0.286
CYP2C19-inhibitor:	0.031
CYP2C19-substrate:	0.891
CYP2C9-inhibitor:	0.104
CYP2C9-substrate:	0.052
CYP2D6-inhibitor:	0.074
CYP2D6-substrate:	0.852
CYP3A4-inhibitor:	0.484
CYP3A4-substrate:	0.517

ADMET: Excretion

Clearance (CL):	18.458
Half-life (T1/2):	0.152

ADMET: Toxicity

hERG Blockers:	0.184
Human Hepatotoxicity (H-HT):	0.379
Drug-inuced Liver Injury (DILI):	0.737
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.361
Maximum Recommended Daily Dose:	0.917
Skin Sensitization:	0.946
Carcinogencity:	0.625
Eye Corrosion:	0.882
Eye Irritation:	0.077
Respiratory Toxicity:	0.968

Download Data

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

Natural Product: NPC242385

Natural Product ID:	NPC242385
*Common Name:**	IQDIERHFZVCNRZ-YUYPDVIUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IQDIERHFZVCNRZ-YUYPDVIUSA-N
Standard InCHI:	InChI=1S/C27H43NO3/c1-15-4-7-25-27(3,31)21-6-5-17-18(20(21)14-28(25)13-15)11-22-19(17)12-24(30)23-10-16(29)8-9-26(22,23)2/h15-23,25,29,31H,4-14H2,1-3H3/p+1/t15-,16-,17+,18+,19-,20-,21-,22-,23+,25-,26+,27-/m0/s1
SMILES:	C[C@H]1CC[C@H]2[C@](C)([C@H]3CC[C@@H]4[C@@H](C[C@H]5[C@H]4CC(=O)[C@H]4C[C@H](CC[C@]54C)O)[C@@H]3C[NH+]2C1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	167691
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002724] Steroidal alkaloids [CHEMONTID:0002729] Cerveratrum-type alkaloids

*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
NPO14849	Fritillaria unibracteata	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10290	Fritillaria ebeiensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18644	Fritillaria walujewii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7844	Fritillaria hupehensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12273	Fritillaria delavayi	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5648	Fritillaria ussuriensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22292	Fritillaria przewalskii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1279	Fritillaria cirrhosa	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5648	Fritillaria ussuriensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1279	Fritillaria cirrhosa	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18644	Fritillaria walujewii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7844	Fritillaria hupehensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10290	Fritillaria ebeiensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12273	Fritillaria delavayi	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14849	Fritillaria unibracteata	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22292	Fritillaria przewalskii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5648	Fritillaria ussuriensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14849	Fritillaria unibracteata	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22292	Fritillaria przewalskii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12556	Fritillaria verticillata	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12273	Fritillaria delavayi	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18644	Fritillaria walujewii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14135	Fritillaria prezewalskii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7844	Fritillaria hupehensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14849	Fritillaria unibracteata	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4487	Fritillaria thunbergii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12556	Fritillaria verticillata	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5648	Fritillaria ussuriensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18644	Fritillaria walujewii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22292	Fritillaria przewalskii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1279	Fritillaria cirrhosa	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12273	Fritillaria delavayi	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25808	Fritillaria taipaiensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25253	Corydalis caseana	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18644	Fritillaria walujewii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22292	Fritillaria przewalskii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25300	Senecio ruderalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26833	Ichnocarpus frutescens	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7844	Fritillaria hupehensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28973	Rhytisma fulvum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26096	Jatropha multiloba	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23477	Anabaena torulosa	Species	0stocaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5648	Fritillaria ussuriensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26065	Elaeocarpus archboldianus	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1279	Fritillaria cirrhosa	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12556	Fritillaria verticillata	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25941	Garcinia yunnanensis	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26340	Chione venosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26765	Litsea pedunculata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25808	Fritillaria taipaiensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12273	Fritillaria delavayi	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26282	Phebalium ovatifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10290	Fritillaria ebeiensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25749	Kielmeyera argentea	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14849	Fritillaria unibracteata	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4487	Fritillaria thunbergii	Species	Liliaceae	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 NPC242385 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	153
0.1-0.2	2514
0.2-0.3	18165
0.3-0.4	11466
0.4-0.5	6221
0.5-0.6	3633
0.6-0.7	503
0.7-0.8	36
0.8-0.85	2
0.85-0.9	1
0.9-0.95	1
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 NPC242385 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	93
0.1-0.2	1335
0.2-0.3	4741
0.3-0.4	2156
0.4-0.5	602
0.5-0.6	161
0.6-0.7	57
0.7-0.8	4
0.8-0.85	1
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