NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	192.15
Volume:	225.729
LogP:	3.535
LogD:	2.938
LogS:	-3.816
# Rotatable Bonds:	2
TPSA:	17.07
# H-Bond Aceptor:	1
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.61
Synthetic Accessibility Score:	2.719
Fsp3:	0.615
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.615
MDCK Permeability:	2.3338247046922334e-05
Pgp-inhibitor:	0.962
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.029
30% Bioavailability (F30%):	0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.107
Plasma Protein Binding (PPB):	93.84461212158203%
Volume Distribution (VD):	2.526
Pgp-substrate:	6.3162031173706055%

ADMET: Metabolism

CYP1A2-inhibitor:	0.446
CYP1A2-substrate:	0.869
CYP2C19-inhibitor:	0.365
CYP2C19-substrate:	0.922
CYP2C9-inhibitor:	0.083
CYP2C9-substrate:	0.798
CYP2D6-inhibitor:	0.301
CYP2D6-substrate:	0.871
CYP3A4-inhibitor:	0.027
CYP3A4-substrate:	0.586

ADMET: Excretion

Clearance (CL):	1.704
Half-life (T1/2):	0.611

ADMET: Toxicity

hERG Blockers:	0.029
Human Hepatotoxicity (H-HT):	0.358
Drug-inuced Liver Injury (DILI):	0.144
AMES Toxicity:	0.089
Rat Oral Acute Toxicity:	0.497
Maximum Recommended Daily Dose:	0.638
Skin Sensitization:	0.805
Carcinogencity:	0.815
Eye Corrosion:	0.553
Eye Irritation:	0.923
Respiratory Toxicity:	0.973

Download Data

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

Natural Product: NPC69898

Natural Product ID:	NPC69898
*Common Name:**	4-(2,6,6-Trimethylcyclohexen-1-Yl)But-3-En-2-One
IUPAC Name:	4-(2,6,6-trimethylcyclohexen-1-yl)but-3-en-2-one
Synonyms:
Standard InCHIKey:	PSQYTAPXSHCGMF-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C13H20O/c1-10-6-5-9-13(3,4)12(10)8-7-11(2)14/h7-8H,5-6,9H2,1-4H3
SMILES:	CC(=O)C=CC1=C(C)CCCC1(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3184146
PubChem CID:	26955
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO28152	Jacaranda caucana	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19361168]
NPO11450	Pseudoceratina purpurea	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[26035239]
NPO11450	Pseudoceratina purpurea	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26838	Adenophora triphylla	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27219	Gonioma kamassi	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8266	Solanum anguivi	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28152	Jacaranda caucana	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27948	Licania carii	Species	Chrysobalanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27381	Hypselodoris webbi	Species	Chromodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27985	Plantago arenaria	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11450	Pseudoceratina purpurea	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1650	Boykinia watanabei	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29214	Teucrium massiliense	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26838	Adenophora triphylla	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28095	Boronia megastigma	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15808	Vibrio gazogenes	Species	Vibrionaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO27879	Ailanthus triphysa	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20978	Alternaria cinerariae	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28117	Tor sinensis	Species	Cyprinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27588	Carpolobia lutea	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23311	Libanothamnus tamanus	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
Potency	2

Activity Type	# Activity
Individual Protein	1
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT163	Individual Protein	Nuclear factor NF-kappa-B p105 subunit	Homo sapiens	Potency	n.a.	10962.2	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	61130.6	nM	PubChem BioAssay data set

