NPASS Compound

Structure

NPC93569 OpenBabel06302215512D 30 34 0 0 1 0 0 0 0 0999 V2000 -1.1420 1.3680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2225 0.9749 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6359 1.4878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3890 0.8299 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3639 1.0524 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7570 1.9719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7529 1.8823 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9754 0.9074 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9117 0.5560 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.7207 1.1438 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.7207 2.1438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5297 0.5560 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4808 0.8650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2898 0.2772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0988 0.8650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0499 0.5560 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7898 1.8161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3776 2.6251 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7898 1.8161 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2898 -0.7228 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4238 -1.2228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2207 -0.3951 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2207 -0.3951 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6698 -1.2296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6738 -1.3193 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9828 -0.5965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1170 0.3945 0.0000 N 0 3 3 0 0 0 0 0 0 0 0 0 0.9960 -0.0896 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 -0.6579 -0.7531 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 29 1 0 0 0 0 4 3 1 1 0 0 0 4 5 1 0 0 0 0 4 28 1 0 0 0 0 5 6 1 6 0 0 0 5 27 1 0 0 0 0 6 7 1 0 0 0 0 8 7 1 1 0 0 0 8 9 1 0 0 0 0 8 27 1 0 0 0 0 9 10 1 0 0 0 0 9 23 1 0 0 0 0 10 11 1 6 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 12 22 1 0 0 0 0 13 19 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 20 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 20 21 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 6 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 M CHG 1 27 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	417.22
Volume:	416.774
LogP:	3.837
LogD:	3.926
LogS:	-4.195
# Rotatable Bonds:	3
TPSA:	81.37
# H-Bond Aceptor:	7
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.752
Synthetic Accessibility Score:	4.941
Fsp3:	0.696
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.847
MDCK Permeability:	6.437245610868558e-05
Pgp-inhibitor:	0.08
Pgp-substrate:	0.124
Human Intestinal Absorption (HIA):	0.029
20% Bioavailability (F20%):	0.15
30% Bioavailability (F30%):	0.956

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.369
Plasma Protein Binding (PPB):	84.49929809570312%
Volume Distribution (VD):	1.655
Pgp-substrate:	16.83538055419922%

ADMET: Metabolism

CYP1A2-inhibitor:	0.123
CYP1A2-substrate:	0.081
CYP2C19-inhibitor:	0.032
CYP2C19-substrate:	0.576
CYP2C9-inhibitor:	0.04
CYP2C9-substrate:	0.2
CYP2D6-inhibitor:	0.731
CYP2D6-substrate:	0.295
CYP3A4-inhibitor:	0.736
CYP3A4-substrate:	0.852

ADMET: Excretion

Clearance (CL):	10.35
Half-life (T1/2):	0.224

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.556
Drug-inuced Liver Injury (DILI):	0.875
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.433
Maximum Recommended Daily Dose:	0.117
Skin Sensitization:	0.495
Carcinogencity:	0.321
Eye Corrosion:	0.004
Eye Irritation:	0.014
Respiratory Toxicity:	0.899

