NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	244.15
Volume:	278.497
LogP:	4.744
LogD:	3.991
LogS:	-3.83
# Rotatable Bonds:	4
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.474
Synthetic Accessibility Score:	3.189
Fsp3:	0.25
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:	-4.83
MDCK Permeability:	2.52157224167604e-05
Pgp-inhibitor:	0.977
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.262
30% Bioavailability (F30%):	0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.083
Plasma Protein Binding (PPB):	99.0932846069336%
Volume Distribution (VD):	1.066
Pgp-substrate:	1.194334626197815%

ADMET: Metabolism

CYP1A2-inhibitor:	0.831
CYP1A2-substrate:	0.92
CYP2C19-inhibitor:	0.32
CYP2C19-substrate:	0.358
CYP2C9-inhibitor:	0.253
CYP2C9-substrate:	0.893
CYP2D6-inhibitor:	0.889
CYP2D6-substrate:	0.913
CYP3A4-inhibitor:	0.164
CYP3A4-substrate:	0.318

ADMET: Excretion

Clearance (CL):	2.513
Half-life (T1/2):	0.537

ADMET: Toxicity

hERG Blockers:	0.045
Human Hepatotoxicity (H-HT):	0.123
Drug-inuced Liver Injury (DILI):	0.029
AMES Toxicity:	0.09
Rat Oral Acute Toxicity:	0.376
Maximum Recommended Daily Dose:	0.859
Skin Sensitization:	0.949
Carcinogencity:	0.377
Eye Corrosion:	0.071
Eye Irritation:	0.942
Respiratory Toxicity:	0.93

Download Data

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

Natural Product: NPC118788

Natural Product ID:	NPC118788
*Common Name:**	2-(2-Methylbut-3-En-2-Yl)-5-(3-Methylbut-2-Enyl)Cyclohexa-2,5-Diene-1,4-Dione
IUPAC Name:	2-(2-methylbut-3-en-2-yl)-5-(3-methylbut-2-enyl)cyclohexa-2,5-diene-1,4-dione
Synonyms:
Standard InCHIKey:	IXIJAOCIIZYSQJ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C16H20O2/c1-6-16(4,5)13-10-14(17)12(9-15(13)18)8-7-11(2)3/h6-7,9-10H,1,8H2,2-5H3
SMILES:	C=CC(C)(C)C1=CC(=O)C(=CC1=O)CC=C(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL403123
PubChem CID:	24180642
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001534] Quinone and hydroquinone lipids [CHEMONTID:0002802] Prenylquinones

*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
NPO30938	Perithalia capillaris	Species	Sporochnaceae	Eukaryota	n.a.	New Zealand	n.a.	PMID[18052030]
NPO30938	Perithalia capillaris	Species	Sporochnaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21348445]
NPO16286	Sporochnus comosus	Species	Sporochnaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21348445]
NPO5730	Lactuca canadensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17827	Scutellaria przewalskii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5730	Lactuca canadensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17845	Rhynchotechum vestitum	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17827	Scutellaria przewalskii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16286	Sporochnus comosus	Species	Sporochnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17714	Blepharispermum zanguebaricum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17950	Siphonoglossa ramosa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO5730	Lactuca canadensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1266	Trigonella polycerata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14726	Alnus subcordata	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13576	Cordylanthus tenuis	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13944	Parkia speciosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17183	Chaetomium coarctatum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17845	Rhynchotechum vestitum	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17827	Scutellaria przewalskii	Species	Lamiaceae	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
GI50	5
IC50	2

Activity Type	# Activity
Cell Line	6
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	340.0	nM	PMID[530484]
NPT395	Cell Line	SF-268	Homo sapiens	GI50	=	17000.0	nM	PMID[530485]
NPT83	Cell Line	MCF7	Homo sapiens	GI50	=	26000.0	nM	PMID[530485]
NPT397	Cell Line	NCI-H460	Homo sapiens	GI50	=	41000.0	nM	PMID[530485]
NPT139	Cell Line	HT-29	Homo sapiens	GI50	=	37000.0	nM	PMID[530485]
NPT913	Cell Line	CHO-K1	Cricetulus griseus	GI50	=	17000.0	nM	PMID[530485]
NPT2	Others	Unspecified		IC50	=	2100.0	nM	PMID[530484]

