NPASS Compound

Structure

CID194750 OpenBabel06191715582D 27 31 0 0 1 0 0 0 0 0999 V2000 -0.9889 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3619 2.2569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0704 -1.5522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1229 2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2764 3.3981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0291 3.3190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6883 2.9218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5054 2.7308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6018 1.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4263 0.3601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5529 1.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4013 -0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7431 1.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6092 2.1691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4752 0.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.0140 1.1691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0140 1.1691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6092 0.1691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4752 1.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7431 0.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.5529 0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4067 -0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4263 1.9781 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 7.3619 0.0813 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0933 -1.7796 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6018 0.3601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 4 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 6 8 1 0 0 0 0 8 23 1 0 0 0 0 9 11 1 0 0 0 0 10 16 1 0 0 0 0 11 2 1 6 0 0 0 11 21 1 0 0 0 0 12 3 1 6 0 0 0 12 18 1 0 0 0 0 12 22 1 0 0 0 0 13 4 1 6 0 0 0 13 14 1 0 0 0 0 13 20 1 0 0 0 0 14 7 1 1 0 0 0 14 19 1 0 0 0 0 15 10 1 6 0 0 0 15 18 1 0 0 0 0 15 19 1 0 0 0 0 16 17 1 0 0 0 0 16 23 1 6 0 0 0 17 9 1 6 0 0 0 17 26 1 0 0 0 0 18 20 1 0 0 0 0 19 23 1 0 0 0 0 20 27 1 0 0 0 0 21 24 2 0 0 0 0 21 26 1 0 0 0 0 22 25 2 0 0 0 0 22 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	375.24
Volume:	387.171
LogP:	4.227
LogD:	4.391
LogS:	-4.029
# Rotatable Bonds:	2
TPSA:	55.84
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.695
Synthetic Accessibility Score:	5.179
Fsp3:	0.909
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:	-4.777
MDCK Permeability:	8.421626262133941e-05
Pgp-inhibitor:	0.766
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.661

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.126
Plasma Protein Binding (PPB):	68.46440887451172%
Volume Distribution (VD):	1.6
Pgp-substrate:	26.179658889770508%

ADMET: Metabolism

CYP1A2-inhibitor:	0.085
CYP1A2-substrate:	0.098
CYP2C19-inhibitor:	0.042
CYP2C19-substrate:	0.851
CYP2C9-inhibitor:	0.059
CYP2C9-substrate:	0.073
CYP2D6-inhibitor:	0.033
CYP2D6-substrate:	0.518
CYP3A4-inhibitor:	0.925
CYP3A4-substrate:	0.816

ADMET: Excretion

Clearance (CL):	13.025
Half-life (T1/2):	0.322

ADMET: Toxicity

hERG Blockers:	0.548
Human Hepatotoxicity (H-HT):	0.834
Drug-inuced Liver Injury (DILI):	0.909
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.299
Maximum Recommended Daily Dose:	0.037
Skin Sensitization:	0.588
Carcinogencity:	0.06
Eye Corrosion:	0.011
Eye Irritation:	0.023
Respiratory Toxicity:	0.943