☑ 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 NPC69898 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	228
0.1-0.2	3530
0.2-0.3	19287
0.3-0.4	12589
0.4-0.5	5420
0.5-0.6	1350
0.6-0.7	238
0.7-0.8	42
0.8-0.85	8
0.85-0.9	3
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC295777
0.8545	High Similarity	NPC321568
0.8545	High Similarity	NPC281986
0.8545	High Similarity	NPC208749
0.8545	High Similarity	NPC22019
0.8491	Intermediate Similarity	NPC14002
0.8491	Intermediate Similarity	NPC37644
0.8333	Intermediate Similarity	NPC5626
0.8269	Intermediate Similarity	NPC228776
0.8148	Intermediate Similarity	NPC23117
0.807	Intermediate Similarity	NPC60772
0.8	Intermediate Similarity	NPC4638
0.7833	Intermediate Similarity	NPC288253
0.7759	Intermediate Similarity	NPC311852
0.7667	Intermediate Similarity	NPC326645
0.7667	Intermediate Similarity	NPC317177
0.7667	Intermediate Similarity	NPC317025
0.7667	Intermediate Similarity	NPC329416
0.7593	Intermediate Similarity	NPC116906
0.7593	Intermediate Similarity	NPC118788
0.7586	Intermediate Similarity	NPC115385
0.75	Intermediate Similarity	NPC127582
0.75	Intermediate Similarity	NPC310992
0.75	Intermediate Similarity	NPC296311
0.746	Intermediate Similarity	NPC92327
0.746	Intermediate Similarity	NPC176171
0.7458	Intermediate Similarity	NPC56905
0.7458	Intermediate Similarity	NPC27610
0.7455	Intermediate Similarity	NPC64866
0.7451	Intermediate Similarity	NPC216921
0.7419	Intermediate Similarity	NPC212210
0.7377	Intermediate Similarity	NPC213152
0.7344	Intermediate Similarity	NPC254886
0.7344	Intermediate Similarity	NPC176107
0.7302	Intermediate Similarity	NPC251118
0.7273	Intermediate Similarity	NPC163984
0.7273	Intermediate Similarity	NPC32351
0.7273	Intermediate Similarity	NPC58970
0.7273	Intermediate Similarity	NPC176819
0.7258	Intermediate Similarity	NPC167256
0.7258	Intermediate Similarity	NPC165695
0.7258	Intermediate Similarity	NPC32285
0.7231	Intermediate Similarity	NPC260474
0.7231	Intermediate Similarity	NPC87141
0.7231	Intermediate Similarity	NPC188292
0.7193	Intermediate Similarity	NPC268564
0.7167	Intermediate Similarity	NPC308108
0.7167	Intermediate Similarity	NPC170799
0.7164	Intermediate Similarity	NPC181204
0.7143	Intermediate Similarity	NPC475124
0.7143	Intermediate Similarity	NPC6697
0.7143	Intermediate Similarity	NPC150162
0.7143	Intermediate Similarity	NPC285371
0.7121	Intermediate Similarity	NPC256846
0.7119	Intermediate Similarity	NPC249645
0.7119	Intermediate Similarity	NPC55412
0.7097	Intermediate Similarity	NPC294304
0.7097	Intermediate Similarity	NPC228574
0.7091	Intermediate Similarity	NPC17810
0.7077	Intermediate Similarity	NPC475523
0.7069	Intermediate Similarity	NPC250539
0.7049	Intermediate Similarity	NPC203233
0.7049	Intermediate Similarity	NPC96551
0.7049	Intermediate Similarity	NPC285594
0.7049	Intermediate Similarity	NPC472304
0.7049	Intermediate Similarity	NPC276764
0.7	Intermediate Similarity	NPC217923
0.7	Intermediate Similarity	NPC192427
0.6984	Remote Similarity	NPC202118
0.6984	Remote Similarity	NPC197238
0.697	Remote Similarity	NPC155198
0.6957	Remote Similarity	NPC474796
0.6957	Remote Similarity	NPC329866
0.6957	Remote Similarity	NPC474797
0.6935	Remote Similarity	NPC25853
0.6923	Remote Similarity	NPC177470
0.6912	Remote Similarity	NPC54123
0.6912	Remote Similarity	NPC95863
0.6912	Remote Similarity	NPC5701
0.6897	Remote Similarity	NPC45283
0.6885	Remote Similarity	NPC266295
0.6885	Remote Similarity	NPC30215
0.6885	Remote Similarity	NPC94991
0.6875	Remote Similarity	NPC226066
0.6875	Remote Similarity	NPC469662
0.6857	Remote Similarity	NPC473171
0.6852	Remote Similarity	NPC191337
0.6852	Remote Similarity	NPC166788
0.6842	Remote Similarity	NPC30433
0.6833	Remote Similarity	NPC473733
0.6825	Remote Similarity	NPC469728
