NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	194.17
Volume:	228.365
LogP:	3.221
LogD:	3.297
LogS:	-3.41
# Rotatable Bonds:	3
TPSA:	17.07
# H-Bond Aceptor:	1
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.625
Synthetic Accessibility Score:	3.265
Fsp3:	0.769
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:	-4.529
MDCK Permeability:	1.556491588416975e-05
Pgp-inhibitor:	0.23
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.952
30% Bioavailability (F30%):	0.091

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.946
Plasma Protein Binding (PPB):	72.19365692138672%
Volume Distribution (VD):	0.797
Pgp-substrate:	36.41202926635742%

ADMET: Metabolism

CYP1A2-inhibitor:	0.232
CYP1A2-substrate:	0.749
CYP2C19-inhibitor:	0.26
CYP2C19-substrate:	0.827
CYP2C9-inhibitor:	0.223
CYP2C9-substrate:	0.864
CYP2D6-inhibitor:	0.019
CYP2D6-substrate:	0.889
CYP3A4-inhibitor:	0.032
CYP3A4-substrate:	0.257

ADMET: Excretion

Clearance (CL):	6.852
Half-life (T1/2):	0.359

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.17
Drug-inuced Liver Injury (DILI):	0.099
AMES Toxicity:	0.021
Rat Oral Acute Toxicity:	0.119
Maximum Recommended Daily Dose:	0.855
Skin Sensitization:	0.177
Carcinogencity:	0.423
Eye Corrosion:	0.82
Eye Irritation:	0.861
Respiratory Toxicity:	0.957

Download Data

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

Natural Product: NPC236623

Natural Product ID:	NPC236623
*Common Name:**	4-(2,2-Dimethyl-6-Methylenecyclohexyl)Butan-2-One
IUPAC Name:	4-[(1S)-2,2-dimethyl-6-methylidenecyclohexyl]butan-2-one
Synonyms:
Standard InCHIKey:	ZLPHULOLXDKCND-GFCCVEGCSA-N
Standard InCHI:	InChI=1S/C13H22O/c1-10-6-5-9-13(3,4)12(10)8-7-11(2)14/h12H,1,5-9H2,2-4H3/t12-/m1/s1
SMILES:	C=C1CCCC(C)(C)[C@@H]1CCC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL220980
PubChem CID:	11264039
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
NPO33073	physeter macrocephalus	Species	Physeteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[17315955]

☑ 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
ED50	4

Activity Type	# Activity
Cell Line	3
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1183	Cell Line	WiDr	Homo sapiens	ED50	>	10.0	ug ml-1	PMID[575302]
NPT81	Cell Line	A549	Homo sapiens	ED50	>	10.0	ug ml-1	PMID[575302]
NPT83	Cell Line	MCF7	Homo sapiens	ED50	>	10.0	ug ml-1	PMID[575302]
NPT27	Others	Unspecified		ED50	>	10.0	ug ml-1	PMID[575302]

