NPASS Compound

Structure

NPC30915 OpenBabel07101718232D 21 22 0 0 1 0 0 0 0 0999 V2000 -6.5604 -0.2864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4315 3.7292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5659 -0.3909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5714 -0.4954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5768 -0.6000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5823 -0.7045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6180 1.9021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9271 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4370 3.6247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6180 1.9021 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3090 0.9511 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5000 1.5388 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3090 0.9511 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2601 1.2601 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -0.1508 4.4337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 2.5388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1180 0.3633 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0302 2.7111 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 3 1 0 0 0 0 2 10 1 0 0 0 0 3 4 3 0 0 0 0 4 5 1 0 0 0 0 5 6 3 0 0 0 0 6 7 1 0 0 0 0 7 11 2 0 0 0 0 8 9 2 0 0 0 0 8 12 1 0 0 0 0 9 19 1 0 0 0 0 10 17 2 0 0 0 0 10 20 1 0 0 0 0 11 13 1 0 0 0 0 11 21 1 0 0 0 0 12 15 1 6 0 0 0 12 20 1 0 0 0 0 13 14 1 0 0 0 0 13 16 1 1 0 0 0 14 15 1 6 0 0 0 14 18 1 0 0 0 0 15 19 1 6 0 0 0 15 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	308.05
Volume:	291.59
LogP:	2.315
LogD:	0.915
LogS:	-3.9
# Rotatable Bonds:	2
TPSA:	64.99
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.446
Synthetic Accessibility Score:	5.839
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.837
MDCK Permeability:	6.348497845465317e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.519
20% Bioavailability (F20%):	0.971
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.086
Plasma Protein Binding (PPB):	99.52214813232422%
Volume Distribution (VD):	1.729
Pgp-substrate:	4.956554889678955%

ADMET: Metabolism

CYP1A2-inhibitor:	0.115
CYP1A2-substrate:	0.075
CYP2C19-inhibitor:	0.797
CYP2C19-substrate:	0.502
CYP2C9-inhibitor:	0.883
CYP2C9-substrate:	0.086
CYP2D6-inhibitor:	0.028
CYP2D6-substrate:	0.127
CYP3A4-inhibitor:	0.793
CYP3A4-substrate:	0.409

ADMET: Excretion

Clearance (CL):	3.645
Half-life (T1/2):	0.408

ADMET: Toxicity

hERG Blockers:	0.017
Human Hepatotoxicity (H-HT):	0.999
Drug-inuced Liver Injury (DILI):	0.988
AMES Toxicity:	0.959
Rat Oral Acute Toxicity:	0.806
Maximum Recommended Daily Dose:	0.869
Skin Sensitization:	0.848
Carcinogencity:	0.677
Eye Corrosion:	0.006
Eye Irritation:	0.064
Respiratory Toxicity:	0.945

Download Data

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

Natural Product: NPC30915

Natural Product ID:	NPC30915
*Common Name:**	Flosculin A
IUPAC Name:	[(2E,3S,4R,5S,9R)-3-chloro-2-hexa-2,4-diynylidene-4-hydroxy-1,6-dioxaspiro[4.4]non-7-en-9-yl] acetate
Synonyms:
Standard InCHIKey:	OMTKEJWBQVTEHK-ZLGGFXMGSA-N
Standard InCHI:	InChI=1S/C15H13ClO5/c1-3-4-5-6-7-11-13(16)14(18)15(21-11)12(8-9-19-15)20-10(2)17/h7-9,12-14,18H,1-2H3/b11-7+/t12-,13-,14+,15-/m1/s1
SMILES:	CC#CC#C/C=C/1[C@H]([C@@H]([C@@]2([C@@H](C=CO2)OC(=O)C)O1)O)Cl
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL452620
PubChem CID:	11630937
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000254] Ethers [CHEMONTID:0001656] Acetals [CHEMONTID:0004472] Ketals

*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
NPO3028	Plagius flosculosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16499337]
NPO3028	Plagius flosculosus	Species	Asteraceae	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	3

Activity Type	# Activity
Cell Line	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT15	Cell Line	Jurkat	Homo sapiens	IC50	=	13200.0	nM	PMID[572998]
NPT15	Cell Line	Jurkat	Homo sapiens	IC50	=	19100.0	nM	PMID[572998]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	18900.0	nM	PMID[572998]