☑ 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 NPC118788 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	191
0.1-0.2	5635
0.2-0.3	20114
0.3-0.4	10033
0.4-0.5	5169
0.5-0.6	1229
0.6-0.7	265
0.7-0.8	43
0.8-0.85	11
0.85-0.9	6
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8913	High Similarity	NPC477686
0.8776	High Similarity	NPC228776
0.8723	High Similarity	NPC166788
0.8723	High Similarity	NPC191337
0.8696	High Similarity	NPC216921
0.8627	High Similarity	NPC37644
0.84	Intermediate Similarity	NPC15325
0.8182	Intermediate Similarity	NPC311852
0.8163	Intermediate Similarity	NPC262558
0.8163	Intermediate Similarity	NPC8610
0.8043	Intermediate Similarity	NPC111474
0.7925	Intermediate Similarity	NPC23117
0.7925	Intermediate Similarity	NPC296311
0.7925	Intermediate Similarity	NPC14002
0.7885	Intermediate Similarity	NPC64866
0.7778	Intermediate Similarity	NPC5626
0.7692	Intermediate Similarity	NPC163984
0.7692	Intermediate Similarity	NPC32351
0.7692	Intermediate Similarity	NPC176819
0.7692	Intermediate Similarity	NPC58970
0.7667	Intermediate Similarity	NPC251118
0.7627	Intermediate Similarity	NPC288253
0.7609	Intermediate Similarity	NPC180840
0.7593	Intermediate Similarity	NPC69898
0.7593	Intermediate Similarity	NPC295777
0.75	Intermediate Similarity	NPC4638
0.7419	Intermediate Similarity	NPC106613
0.7414	Intermediate Similarity	NPC203233
0.74	Intermediate Similarity	NPC25771
0.74	Intermediate Similarity	NPC471753
0.7391	Intermediate Similarity	NPC185839
0.7333	Intermediate Similarity	NPC32285
0.7302	Intermediate Similarity	NPC260474
0.7302	Intermediate Similarity	NPC188292
0.7302	Intermediate Similarity	NPC87141
0.7292	Intermediate Similarity	NPC113082
0.7273	Intermediate Similarity	NPC268564
0.7241	Intermediate Similarity	NPC60772
0.7222	Intermediate Similarity	NPC30433
0.7213	Intermediate Similarity	NPC212210
0.72	Intermediate Similarity	NPC301972
0.72	Intermediate Similarity	NPC292463
0.7193	Intermediate Similarity	NPC473733
0.7188	Intermediate Similarity	NPC256846
0.7174	Intermediate Similarity	NPC38497
0.7167	Intermediate Similarity	NPC97322
0.7119	Intermediate Similarity	NPC259261
0.7115	Intermediate Similarity	NPC471752
0.7115	Intermediate Similarity	NPC100380
0.7091	Intermediate Similarity	NPC471751
0.7083	Intermediate Similarity	NPC217923
0.7069	Intermediate Similarity	NPC281986
0.7069	Intermediate Similarity	NPC22019
0.7069	Intermediate Similarity	NPC283502
0.7069	Intermediate Similarity	NPC268185
0.7069	Intermediate Similarity	NPC208749
0.7069	Intermediate Similarity	NPC321568
0.7069	Intermediate Similarity	NPC115385
0.7069	Intermediate Similarity	NPC71755
0.7049	Intermediate Similarity	NPC165695
0.7037	Intermediate Similarity	NPC225974
0.7031	Intermediate Similarity	NPC155198
0.7	Intermediate Similarity	NPC25853
0.7	Intermediate Similarity	NPC127582
0.6981	Remote Similarity	NPC91962
0.697	Remote Similarity	NPC54123
0.6964	Remote Similarity	NPC474805
0.6964	Remote Similarity	NPC45283
0.6957	Remote Similarity	NPC269641
0.6949	Remote Similarity	NPC56905
0.6949	Remote Similarity	NPC94991
0.6949	Remote Similarity	NPC266295
0.6949	Remote Similarity	NPC27610
0.6949	Remote Similarity	NPC30215
0.6949	Remote Similarity	NPC308108
0.6949	Remote Similarity	NPC170799
0.6923	Remote Similarity	NPC136473
0.6885	Remote Similarity	NPC213152
0.6885	Remote Similarity	NPC294304
0.6885	Remote Similarity	NPC475795
0.6885	Remote Similarity	NPC228574
0.6885	Remote Similarity	NPC260573
0.6875	Remote Similarity	NPC155880
0.6875	Remote Similarity	NPC475523
0.6875	Remote Similarity	NPC92863
0.6866	Remote Similarity	NPC276336
0.6866	Remote Similarity	NPC153660
0.6852	Remote Similarity	NPC145311
0.6842	Remote Similarity	NPC474127
0.6842	Remote Similarity	NPC317796
0.6833	Remote Similarity	NPC285594
