NPASS Compound

Structure

CID312637 OpenBabel06191716122D 31 35 0 0 1 0 0 0 0 0999 V2000 6.5218 4.6233 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6247 0.5746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4136 0.9593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8766 -0.5061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1686 1.2620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9780 3.9360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3823 2.9295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5370 3.4175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4045 3.1466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8453 -1.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6912 0.0003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 -0.9762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5370 0.4887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6914 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.9534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3452 2.9427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9484 3.8340 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2279 1.4659 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6911 -0.9757 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8459 1.4651 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3829 1.9538 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6917 1.9535 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8459 0.4884 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8458 0.4883 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.8014 2.2553 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8458 1.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5370 1.4654 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.7717 2.1533 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.5571 -1.4757 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7118 1.9651 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5 29 1 0 0 0 0 6 9 1 0 0 0 0 6 17 1 0 0 0 0 7 8 1 0 0 0 0 7 21 1 0 0 0 0 8 22 1 0 0 0 0 9 25 1 0 0 0 0 10 12 1 0 0 0 0 10 19 1 0 0 0 0 11 13 1 0 0 0 0 11 23 1 0 0 0 0 12 28 1 0 0 0 0 13 27 1 0 0 0 0 14 19 1 0 0 0 0 14 24 1 0 0 0 0 15 26 1 0 0 0 0 16 17 1 0 0 0 0 16 29 1 0 0 0 0 17 1 1 1 0 0 0 18 2 1 1 0 0 0 18 21 1 0 0 0 0 19 30 1 6 0 0 0 20 15 1 1 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 21 27 1 1 0 0 0 22 27 1 6 0 0 0 23 28 1 6 0 0 0 24 26 1 0 0 0 0 24 28 1 6 0 0 0 25 18 1 6 0 0 0 25 29 1 0 0 0 0 26 31 2 0 0 0 0 27 3 1 6 0 0 0 28 4 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	429.36
Volume:	476.003
LogP:	5.235
LogD:	4.762
LogS:	-4.405
# Rotatable Bonds:	2
TPSA:	40.54
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.625
Synthetic Accessibility Score:	4.791
Fsp3:	0.964
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:	-4.726
MDCK Permeability:	1.1368587365723215e-05
Pgp-inhibitor:	0.996
Pgp-substrate:	0.981
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.806
30% Bioavailability (F30%):	0.67

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.703
Plasma Protein Binding (PPB):	72.24365234375%
Volume Distribution (VD):	2.277
Pgp-substrate:	8.963756561279297%

ADMET: Metabolism

CYP1A2-inhibitor:	0.053
CYP1A2-substrate:	0.231
CYP2C19-inhibitor:	0.058
CYP2C19-substrate:	0.956
CYP2C9-inhibitor:	0.107
CYP2C9-substrate:	0.044
CYP2D6-inhibitor:	0.822
CYP2D6-substrate:	0.865
CYP3A4-inhibitor:	0.788
CYP3A4-substrate:	0.775

ADMET: Excretion

Clearance (CL):	20.761
Half-life (T1/2):	0.077

ADMET: Toxicity

hERG Blockers:	0.975
Human Hepatotoxicity (H-HT):	0.374
Drug-inuced Liver Injury (DILI):	0.85
AMES Toxicity:	0.021
Rat Oral Acute Toxicity:	0.847
Maximum Recommended Daily Dose:	0.868
Skin Sensitization:	0.954
Carcinogencity:	0.472
Eye Corrosion:	0.962
Eye Irritation:	0.058
Respiratory Toxicity:	0.962

Download Data

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

Natural Product: NPC312637

Natural Product ID:	NPC312637
*Common Name:**	Puqietinone
IUPAC Name:	(3S,5S,8S,9S,10R,13S,14S,17S)-17-[(1S)-1-[(2S,5R)-1,5-dimethylpiperidin-2-yl]ethyl]-3-hydroxy-10,13-dimethyl-1,2,3,4,5,7,8,9,11,12,14,15,16,17-tetradecahydrocyclopenta[a]phenanthren-6-one
Synonyms:	Puqietinone
Standard InCHIKey:	HEOBUSMYCWXIQQ-OXZWOSNHSA-N
Standard InCHI:	InChI=1S/C28H47NO2/c1-17-6-9-25(29(5)16-17)18(2)21-7-8-22-20-15-26(31)24-14-19(30)10-12-28(24,4)23(20)11-13-27(21,22)3/h17-25,30H,6-16H2,1-5H3/t17-,18+,19+,20+,21+,22+,23+,24-,25+,27-,28-/m1/s1
SMILES:	C[C@@H]1CC[C@@H]([C@@H](C)[C@@H]2CC[C@H]3[C@@H]4CC(=O)[C@H]5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O)N(C)C1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL498633
PubChem CID:	44583920
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002724] Steroidal alkaloids [CHEMONTID:0002732] 22,26-epiminocholestanes

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO20194	Fritillaria puqiensis	Species	Liliaceae	Eukaryota	bulbs	n.a.	n.a.	PMID[15730259]
NPO11228	Fritillaria pallidiflora	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]
NPO22292	Fritillaria przewalskii	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]
NPO20194	Fritillaria puqiensis	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]
NPO14849	Fritillaria unibracteata	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]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

Activity Type	# Activity
Others	2

Activity Type	# Activity
Organism	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	11.0	n.a.	PMID[475582]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	17.0	n.a.	PMID[475582]

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☑ 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 NPC312637 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	139
0.1-0.2	1961
0.2-0.3	16876
0.3-0.4	11364
0.4-0.5	6217
0.5-0.6	4744
0.6-0.7	1206
0.7-0.8	173
0.8-0.85	13
0.85-0.9	0
0.9-0.95	3
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9326	High Similarity	NPC174117
0.9231	High Similarity	NPC220111
0.8557	High Similarity	NPC475239
0.8077	Intermediate Similarity	NPC28224
0.8068	Intermediate Similarity	NPC109533

Showing 1 to 5 of 200 entries

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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 NPC312637 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	97
0.1-0.2	1408
0.2-0.3	4743
0.3-0.4	2046
0.4-0.5	523
0.5-0.6	244
0.6-0.7	62
0.7-0.8	25
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8469	Intermediate Similarity	NPD6920	Discontinued
0.83	Intermediate Similarity	NPD6415	Discontinued
0.7857	Intermediate Similarity	NPD4808	Clinical (unspecified phase)
0.7857	Intermediate Similarity	NPD4809	Clinical (unspecified phase)
0.7619	Intermediate Similarity	NPD3700	Clinical (unspecified phase)

Showing 1 to 5 of 149 entries

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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