☑ 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 NPC30915 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	208
0.1-0.2	3026
0.2-0.3	11277
0.3-0.4	18047
0.4-0.5	7864
0.5-0.6	1976
0.6-0.7	296
0.7-0.8	2
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.7176	Intermediate Similarity	NPC477422
0.7093	Intermediate Similarity	NPC477421
0.6977	Remote Similarity	NPC472174
0.6951	Remote Similarity	NPC276299
0.6782	Remote Similarity	NPC472173
0.6778	Remote Similarity	NPC179933
0.6739	Remote Similarity	NPC251026
0.6701	Remote Similarity	NPC118078
0.6667	Remote Similarity	NPC142111
0.6667	Remote Similarity	NPC473315
0.6632	Remote Similarity	NPC477428
0.663	Remote Similarity	NPC469469
0.6629	Remote Similarity	NPC326661
0.6596	Remote Similarity	NPC473308
0.6593	Remote Similarity	NPC473947
0.6585	Remote Similarity	NPC474729
0.6585	Remote Similarity	NPC474723
0.6556	Remote Similarity	NPC474026
0.6522	Remote Similarity	NPC121374
0.6522	Remote Similarity	NPC163362
0.6522	Remote Similarity	NPC127295
0.6506	Remote Similarity	NPC294813
0.6506	Remote Similarity	NPC90463
0.6506	Remote Similarity	NPC13143
0.6484	Remote Similarity	NPC248775
0.6484	Remote Similarity	NPC133377
0.6484	Remote Similarity	NPC28049
0.6477	Remote Similarity	NPC132938
0.6458	Remote Similarity	NPC208473
0.6429	Remote Similarity	NPC478110
0.6429	Remote Similarity	NPC470123
0.6429	Remote Similarity	NPC19769
0.6421	Remote Similarity	NPC266718
0.6421	Remote Similarity	NPC475035
0.6413	Remote Similarity	NPC477088
0.6413	Remote Similarity	NPC470148
0.6413	Remote Similarity	NPC470149
0.6413	Remote Similarity	NPC180725
0.6404	Remote Similarity	NPC474280
0.64	Remote Similarity	NPC473663
0.64	Remote Similarity	NPC475173
0.64	Remote Similarity	NPC473723
0.64	Remote Similarity	NPC61201
0.64	Remote Similarity	NPC473561
0.6374	Remote Similarity	NPC475711
0.6374	Remote Similarity	NPC110813
0.6373	Remote Similarity	NPC473333
0.6364	Remote Similarity	NPC473904
0.6354	Remote Similarity	NPC471567
0.6354	Remote Similarity	NPC470124
0.6354	Remote Similarity	NPC120398
0.6354	Remote Similarity	NPC322529
0.6344	Remote Similarity	NPC470147
0.6344	Remote Similarity	NPC133226
0.6337	Remote Similarity	NPC256368
0.6327	Remote Similarity	NPC20339
0.6327	Remote Similarity	NPC21208
0.6327	Remote Similarity	NPC40376
0.6327	Remote Similarity	NPC470137
0.6327	Remote Similarity	NPC48338
0.6327	Remote Similarity	NPC233551
0.6327	Remote Similarity	NPC280621
0.6316	Remote Similarity	NPC109603
0.6316	Remote Similarity	NPC93688
0.6311	Remote Similarity	NPC2666
0.6311	Remote Similarity	NPC471490
0.63	Remote Similarity	NPC9447
0.63	Remote Similarity	NPC473707
0.6289	Remote Similarity	NPC478112
0.6289	Remote Similarity	NPC171174
0.6289	Remote Similarity	NPC114694
0.6289	Remote Similarity	NPC240695
0.6289	Remote Similarity	NPC62118
0.6289	Remote Similarity	NPC142117
0.6289	Remote Similarity	NPC279267
0.6289	Remote Similarity	NPC69082
0.6289	Remote Similarity	NPC232555
0.6289	Remote Similarity	NPC475581
0.6289	Remote Similarity	NPC231096
0.6289	Remote Similarity	NPC107717
0.6277	Remote Similarity	NPC297440
0.6275	Remote Similarity	NPC471492
0.6264	Remote Similarity	NPC229655
0.6263	Remote Similarity	NPC139418
0.625	Remote Similarity	NPC163093
0.625	Remote Similarity	NPC476012
0.625	Remote Similarity	NPC323677
0.625	Remote Similarity	NPC477429
0.625	Remote Similarity	NPC32676
0.625	Remote Similarity	NPC156804
0.6238	Remote Similarity	NPC473520
0.6237	Remote Similarity	NPC1180
0.6226	Remote Similarity	NPC310804
0.6226	Remote Similarity	NPC261117
0.6224	Remote Similarity	NPC475037
0.6224	Remote Similarity	NPC178215
0.6211	Remote Similarity	NPC475046
0.6211	Remote Similarity	NPC310450
0.6211	Remote Similarity	NPC11383
0.6211	Remote Similarity	NPC474959
0.6207	Remote Similarity	NPC63873
0.62	Remote Similarity	NPC239517
0.62	Remote Similarity	NPC6414
0.62	Remote Similarity	NPC327253
0.62	Remote Similarity	NPC303451
0.62	Remote Similarity	NPC473311