Download Data

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

Natural Product: NPC194750

Natural Product ID:	NPC194750
*Common Name:**	Tuberostemonine
IUPAC Name:	n.a.
Synonyms:	Tuberostemonine
Standard InCHIKey:	GYOGHROCTSEKDY-JJDZUBOLSA-N
Standard InCHI:	InChI=1S/C22H33NO4/c1-4-13-14-7-5-6-8-23-16(17-9-11(2)21(24)26-17)10-15(19(14)23)18-12(3)22(25)27-20(13)18/h11-20H,4-10H2,1-3H3/p+1/t11-,12-,13+,14+,15+,16-,17-,18+,19+,20-/m0/s1
SMILES:	CC[C@@H]1[C@H]2CCCC[NH+]3[C@@H](C[C@H]([C@H]4[C@H](C)C(=O)O[C@@H]14)[C@@H]23)[C@@H]1C[C@H](C)C(=O)O1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL517375
PubChem CID:	100781
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0003427] Stemona alkaloids [CHEMONTID:0003914] Stemoamide-type alkaloids [CHEMONTID:0003429] Stichoneurine-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
NPO30254	Stemona collinsae	Species	Stemonaceae	Eukaryota	Leaves, rhizomes, and roots	southeast Thailand near Chonburi	2000-Feb, 2001-Jan	PMID[12088422]
NPO8753	Axinyssa ambrosia	Species	Halichondriidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12088426]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679323]
NPO30254	Stemona collinsae	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679323]
NPO30254	Stemona collinsae	Species	Stemonaceae	Eukaryota	slowly dried tubers	Bangkok, Thailand	n.a.	PMID[15679323]
NPO30254	Stemona collinsae	Species	Stemonaceae	Eukaryota	n.a.	Southeast Thailand near Chonburi, Khao Khieo, close to the Chanthathen waterfall and Sri Racha	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]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21902195]
NPO15783	Stemona phyllantha	Species	Stemonaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21902195]
NPO15783	Stemona phyllantha	Species	Stemonaceae	Eukaryota	n.a.	tuberous root	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]
NPO19620	Stemona tuberosa	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]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28230	Stemona japonica	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]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
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]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30254	Stemona collinsae	Species	Stemonaceae	Eukaryota	leaf and root	n.a.	n.a.	Database[Title]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28230	Stemona japonica	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]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8753	Axinyssa ambrosia	Species	Halichondriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4458	Tarenna bipindensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15783	Stemona phyllantha	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7468	Trichogonia gardneri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5767	Alibertia edulis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6018	Crepis virens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19620	Stemona tuberosa	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]

☑ 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

Activity Type	# Activity
IC50	1
Others	3

Activity Type	# Activity
Organism	3
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		IC50	>	50000.0	nM	PMID[573218]
NPT776	Organism	Spodoptera littoralis	Spodoptera littoralis	Survival	=	100.0	%	PMID[573219]
NPT776	Organism	Spodoptera littoralis	Spodoptera littoralis	LC50	=	500.0	ppm	PMID[573219]
NPT776	Organism	Spodoptera littoralis	Spodoptera littoralis	LC50	>	500.0	ppm	PMID[573219]

☑ 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 NPC194750 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	243
0.1-0.2	3446
0.2-0.3	18846
0.3-0.4	14302
0.4-0.5	5333
0.5-0.6	454
0.6-0.7	55
0.7-0.8	13
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC233274
1.0	High Similarity	NPC287638
0.8485	Intermediate Similarity	NPC471843
0.785	Intermediate Similarity	NPC471844
0.7766	Intermediate Similarity	NPC216090
0.7544	Intermediate Similarity	NPC470538
0.7241	Intermediate Similarity	NPC39041
0.7241	Intermediate Similarity	NPC471845
0.7241	Intermediate Similarity	NPC202722
0.7241	Intermediate Similarity	NPC471846
0.7241	Intermediate Similarity	NPC241294
0.6875	Remote Similarity	NPC97336
0.6833	Remote Similarity	NPC174463
0.6822	Remote Similarity	NPC469998
0.68	Remote Similarity	NPC280903
0.6726	Remote Similarity	NPC265094
0.6721	Remote Similarity	NPC11379
0.6721	Remote Similarity	NPC230849
0.6694	Remote Similarity	NPC473477
0.6667	Remote Similarity	NPC470537
0.6614	Remote Similarity	NPC173173
0.6604	Remote Similarity	NPC322966
0.6381	Remote Similarity	NPC277918
0.6357	Remote Similarity	NPC212106
0.633	Remote Similarity	NPC476019
0.6136	Remote Similarity	NPC215507
0.6134	Remote Similarity	NPC271562
0.6	Remote Similarity	NPC203170
0.6	Remote Similarity	NPC469999
0.5954	Remote Similarity	NPC474371
0.5948	Remote Similarity	NPC220111
0.5917	Remote Similarity	NPC86906
0.5909	Remote Similarity	NPC52533
0.5893	Remote Similarity	NPC312637
0.5887	Remote Similarity	NPC469466
0.5854	Remote Similarity	NPC63511
0.584	Remote Similarity	NPC477963
0.5814	Remote Similarity	NPC470593
0.5814	Remote Similarity	NPC470594
0.5806	Remote Similarity	NPC58281
0.5806	Remote Similarity	NPC474459
0.5797	Remote Similarity	NPC474210
0.5794	Remote Similarity	NPC135431
0.5785	Remote Similarity	NPC233256
0.5785	Remote Similarity	NPC195841
0.5784	Remote Similarity	NPC109510
0.5784	Remote Similarity	NPC208657
0.576	Remote Similarity	NPC474452
0.5758	Remote Similarity	NPC211848
0.5755	Remote Similarity	NPC474754
0.5748	Remote Similarity	NPC271115
0.5748	Remote Similarity	NPC209252
0.5736	Remote Similarity	NPC475340
0.5728	Remote Similarity	NPC55508
0.5726	Remote Similarity	NPC472313
0.5714	Remote Similarity	NPC474348
0.5714	Remote Similarity	NPC325117
0.5714	Remote Similarity	NPC233108
0.5714	Remote Similarity	NPC326651
0.5714	Remote Similarity	NPC322319
0.5714	Remote Similarity	NPC309731
0.5704	Remote Similarity	NPC309249
0.5703	Remote Similarity	NPC28542
0.5702	Remote Similarity	NPC475239
0.5701	Remote Similarity	NPC134227
0.5692	Remote Similarity	NPC88190
0.568	Remote Similarity	NPC79238
0.5678	Remote Similarity	NPC220234
0.5672	Remote Similarity	NPC476501
0.5669	Remote Similarity	NPC470540
0.5664	Remote Similarity	NPC323156
0.5662	Remote Similarity	NPC307165
0.5659	Remote Similarity	NPC476952
0.5649	Remote Similarity	NPC238323
0.5645	Remote Similarity	NPC473994
0.5636	Remote Similarity	NPC65133
0.5635	Remote Similarity	NPC43648
0.5631	Remote Similarity	NPC474755
0.563	Remote Similarity	NPC476497
0.5619	Remote Similarity	NPC471046
0.5615	Remote Similarity	NPC138534
0.5615	Remote Similarity	NPC477986
0.5607	Remote Similarity	NPC73013