Download Data

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

Natural Product: NPC93569

Natural Product ID:	NPC93569
*Common Name:**	JDGNFRYDHRYXNL-BBDFNLGKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JDGNFRYDHRYXNL-BBDFNLGKSA-N
Standard InCHI:	InChI=1S/C23H31NO6/c1-11-10-17(29-22(11)25)14-7-8-15-18-12(2)20(28-16(18)6-5-9-24(14)15)21-19(27-4)13(3)23(26)30-21/h11-12,14-18H,5-10H2,1-4H3/p+1/b21-20+/t11-,12-,14-,15-,16+,17-,18+/m0/s1
SMILES:	C[C@H]1C[C@@H]([C@@H]2CC[C@H]3[C@H]4[C@H](C)/C(=C5/C(=C(C)C(=O)O5)OC)/O[C@@H]4CCC[NH+]23)OC1=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10024975
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0003427] Stemona alkaloids [CHEMONTID:0003914] Stemoamide-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
NPO8753	Axinyssa ambrosia	Species	Halichondriidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12088426]
NPO1235	Stemona curtisii	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104502]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679323]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	roots	n.a.	n.a.	PMID[16643052]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	Roots; Stems; Tubers	n.a.	n.a.	PMID[16872143]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	stems and leaves	n.a.	n.a.	PMID[18163592]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	roots	n.a.	n.a.	PMID[18452334]
NPO29935	Caesalpinia sappan	Species	Fabaceae	Eukaryota	n.a.	heartwood	n.a.	PMID[19420770]
NPO1235	Stemona curtisii	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21049906]
NPO27067	Stemona cochinchinensis	Species	Stemonaceae	Eukaryota	n.a.	root	n.a.	PMID[21049906]
NPO1235	Stemona curtisii	Species	Stemonaceae	Eukaryota	n.a.	root	n.a.	PMID[21049906]
NPO24472	Stemona kerrii	Species	Stemonaceae	Eukaryota	n.a.	root	n.a.	PMID[21049906]
NPO29935	Caesalpinia sappan	Species	Fabaceae	Eukaryota	n.a.	heartwood	n.a.	PMID[21800859]
NPO29935	Caesalpinia sappan	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21800859]
NPO24472	Stemona kerrii	Species	Stemonaceae	Eukaryota	n.a.	tuberous root	n.a.	PMID[21902195]
NPO1235	Stemona curtisii	Species	Stemonaceae	Eukaryota	n.a.	tuberous root	n.a.	PMID[21902195]
NPO1235	Stemona curtisii	Species	Stemonaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21902195]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	tuberous root	n.a.	PMID[21902195]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	root	n.a.	PMID[21902195]
NPO1235	Stemona curtisii	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21902195]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21902195]
NPO24472	Stemona kerrii	Species	Stemonaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21902195]
NPO29935	Caesalpinia sappan	Species	Fabaceae	Eukaryota	heartwood	n.a.	n.a.	PMID[23127886]
NPO29935	Caesalpinia sappan	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23234407]
NPO19476	Gnidia polycephala	Species	Thymelaeaceae	Eukaryota	roots	n.a.	n.a.	PMID[26091146]
NPO29935	Caesalpinia sappan	Species	Fabaceae	Eukaryota	seeds	Nanning, Guangxi Province, China	2013-APR	PMID[26398312]
NPO1235	Stemona curtisii	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24472	Stemona kerrii	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12104	Stemona cf. pierrei	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29935	Caesalpinia sappan	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27067	Stemona cochinchinensis	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19476	Gnidia polycephala	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2554	Biancaea sappan	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24472	Stemona kerrii	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1235	Stemona curtisii	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14009	Brosimum acutifolium	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20195	Radix stemonae preparata	Species	Lymnaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27067	Stemona cochinchinensis	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12104	Stemona cf. pierrei	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29935	Caesalpinia sappan	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2554	Biancaea sappan	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO6018	Crepis virens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8753	Axinyssa ambrosia	Species	Halichondriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14009	Brosimum acutifolium	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11655	Pygeum acuminatum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1235	Stemona curtisii	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11455	Drechslera turcica	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19137	Crinodendron patagua	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27067	Stemona cochinchinensis	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11929	Drosera gigantea	Species	Droseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15993	Thyrsanthera suborbicularis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19523	Turbinellus kauffmanii	Species	Gomphaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2554	Biancaea sappan	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4458	Tarenna bipindensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7468	Trichogonia gardneri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19275	Leandra lacunosa	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19476	Gnidia polycephala	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24472	Stemona kerrii	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5767	Alibertia edulis	Species	Rubiaceae	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 NPC93569 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	129
0.1-0.2	1096
0.2-0.3	11432
0.3-0.4	21462
0.4-0.5	7591
0.5-0.6	887
0.6-0.7	58
0.7-0.8	37
0.8-0.85	2
0.85-0.9	3
0.9-0.95	0
0.95-1	0

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 NPC93569 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	752
0.2-0.3	3454
0.3-0.4	3888
0.4-0.5	883
0.5-0.6	75
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
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