☑ 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 NPC236623 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	186
0.1-0.2	4019
0.2-0.3	18770
0.3-0.4	10146
0.4-0.5	6648
0.5-0.6	2433
0.6-0.7	421
0.7-0.8	64
0.8-0.85	6
0.85-0.9	2
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9216	High Similarity	NPC200258
0.8393	Intermediate Similarity	NPC127582
0.8364	Intermediate Similarity	NPC56905
0.8364	Intermediate Similarity	NPC27610
0.8246	Intermediate Similarity	NPC60565
0.8235	Intermediate Similarity	NPC116906
0.8182	Intermediate Similarity	NPC192427
0.8182	Intermediate Similarity	NPC115385
0.8103	Intermediate Similarity	NPC202118
0.8103	Intermediate Similarity	NPC197238
0.807	Intermediate Similarity	NPC270042
0.7966	Intermediate Similarity	NPC469662
0.7966	Intermediate Similarity	NPC475124
0.7966	Intermediate Similarity	NPC285371
0.7931	Intermediate Similarity	NPC213152
0.7895	Intermediate Similarity	NPC276764
0.7895	Intermediate Similarity	NPC472304
0.7857	Intermediate Similarity	NPC49575
0.7857	Intermediate Similarity	NPC267626
0.7857	Intermediate Similarity	NPC55004
0.7857	Intermediate Similarity	NPC230823
0.7755	Intermediate Similarity	NPC171783
0.7736	Intermediate Similarity	NPC27438
0.7719	Intermediate Similarity	NPC266295
0.7719	Intermediate Similarity	NPC30215
0.7719	Intermediate Similarity	NPC94991
0.7705	Intermediate Similarity	NPC107704
0.7705	Intermediate Similarity	NPC189917
0.7705	Intermediate Similarity	NPC168824
0.7705	Intermediate Similarity	NPC103734
0.7705	Intermediate Similarity	NPC43300
0.7705	Intermediate Similarity	NPC96812
0.7705	Intermediate Similarity	NPC39462
0.7667	Intermediate Similarity	NPC6697
0.7667	Intermediate Similarity	NPC212210
0.7636	Intermediate Similarity	NPC202850
0.7636	Intermediate Similarity	NPC63396
0.7586	Intermediate Similarity	NPC285594
0.7586	Intermediate Similarity	NPC259261
0.7586	Intermediate Similarity	NPC96551
0.7581	Intermediate Similarity	NPC263161
0.75	Intermediate Similarity	NPC59570
0.75	Intermediate Similarity	NPC472306
0.75	Intermediate Similarity	NPC45270
0.75	Intermediate Similarity	NPC165695
0.75	Intermediate Similarity	NPC215118
0.75	Intermediate Similarity	NPC288253
0.75	Intermediate Similarity	NPC135077
0.746	Intermediate Similarity	NPC188292
0.746	Intermediate Similarity	NPC39157
0.746	Intermediate Similarity	NPC82477
0.746	Intermediate Similarity	NPC310992
0.746	Intermediate Similarity	NPC296697
0.746	Intermediate Similarity	NPC142754
0.746	Intermediate Similarity	NPC260474
0.746	Intermediate Similarity	NPC20610
0.746	Intermediate Similarity	NPC155198
0.7458	Intermediate Similarity	NPC25853
0.7455	Intermediate Similarity	NPC268564
0.7455	Intermediate Similarity	NPC474141
0.7419	Intermediate Similarity	NPC323005
0.7414	Intermediate Similarity	NPC170799
0.7414	Intermediate Similarity	NPC308108
0.7414	Intermediate Similarity	NPC311852
0.7368	Intermediate Similarity	NPC20603
0.7344	Intermediate Similarity	NPC286814
0.7344	Intermediate Similarity	NPC477857
0.7344	Intermediate Similarity	NPC139397
0.7344	Intermediate Similarity	NPC182815
0.7333	Intermediate Similarity	NPC475795
0.7308	Intermediate Similarity	NPC4079
0.7308	Intermediate Similarity	NPC14917
0.7308	Intermediate Similarity	NPC236355
0.7302	Intermediate Similarity	NPC475523
0.7302	Intermediate Similarity	NPC220210
0.7302	Intermediate Similarity	NPC469868
0.7302	Intermediate Similarity	NPC20181
0.7273	Intermediate Similarity	NPC22182
0.7258	Intermediate Similarity	NPC251118
0.7258	Intermediate Similarity	NPC268039
0.7241	Intermediate Similarity	NPC193695
0.7231	Intermediate Similarity	NPC35734
0.7231	Intermediate Similarity	NPC265782
0.7231	Intermediate Similarity	NPC477856
0.7231	Intermediate Similarity	NPC307176
0.7231	Intermediate Similarity	NPC260040
0.7231	Intermediate Similarity	NPC163020
0.7231	Intermediate Similarity	NPC159577
0.7231	Intermediate Similarity	NPC251929
0.7231	Intermediate Similarity	NPC2634
0.7231	Intermediate Similarity	NPC214770
