NPASS Compound

Structure

NPC23733 OpenBabel06302215512D 30 35 0 0 1 0 0 0 0 0999 V2000 0.8436 -1.5086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8435 -0.4868 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6868 0.0002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6867 0.9741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8432 1.4609 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8431 2.4348 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7279 2.9458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0004 2.9217 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0004 3.8962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8438 4.3831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6877 3.8961 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6876 2.9216 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5310 2.4345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3749 2.9215 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3750 3.8960 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2189 4.3829 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0622 3.8959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9283 4.3958 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0622 2.9214 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9056 2.4344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9056 1.4605 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0622 0.9736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2188 1.4605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2188 2.4344 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3527 1.9344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7905 0.9497 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8437 2.4346 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8436 1.4607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0001 0.9739 0.0000 N 0 0 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 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 0 0 0 0 6 8 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 END $$$$

Physi-Chem Properties

Molecular Weight:	126.03
Volume:	122.237
LogP:	-0.448
LogD:	-0.36
LogS:	-0.915
# Rotatable Bonds:	1
TPSA:	43.37
# H-Bond Aceptor:	3
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.364
Synthetic Accessibility Score:	4.492
Fsp3:	0.333
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.565
MDCK Permeability:	1.751021045492962e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.099

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.733
Plasma Protein Binding (PPB):	49.2286376953125%
Volume Distribution (VD):	0.714
Pgp-substrate:	63.102210998535156%

ADMET: Metabolism

CYP1A2-inhibitor:	0.036
CYP1A2-substrate:	0.44
CYP2C19-inhibitor:	0.029
CYP2C19-substrate:	0.318
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.078
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.143
CYP3A4-inhibitor:	0.018
CYP3A4-substrate:	0.268

ADMET: Excretion

Clearance (CL):	6.324
Half-life (T1/2):	0.862

ADMET: Toxicity

hERG Blockers:	0.034
Human Hepatotoxicity (H-HT):	0.125
Drug-inuced Liver Injury (DILI):	0.47
AMES Toxicity:	0.952
Rat Oral Acute Toxicity:	0.194
Maximum Recommended Daily Dose:	0.367
Skin Sensitization:	0.96
Carcinogencity:	0.892
Eye Corrosion:	0.709
Eye Irritation:	0.887
Respiratory Toxicity:	0.808

Download Data

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

Natural Product: NPC23733

Natural Product ID:	NPC23733
*Common Name:**	MWBJDDYEYGDWCZ-PZCFKJIRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MWBJDDYEYGDWCZ-PZCFKJIRSA-N
Standard InCHI:	InChI=1S/C27H43NO2/c1-15-4-7-25-16(2)18-5-6-19-20(22(18)14-28(25)13-15)11-23-21(19)12-26(30)24-10-17(29)8-9-27(23,24)3/h15-25,29H,4-14H2,1-3H3/t15-,16?,17-,18+,19+,20+,21-,22+,23-,24+,25-,27+/m0/s1
SMILES:	C[C@H]1CC[C@H]2C(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]3CN2C1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102062796
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
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]
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]
NPO1279	Fritillaria cirrhosa	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14849	Fritillaria unibracteata	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7844	Fritillaria hupehensis	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]
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]
NPO11228	Fritillaria pallidiflora	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]
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]
NPO25334	Bulbus fritillariae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO12273	Fritillaria delavayi	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]
NPO11228	Fritillaria pallidiflora	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]
NPO14849	Fritillaria unibracteata	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]
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[TM-MC]
NPO7844	Fritillaria hupehensis	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]
NPO1279	Fritillaria cirrhosa	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]
NPO18644	Fritillaria walujewii	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]
NPO5648	Fritillaria ussuriensis	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]
NPO14135	Fritillaria prezewalskii	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]
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[UNPD]
NPO14849	Fritillaria unibracteata	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]
NPO18644	Fritillaria walujewii	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]
NPO7844	Fritillaria hupehensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5648	Fritillaria ussuriensis	Species	Liliaceae	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]
NPO22292	Fritillaria przewalskii	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25808	Fritillaria taipaiensis	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 NPC23733 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	154
0.1-0.2	2259
0.2-0.3	17464
0.3-0.4	11268
0.4-0.5	5694
0.5-0.6	4682
0.6-0.7	1051
0.7-0.8	116
0.8-0.85	3
0.85-0.9	3
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 NPC23733 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	103
0.1-0.2	1552
0.2-0.3	4847
0.3-0.4	1867
0.4-0.5	500
0.5-0.6	207
0.6-0.7	51
0.7-0.8	21
0.8-0.85	2
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