0.6825	Remote Similarity	NPC97322
0.6812	Remote Similarity	NPC251705
0.6812	Remote Similarity	NPC470045
0.6812	Remote Similarity	NPC276336
0.6812	Remote Similarity	NPC470044
0.6812	Remote Similarity	NPC153660
0.6774	Remote Similarity	NPC259261
0.6774	Remote Similarity	NPC143834
0.6769	Remote Similarity	NPC470329
0.6765	Remote Similarity	NPC265782
0.6765	Remote Similarity	NPC2634
0.6765	Remote Similarity	NPC251929
0.6761	Remote Similarity	NPC250621
0.6761	Remote Similarity	NPC469793
0.6761	Remote Similarity	NPC469796
0.6731	Remote Similarity	NPC144023
0.6731	Remote Similarity	NPC7754
0.6731	Remote Similarity	NPC270170
0.6727	Remote Similarity	NPC100380
0.6727	Remote Similarity	NPC4079
0.6727	Remote Similarity	NPC236355
0.6727	Remote Similarity	NPC262558
0.6727	Remote Similarity	NPC14917
0.6727	Remote Similarity	NPC8610
0.6724	Remote Similarity	NPC22182
0.6716	Remote Similarity	NPC117804
0.6714	Remote Similarity	NPC309852
0.6667	Remote Similarity	NPC176621
0.6667	Remote Similarity	NPC470078
0.6667	Remote Similarity	NPC474562
0.6667	Remote Similarity	NPC234707
0.6667	Remote Similarity	NPC225467
0.6667	Remote Similarity	NPC5734
0.6667	Remote Similarity	NPC275472
0.6667	Remote Similarity	NPC477686
0.6667	Remote Similarity	NPC267514
0.6667	Remote Similarity	NPC305501
0.6667	Remote Similarity	NPC200258
0.6667	Remote Similarity	NPC145755
0.6667	Remote Similarity	NPC255781
0.6667	Remote Similarity	NPC115023
0.6667	Remote Similarity	NPC25771
0.6667	Remote Similarity	NPC15325
0.6667	Remote Similarity	NPC181587
0.662	Remote Similarity	NPC476346
0.662	Remote Similarity	NPC293803
0.6618	Remote Similarity	NPC139397
0.6618	Remote Similarity	NPC136473
0.6618	Remote Similarity	NPC474060
0.6615	Remote Similarity	NPC52449
0.6615	Remote Similarity	NPC169275
0.661	Remote Similarity	NPC474141
0.6607	Remote Similarity	NPC91962
0.6575	Remote Similarity	NPC189485
0.6571	Remote Similarity	NPC474228
0.6571	Remote Similarity	NPC303613
0.6567	Remote Similarity	NPC290350
0.6567	Remote Similarity	NPC4370
0.6562	Remote Similarity	NPC260573
0.6562	Remote Similarity	NPC60565
0.6562	Remote Similarity	NPC475795
0.6552	Remote Similarity	NPC27438
0.6552	Remote Similarity	NPC236623
0.6545	Remote Similarity	NPC86683
0.6538	Remote Similarity	NPC111474
0.6538	Remote Similarity	NPC183670
0.6528	Remote Similarity	NPC1254
0.6528	Remote Similarity	NPC112680
0.6528	Remote Similarity	NPC69408
0.6528	Remote Similarity	NPC110725
0.6528	Remote Similarity	NPC474463
0.6528	Remote Similarity	NPC292589
0.6522	Remote Similarity	NPC260040
0.6522	Remote Similarity	NPC35734
0.6522	Remote Similarity	NPC307176
0.6522	Remote Similarity	NPC282593
0.6522	Remote Similarity	NPC159577
0.6515	Remote Similarity	NPC268039
0.6515	Remote Similarity	NPC183422
0.6491	Remote Similarity	NPC145311
0.6486	Remote Similarity	NPC27817
0.6486	Remote Similarity	NPC170793
0.6481	Remote Similarity	NPC292463
0.6481	Remote Similarity	NPC301972
0.6479	Remote Similarity	NPC255021
0.6471	Remote Similarity	NPC239039
0.6462	Remote Similarity	NPC472306
0.6452	Remote Similarity	NPC49575
0.6452	Remote Similarity	NPC267626
0.6452	Remote Similarity	NPC193695
0.6452	Remote Similarity	NPC230823
0.6452	Remote Similarity	NPC55004
0.6441	Remote Similarity	NPC471751
0.6429	Remote Similarity	NPC474539
0.6429	Remote Similarity	NPC21944
0.6429	Remote Similarity	NPC190035
0.6418	Remote Similarity	NPC323005
0.6418	Remote Similarity	NPC259156
0.6418	Remote Similarity	NPC242945
0.64	Remote Similarity	NPC74086
0.64	Remote Similarity	NPC469798
0.64	Remote Similarity	NPC469797
0.6393	Remote Similarity	NPC470893
0.6393	Remote Similarity	NPC188789
0.6393	Remote Similarity	NPC297280
0.6389	Remote Similarity	NPC225665
0.6389	Remote Similarity	NPC169056
0.6389	Remote Similarity	NPC166018
0.6377	Remote Similarity	NPC182815