0.6833	Remote Similarity	NPC96551
0.6825	Remote Similarity	NPC470329
0.6818	Remote Similarity	NPC2634
0.6818	Remote Similarity	NPC265782
0.6818	Remote Similarity	NPC251929
0.6792	Remote Similarity	NPC14917
0.6792	Remote Similarity	NPC4079
0.6792	Remote Similarity	NPC236355
0.6786	Remote Similarity	NPC137396
0.678	Remote Similarity	NPC224103
0.678	Remote Similarity	NPC200831
0.678	Remote Similarity	NPC299369
0.6774	Remote Similarity	NPC167256
0.6774	Remote Similarity	NPC202118
0.6774	Remote Similarity	NPC197238
0.6774	Remote Similarity	NPC322457
0.6769	Remote Similarity	NPC310992
0.6765	Remote Similarity	NPC309852
0.6739	Remote Similarity	NPC12889
0.6731	Remote Similarity	NPC145755
0.6731	Remote Similarity	NPC267514
0.6727	Remote Similarity	NPC474391
0.6727	Remote Similarity	NPC220191
0.6727	Remote Similarity	NPC116906
0.6724	Remote Similarity	NPC275472
0.6721	Remote Similarity	NPC79756
0.6719	Remote Similarity	NPC92327
0.6719	Remote Similarity	NPC137163
0.6719	Remote Similarity	NPC176171
0.6716	Remote Similarity	NPC474539
0.6716	Remote Similarity	NPC181204
0.6716	Remote Similarity	NPC5701
0.6667	Remote Similarity	NPC285371
0.6667	Remote Similarity	NPC476346
0.6667	Remote Similarity	NPC24833
0.6667	Remote Similarity	NPC169275
0.6667	Remote Similarity	NPC52449
0.6667	Remote Similarity	NPC474141
0.6667	Remote Similarity	NPC475124
0.6667	Remote Similarity	NPC139397
0.6667	Remote Similarity	NPC150162
0.6667	Remote Similarity	NPC324812
0.6667	Remote Similarity	NPC281195
0.6667	Remote Similarity	NPC473603
0.6667	Remote Similarity	NPC469662
0.6667	Remote Similarity	NPC473902
0.6667	Remote Similarity	NPC476059
0.6667	Remote Similarity	NPC6697
0.6618	Remote Similarity	NPC470044
0.6618	Remote Similarity	NPC303613
0.6618	Remote Similarity	NPC251705
0.6618	Remote Similarity	NPC470045
0.6618	Remote Similarity	NPC474228
0.6615	Remote Similarity	NPC254886
0.6615	Remote Similarity	NPC176107
0.6613	Remote Similarity	NPC329416
0.6613	Remote Similarity	NPC317177
0.6613	Remote Similarity	NPC317025
0.6613	Remote Similarity	NPC326645
0.6613	Remote Similarity	NPC60565
0.6607	Remote Similarity	NPC22329
0.6607	Remote Similarity	NPC477458
0.66	Remote Similarity	NPC12319
0.66	Remote Similarity	NPC18205
0.66	Remote Similarity	NPC101147
0.6571	Remote Similarity	NPC69408
0.6571	Remote Similarity	NPC40353
0.6571	Remote Similarity	NPC1254
0.6567	Remote Similarity	NPC203819
0.6567	Remote Similarity	NPC260040
0.6567	Remote Similarity	NPC307176
0.6562	Remote Similarity	NPC470688
0.6557	Remote Similarity	NPC472304
0.6557	Remote Similarity	NPC276764
0.6557	Remote Similarity	NPC38455
0.6552	Remote Similarity	NPC100809
0.6552	Remote Similarity	NPC300121
0.6552	Remote Similarity	NPC209431
0.6552	Remote Similarity	NPC322461
0.6545	Remote Similarity	NPC267110
0.6538	Remote Similarity	NPC106819
0.6531	Remote Similarity	NPC130923
0.6522	Remote Similarity	NPC304788
0.6522	Remote Similarity	NPC474797
0.6522	Remote Similarity	NPC266979
0.6522	Remote Similarity	NPC147438
0.6522	Remote Similarity	NPC329866
0.6522	Remote Similarity	NPC474796
0.6515	Remote Similarity	NPC117804
0.6508	Remote Similarity	NPC477830
0.6508	Remote Similarity	NPC477707
0.65	Remote Similarity	NPC192843
0.65	Remote Similarity	NPC192427
0.65	Remote Similarity	NPC267626
0.65	Remote Similarity	NPC55004
0.65	Remote Similarity	NPC230823
0.65	Remote Similarity	NPC49575
0.65	Remote Similarity	NPC193695
0.65	Remote Similarity	NPC281230
0.6491	Remote Similarity	NPC151919
0.6471	Remote Similarity	NPC234707
0.6471	Remote Similarity	NPC190035
0.6471	Remote Similarity	NPC225467
0.6471	Remote Similarity	NPC95863
0.6471	Remote Similarity	NPC305501
0.6471	Remote Similarity	NPC474562
0.6471	Remote Similarity	NPC115023
0.6462	Remote Similarity	NPC16119
0.6441	Remote Similarity	NPC188789