0.7231	Intermediate Similarity	NPC282593
0.7222	Intermediate Similarity	NPC32351
0.7213	Intermediate Similarity	NPC32285
0.7193	Intermediate Similarity	NPC275472
0.7188	Intermediate Similarity	NPC87141
0.717	Intermediate Similarity	NPC91962
0.7143	Intermediate Similarity	NPC62086
0.7143	Intermediate Similarity	NPC227632
0.7143	Intermediate Similarity	NPC78551
0.7143	Intermediate Similarity	NPC23117
0.7121	Intermediate Similarity	NPC470078
0.7121	Intermediate Similarity	NPC21944
0.7121	Intermediate Similarity	NPC474562
0.7121	Intermediate Similarity	NPC54123
0.7121	Intermediate Similarity	NPC190035
0.7121	Intermediate Similarity	NPC133253
0.7121	Intermediate Similarity	NPC115023
0.7119	Intermediate Similarity	NPC60772
0.7097	Intermediate Similarity	NPC473902
0.7091	Intermediate Similarity	NPC64866
0.7091	Intermediate Similarity	NPC274182
0.7077	Intermediate Similarity	NPC256846
0.7049	Intermediate Similarity	NPC97322
0.7031	Intermediate Similarity	NPC193770
0.7031	Intermediate Similarity	NPC290350
0.7031	Intermediate Similarity	NPC4370
0.7018	Intermediate Similarity	NPC250539
0.7015	Intermediate Similarity	NPC474228
0.7015	Intermediate Similarity	NPC303613
0.7015	Intermediate Similarity	NPC180015
0.7015	Intermediate Similarity	NPC474488
0.7015	Intermediate Similarity	NPC109576
0.7015	Intermediate Similarity	NPC130016
0.7015	Intermediate Similarity	NPC251705
0.7015	Intermediate Similarity	NPC470045
0.7015	Intermediate Similarity	NPC472813
0.7015	Intermediate Similarity	NPC56747
0.7015	Intermediate Similarity	NPC470044
0.7	Intermediate Similarity	NPC143834
0.7	Intermediate Similarity	NPC103290
0.6984	Remote Similarity	NPC470329
0.697	Remote Similarity	NPC151045
0.697	Remote Similarity	NPC40574
0.697	Remote Similarity	NPC246722
0.6939	Remote Similarity	NPC141634
0.6935	Remote Similarity	NPC167256
0.6923	Remote Similarity	NPC36616
0.6923	Remote Similarity	NPC290445
0.6912	Remote Similarity	NPC474796
0.6912	Remote Similarity	NPC159497
0.6912	Remote Similarity	NPC329866
0.6912	Remote Similarity	NPC20025
0.6912	Remote Similarity	NPC474797
0.6912	Remote Similarity	NPC309852
0.6885	Remote Similarity	NPC40206
0.6866	Remote Similarity	NPC225467
0.6866	Remote Similarity	NPC181204
0.6866	Remote Similarity	NPC234707
0.6863	Remote Similarity	NPC193180
0.6863	Remote Similarity	NPC190232
0.6863	Remote Similarity	NPC105246
0.6852	Remote Similarity	NPC294440
0.6842	Remote Similarity	NPC296311
0.6842	Remote Similarity	NPC14002
0.6825	Remote Similarity	NPC4638
0.6818	Remote Similarity	NPC475952
0.6812	Remote Similarity	NPC65650
0.6812	Remote Similarity	NPC293803
0.6812	Remote Similarity	NPC473171
0.6812	Remote Similarity	NPC476346
0.678	Remote Similarity	NPC473733
0.6765	Remote Similarity	NPC52667
0.6735	Remote Similarity	NPC223315
0.6727	Remote Similarity	NPC247786
0.6727	Remote Similarity	NPC258672
0.6727	Remote Similarity	NPC293343
0.6724	Remote Similarity	NPC5626
0.6724	Remote Similarity	NPC288296
0.6724	Remote Similarity	NPC53245
0.6716	Remote Similarity	NPC91369
0.6716	Remote Similarity	NPC235586
0.6714	Remote Similarity	NPC69408
0.6714	Remote Similarity	NPC263582
0.6714	Remote Similarity	NPC20466
0.6714	Remote Similarity	NPC1254
0.6714	Remote Similarity	NPC469793
0.6714	Remote Similarity	NPC469796
0.6714	Remote Similarity	NPC180886
0.6667	Remote Similarity	NPC173996
0.6667	Remote Similarity	NPC255021
0.6667	Remote Similarity	NPC131981
0.6667	Remote Similarity	NPC102313
0.6667	Remote Similarity	NPC83187
0.6667	Remote Similarity	NPC18819
0.6667	Remote Similarity	NPC40249
0.6667	Remote Similarity	NPC46610
0.6667	Remote Similarity	NPC199316
0.6667	Remote Similarity	NPC98246
0.6667	Remote Similarity	NPC285814
0.662	Remote Similarity	NPC212661
0.662	Remote Similarity	NPC471035
0.662	Remote Similarity	NPC74995
0.662	Remote Similarity	NPC325946
0.662	Remote Similarity	NPC257666
0.662	Remote Similarity	NPC266193
0.662	Remote Similarity	NPC472300
0.662	Remote Similarity	NPC165711
0.662	Remote Similarity	NPC476608
0.662	Remote Similarity	NPC91665