0.6196	Remote Similarity	NPC474278
0.619	Remote Similarity	NPC475073
0.6186	Remote Similarity	NPC286338
0.6186	Remote Similarity	NPC1083
0.6186	Remote Similarity	NPC132496
0.6186	Remote Similarity	NPC470658
0.6186	Remote Similarity	NPC329838
0.6186	Remote Similarity	NPC329615
0.6186	Remote Similarity	NPC283085
0.6186	Remote Similarity	NPC477013
0.6186	Remote Similarity	NPC107986
0.6186	Remote Similarity	NPC66346
0.6186	Remote Similarity	NPC223871
0.6186	Remote Similarity	NPC473651
0.6186	Remote Similarity	NPC473669
0.6186	Remote Similarity	NPC231009
0.6186	Remote Similarity	NPC477014
0.6186	Remote Similarity	NPC473478
0.6186	Remote Similarity	NPC103284
0.6186	Remote Similarity	NPC82795
0.6186	Remote Similarity	NPC110710
0.6173	Remote Similarity	NPC223804
0.6163	Remote Similarity	NPC201356
0.6162	Remote Similarity	NPC81045
0.6162	Remote Similarity	NPC39754
0.6162	Remote Similarity	NPC172821
0.6162	Remote Similarity	NPC287164
0.6162	Remote Similarity	NPC320458
0.6162	Remote Similarity	NPC151403
0.6162	Remote Similarity	NPC274446
0.6162	Remote Similarity	NPC89001
0.6162	Remote Similarity	NPC169511
0.6162	Remote Similarity	NPC61257
0.6162	Remote Similarity	NPC473905
0.6162	Remote Similarity	NPC100454
0.6162	Remote Similarity	NPC234077
0.6162	Remote Similarity	NPC191929
0.6162	Remote Similarity	NPC171135
0.6162	Remote Similarity	NPC320569
0.6162	Remote Similarity	NPC261952
0.6162	Remote Similarity	NPC242364
0.6162	Remote Similarity	NPC133730
0.6161	Remote Similarity	NPC258711
0.6161	Remote Similarity	NPC35069
0.6154	Remote Similarity	NPC473948
0.6154	Remote Similarity	NPC52781
0.6146	Remote Similarity	NPC253801
0.6146	Remote Similarity	NPC286770
0.6146	Remote Similarity	NPC229799
0.6146	Remote Similarity	NPC284472
0.6145	Remote Similarity	NPC477424
0.6136	Remote Similarity	NPC316572
0.6122	Remote Similarity	NPC293136
0.6122	Remote Similarity	NPC134807
0.6122	Remote Similarity	NPC112685
0.6122	Remote Similarity	NPC184461
0.6122	Remote Similarity	NPC477015
0.6122	Remote Similarity	NPC219498
0.6122	Remote Similarity	NPC308412
0.6122	Remote Similarity	NPC134885
0.6122	Remote Similarity	NPC103523
0.6122	Remote Similarity	NPC134865
0.6122	Remote Similarity	NPC210218
0.6122	Remote Similarity	NPC204686
0.6122	Remote Similarity	NPC132940
0.6122	Remote Similarity	NPC309211
0.6122	Remote Similarity	NPC278283
0.6122	Remote Similarity	NPC473687
0.6122	Remote Similarity	NPC241360
0.6118	Remote Similarity	NPC31496
0.6117	Remote Similarity	NPC170204
0.6111	Remote Similarity	NPC86095
0.6111	Remote Similarity	NPC327383
0.6111	Remote Similarity	NPC185186
0.6111	Remote Similarity	NPC329914
0.6105	Remote Similarity	NPC236649
0.6105	Remote Similarity	NPC280367
0.6105	Remote Similarity	NPC21693
0.61	Remote Similarity	NPC133450
0.61	Remote Similarity	NPC20621
0.61	Remote Similarity	NPC91067
0.61	Remote Similarity	NPC477017
0.61	Remote Similarity	NPC93794
0.61	Remote Similarity	NPC477016
0.61	Remote Similarity	NPC81778
0.61	Remote Similarity	NPC40066
0.61	Remote Similarity	NPC473504
0.61	Remote Similarity	NPC477011
0.61	Remote Similarity	NPC42598
0.61	Remote Similarity	NPC318963
0.6095	Remote Similarity	NPC223700
0.6092	Remote Similarity	NPC478100
0.6092	Remote Similarity	NPC25298
0.6078	Remote Similarity	NPC156553

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 NPC30915 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	165
0.1-0.2	3303
0.2-0.3	4060
0.3-0.4	1326
0.4-0.5	252
0.5-0.6	43
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
0.6	Remote Similarity	NPD847	Phase 1
0.596	Remote Similarity	NPD4249	Approved
0.5905	Remote Similarity	NPD4792	Clinical (unspecified phase)
0.5904	Remote Similarity	NPD9119	Approved
0.5904	Remote Similarity	NPD69	Approved
0.59	Remote Similarity	NPD4250	Approved
0.59	Remote Similarity	NPD4251	Approved
0.5783	Remote Similarity	NPD9118	Approved
0.5728	Remote Similarity	NPD7838	Discovery

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