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 NPC118788 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	171
0.1-0.2	4120
0.2-0.3	3933
0.3-0.4	600
0.4-0.5	261
0.5-0.6	49
0.6-0.7	15
0.7-0.8	1
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
0.7447	Intermediate Similarity	NPD5783	Phase 3
0.6949	Remote Similarity	NPD287	Approved
0.6818	Remote Similarity	NPD4691	Approved
0.678	Remote Similarity	NPD8779	Phase 3
0.6765	Remote Similarity	NPD4058	Approved
0.6667	Remote Similarity	NPD4137	Phase 3
0.6613	Remote Similarity	NPD4193	Approved
0.6613	Remote Similarity	NPD4191	Approved
0.6613	Remote Similarity	NPD4192	Approved
0.6613	Remote Similarity	NPD4194	Approved
0.6567	Remote Similarity	NPD4747	Approved
0.6522	Remote Similarity	NPD4687	Approved
0.6471	Remote Similarity	NPD5276	Approved
0.6462	Remote Similarity	NPD7331	Phase 2
0.6462	Remote Similarity	NPD6108	Clinical (unspecified phase)
0.6286	Remote Similarity	NPD5733	Approved
0.6271	Remote Similarity	NPD539	Approved
0.625	Remote Similarity	NPD4220	Pre-registration
0.625	Remote Similarity	NPD2664	Clinical (unspecified phase)
0.6167	Remote Similarity	NPD4627	Clinical (unspecified phase)
0.6119	Remote Similarity	NPD3709	Clinical (unspecified phase)
0.6029	Remote Similarity	NPD3621	Clinical (unspecified phase)
0.6	Remote Similarity	NPD4222	Approved
0.6	Remote Similarity	NPD3174	Discontinued
0.6	Remote Similarity	NPD39	Approved
0.6	Remote Similarity	NPD4695	Discontinued
0.6	Remote Similarity	NPD8259	Clinical (unspecified phase)
0.5974	Remote Similarity	NPD3527	Clinical (unspecified phase)
0.5926	Remote Similarity	NPD5326	Phase 3
0.5909	Remote Similarity	NPD5325	Clinical (unspecified phase)
0.5867	Remote Similarity	NPD4195	Approved
0.5821	Remote Similarity	NPD7341	Phase 2
0.5818	Remote Similarity	NPD6096	Approved
0.5818	Remote Similarity	NPD6097	Approved
0.5806	Remote Similarity	NPD4219	Approved
0.5789	Remote Similarity	NPD5343	Approved
0.5763	Remote Similarity	NPD6927	Phase 3
0.575	Remote Similarity	NPD5690	Phase 2
0.5714	Remote Similarity	NPD8028	Phase 2
0.569	Remote Similarity	NPD3173	Approved
0.569	Remote Similarity	NPD8262	Approved
0.5686	Remote Similarity	NPD319	Phase 1
0.5679	Remote Similarity	NPD3573	Approved
0.5672	Remote Similarity	NPD1984	Approved
0.5641	Remote Similarity	NPD4221	Approved
0.5641	Remote Similarity	NPD5209	Approved
0.5641	Remote Similarity	NPD4223	Phase 3

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