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 NPC236623 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	194
0.1-0.2	3766
0.2-0.3	3815
0.3-0.4	912
0.4-0.5	339
0.5-0.6	113
0.6-0.7	11
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
0.746	Intermediate Similarity	NPD3621	Clinical (unspecified phase)
0.7414	Intermediate Similarity	NPD287	Approved
0.7344	Intermediate Similarity	NPD4137	Phase 3
0.7231	Intermediate Similarity	NPD4691	Approved
0.7231	Intermediate Similarity	NPD4747	Approved
0.7121	Intermediate Similarity	NPD5276	Approved
0.6912	Remote Similarity	NPD5733	Approved
0.6912	Remote Similarity	NPD4687	Approved
0.6912	Remote Similarity	NPD4058	Approved
0.6863	Remote Similarity	NPD1799	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD345	Approved
0.6667	Remote Similarity	NPD343	Approved
0.6667	Remote Similarity	NPD344	Approved
0.6351	Remote Similarity	NPD4695	Discontinued
0.6184	Remote Similarity	NPD4223	Phase 3
0.6184	Remote Similarity	NPD3667	Approved
0.6184	Remote Similarity	NPD4221	Approved
0.6119	Remote Similarity	NPD7331	Phase 2
0.6104	Remote Similarity	NPD4788	Approved
0.6104	Remote Similarity	NPD3527	Clinical (unspecified phase)
0.6081	Remote Similarity	NPD3617	Approved
0.6053	Remote Similarity	NPD8028	Phase 2
0.6026	Remote Similarity	NPD4197	Approved
0.6026	Remote Similarity	NPD3666	Approved
0.6026	Remote Similarity	NPD4786	Approved
0.6026	Remote Similarity	NPD3668	Phase 3
0.6026	Remote Similarity	NPD3133	Approved
0.6026	Remote Similarity	NPD3665	Phase 1
0.597	Remote Similarity	NPD7341	Phase 2
0.5949	Remote Similarity	NPD5329	Approved
0.5875	Remote Similarity	NPD6098	Approved
0.5875	Remote Similarity	NPD7146	Approved
0.5875	Remote Similarity	NPD4693	Phase 3
0.5875	Remote Similarity	NPD5280	Approved
0.5875	Remote Similarity	NPD4688	Approved
0.5875	Remote Similarity	NPD4694	Approved
0.5875	Remote Similarity	NPD6684	Approved
0.5875	Remote Similarity	NPD5690	Phase 2
0.5875	Remote Similarity	NPD7521	Approved
0.5875	Remote Similarity	NPD5330	Approved
0.5875	Remote Similarity	NPD4689	Approved
0.5875	Remote Similarity	NPD3618	Phase 1
0.5875	Remote Similarity	NPD7334	Approved
0.5875	Remote Similarity	NPD5279	Phase 3
0.5875	Remote Similarity	NPD4623	Approved
0.5875	Remote Similarity	NPD6409	Approved
0.5875	Remote Similarity	NPD4138	Approved
0.5875	Remote Similarity	NPD4690	Approved
0.5875	Remote Similarity	NPD4519	Discontinued
0.5875	Remote Similarity	NPD5205	Approved
0.5844	Remote Similarity	NPD4692	Approved
0.5844	Remote Similarity	NPD4139	Approved
0.5802	Remote Similarity	NPD3573	Approved
0.5769	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.575	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.5735	Remote Similarity	NPD3171	Clinical (unspecified phase)
0.5732	Remote Similarity	NPD6903	Approved
0.5732	Remote Similarity	NPD5208	Approved
0.5732	Remote Similarity	NPD5737	Approved
0.5732	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.5732	Remote Similarity	NPD6672	Approved
0.5679	Remote Similarity	NPD3574	Clinical (unspecified phase)
0.5676	Remote Similarity	NPD8039	Approved
0.5663	Remote Similarity	NPD6080	Approved
0.5663	Remote Similarity	NPD4753	Phase 2
0.5663	Remote Similarity	NPD6673	Approved
0.5663	Remote Similarity	NPD6904	Approved
0.5663	Remote Similarity	NPD5328	Approved
0.566	Remote Similarity	NPD5783	Phase 3
0.5658	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.5652	Remote Similarity	NPD4224	Phase 2
0.5645	Remote Similarity	NPD615	Clinical (unspecified phase)
0.5636	Remote Similarity	NPD387	Clinical (unspecified phase)

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