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 NPC69898 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	231
0.1-0.2	3159
0.2-0.3	4233
0.3-0.4	1143
0.4-0.5	316
0.5-0.6	53
0.6-0.7	10
0.7-0.8	5
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
0.7667	Intermediate Similarity	NPD4191	Approved
0.7667	Intermediate Similarity	NPD4193	Approved
0.7667	Intermediate Similarity	NPD4192	Approved
0.7667	Intermediate Similarity	NPD4194	Approved
0.7206	Intermediate Similarity	NPD4058	Approved
0.7167	Intermediate Similarity	NPD287	Approved
0.7119	Intermediate Similarity	NPD4219	Approved
0.7091	Intermediate Similarity	NPD8262	Approved
0.6957	Remote Similarity	NPD4687	Approved
0.6912	Remote Similarity	NPD5276	Approved
0.6875	Remote Similarity	NPD5325	Clinical (unspecified phase)
0.6765	Remote Similarity	NPD4691	Approved
0.6714	Remote Similarity	NPD5733	Approved
0.6618	Remote Similarity	NPD4137	Phase 3
0.6522	Remote Similarity	NPD4747	Approved
0.64	Remote Similarity	NPD8259	Clinical (unspecified phase)
0.6364	Remote Similarity	NPD3527	Clinical (unspecified phase)
0.6267	Remote Similarity	NPD4195	Approved
0.6232	Remote Similarity	NPD3621	Clinical (unspecified phase)
0.6176	Remote Similarity	NPD7331	Phase 2
0.6087	Remote Similarity	NPD3709	Clinical (unspecified phase)
0.6	Remote Similarity	NPD1799	Clinical (unspecified phase)
0.6	Remote Similarity	NPD1696	Phase 3
0.5974	Remote Similarity	NPD4695	Discontinued
0.5962	Remote Similarity	NPD319	Phase 1
0.5946	Remote Similarity	NPD8039	Approved
0.5897	Remote Similarity	NPD8028	Phase 2
0.5833	Remote Similarity	NPD7143	Approved
0.5833	Remote Similarity	NPD7144	Approved
0.5797	Remote Similarity	NPD7341	Phase 2
0.5783	Remote Similarity	NPD4518	Approved
0.5753	Remote Similarity	NPD7152	Approved
0.5753	Remote Similarity	NPD7150	Approved
0.5753	Remote Similarity	NPD7151	Approved
0.5741	Remote Similarity	NPD5783	Phase 3
0.5735	Remote Similarity	NPD2664	Clinical (unspecified phase)
0.5733	Remote Similarity	NPD8264	Approved
0.5732	Remote Similarity	NPD5280	Approved
0.5732	Remote Similarity	NPD5690	Phase 2
0.5732	Remote Similarity	NPD5279	Phase 3
0.5732	Remote Similarity	NPD4694	Approved
0.5714	Remote Similarity	NPD539	Approved
0.5714	Remote Similarity	NPD6108	Clinical (unspecified phase)
0.5694	Remote Similarity	NPD6922	Approved
0.5694	Remote Similarity	NPD6923	Approved
0.5667	Remote Similarity	NPD4220	Pre-registration
0.5663	Remote Similarity	NPD3573	Approved
0.5647	Remote Similarity	NPD5207	Approved
0.5625	Remote Similarity	NPD4627	Clinical (unspecified phase)
0.5625	Remote Similarity	NPD5209	Approved
0.5625	Remote Similarity	NPD4223	Phase 3
0.5625	Remote Similarity	NPD4221	Approved
0.561	Remote Similarity	NPD1694	Approved

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