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 NPC194750 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	126
0.1-0.2	1754
0.2-0.3	4788
0.3-0.4	1973
0.4-0.5	428
0.5-0.6	74
0.6-0.7	7
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
0.6577	Remote Similarity	NPD3715	Approved
0.6577	Remote Similarity	NPD3713	Approved
0.6577	Remote Similarity	NPD3714	Approved
0.65	Remote Similarity	NPD8144	Approved
0.65	Remote Similarity	NPD8143	Approved
0.6339	Remote Similarity	NPD5349	Clinical (unspecified phase)
0.6325	Remote Similarity	NPD8040	Discontinued
0.6325	Remote Similarity	NPD6920	Discontinued
0.6289	Remote Similarity	NPD2696	Approved
0.6289	Remote Similarity	NPD2694	Approved
0.6289	Remote Similarity	NPD2697	Approved
0.6289	Remote Similarity	NPD2695	Approved
0.6154	Remote Similarity	NPD7911	Approved
0.6154	Remote Similarity	NPD7986	Approved
0.6154	Remote Similarity	NPD7987	Approved
0.6154	Remote Similarity	NPD7912	Approved
0.6122	Remote Similarity	NPD3725	Approved
0.6122	Remote Similarity	NPD3726	Approved
0.6036	Remote Similarity	NPD2682	Approved
0.6	Remote Similarity	NPD7755	Approved
0.6	Remote Similarity	NPD7990	Approved
0.6	Remote Similarity	NPD7989	Approved
0.6	Remote Similarity	NPD7754	Approved
0.6	Remote Similarity	NPD7646	Clinical (unspecified phase)
0.5968	Remote Similarity	NPD8298	Phase 2
0.5962	Remote Similarity	NPD617	Approved
0.5897	Remote Similarity	NPD8418	Phase 2
0.5887	Remote Similarity	NPD8077	Approved
0.5887	Remote Similarity	NPD8078	Approved
0.582	Remote Similarity	NPD6415	Discontinued
0.5736	Remote Similarity	NPD7519	Approved
0.5736	Remote Similarity	NPD7518	Approved
0.5736	Remote Similarity	NPD7517	Approved
0.5669	Remote Similarity	NPD7916	Approved
0.5669	Remote Similarity	NPD7915	Approved
0.561	Remote Similarity	NPD8140	Approved
0.561	Remote Similarity	NPD8307	Discontinued

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