NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	222.16
Volume:	245.895
LogP:	2.209
LogD:	1.819
LogS:	-2.004
# Rotatable Bonds:	0
TPSA:	37.3
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.64
Synthetic Accessibility Score:	4.691
Fsp3:	0.786
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.565
MDCK Permeability:	1.8871500287787057e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.443
30% Bioavailability (F30%):	0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.527
Plasma Protein Binding (PPB):	70.99787139892578%
Volume Distribution (VD):	0.524
Pgp-substrate:	31.096141815185547%

ADMET: Metabolism

CYP1A2-inhibitor:	0.031
CYP1A2-substrate:	0.505
CYP2C19-inhibitor:	0.034
CYP2C19-substrate:	0.813
CYP2C9-inhibitor:	0.039
CYP2C9-substrate:	0.259
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.69
CYP3A4-inhibitor:	0.139
CYP3A4-substrate:	0.385

ADMET: Excretion

Clearance (CL):	9.077
Half-life (T1/2):	0.873

ADMET: Toxicity

hERG Blockers:	0.026
Human Hepatotoxicity (H-HT):	0.531
Drug-inuced Liver Injury (DILI):	0.326
AMES Toxicity:	0.013
Rat Oral Acute Toxicity:	0.246
Maximum Recommended Daily Dose:	0.847
Skin Sensitization:	0.104
Carcinogencity:	0.811
Eye Corrosion:	0.042
Eye Irritation:	0.541
Respiratory Toxicity:	0.345

Download Data

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

Natural Product: NPC40206

Natural Product ID:	NPC40206
*Common Name:**	Nanonorcaryophyllene B
IUPAC Name:	(1R,4S,9R,11S)-11-hydroxy-4,11-dimethyl-8-methylidenebicyclo[7.2.0]undecan-5-one
Synonyms:
Standard InCHIKey:	SNRJRYXYMKILLJ-FMSGJZPZSA-N
Standard InCHI:	InChI=1S/C14H22O2/c1-9-5-7-13(15)10(2)4-6-12-11(9)8-14(12,3)16/h10-12,16H,1,4-8H2,2-3H3/t10-,11-,12+,14-/m0/s1
SMILES:	C=C1CCC(=O)[C@@H](C)CC[C@@H]2[C@H]1C[C@]2(C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL508889
PubChem CID:	11218327
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000129] Alcohols and polyols [CHEMONTID:0001670] Tertiary alcohols

*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
NPO22870	Sinularia nanolobata	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104488]
NPO22870	Sinularia nanolobata	Species	Alcyoniidae	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
ED50	6

Activity Type	# Activity
Cell Line	4
NON-MOLECULAR	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT91	Cell Line	KB	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[475458]
NPT2356	Cell Line	NCI-H661	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[475458]
NPT579	Cell Line	DLD-1	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[475458]
NPT165	Cell Line	HeLa	Homo sapiens	ED50	=	16.9	ug ml-1	PMID[475458]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	ED50	=	18.5	ug ml-1	PMID[475458]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	ED50	>	20.0	ug ml-1	PMID[475458]

☑ 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 NPC40206 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	210
0.1-0.2	2805
0.2-0.3	15766
0.3-0.4	13711
0.4-0.5	7574
0.5-0.6	2424
0.6-0.7	191
0.7-0.8	14
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8	Intermediate Similarity	NPC103734
0.7879	Intermediate Similarity	NPC263161
0.7727	Intermediate Similarity	NPC197089
0.7612	Intermediate Similarity	NPC278895
0.7536	Intermediate Similarity	NPC163020
0.7429	Intermediate Similarity	NPC40327
0.7397	Intermediate Similarity	NPC211279
0.7391	Intermediate Similarity	NPC469914
0.7391	Intermediate Similarity	NPC475952
0.7377	Intermediate Similarity	NPC286752
0.7361	Intermediate Similarity	NPC474419
0.7313	Intermediate Similarity	NPC474329
0.7313	Intermediate Similarity	NPC61473
0.7313	Intermediate Similarity	NPC474304
0.7297	Intermediate Similarity	NPC321180
0.7286	Intermediate Similarity	NPC18543
0.7273	Intermediate Similarity	NPC50435
0.7246	Intermediate Similarity	NPC476629
0.7222	Intermediate Similarity	NPC7382
0.7222	Intermediate Similarity	NPC206875
0.7183	Intermediate Similarity	NPC469737
0.7164	Intermediate Similarity	NPC234767
0.7143	Intermediate Similarity	NPC145963
0.7101	Intermediate Similarity	NPC476626
0.7083	Intermediate Similarity	NPC300940
0.7042	Intermediate Similarity	NPC280256
0.7027	Intermediate Similarity	NPC76966
0.7027	Intermediate Similarity	NPC472305
0.7027	Intermediate Similarity	NPC78935
0.7027	Intermediate Similarity	NPC186554
0.7	Intermediate Similarity	NPC290445
0.7	Intermediate Similarity	NPC476614
0.7	Intermediate Similarity	NPC36616
0.6986	Remote Similarity	NPC46610
0.6986	Remote Similarity	NPC18819
0.6944	Remote Similarity	NPC29328
0.6933	Remote Similarity	NPC34110
0.6933	Remote Similarity	NPC257666
0.6933	Remote Similarity	NPC266193
0.6933	Remote Similarity	NPC266124
0.6933	Remote Similarity	NPC476608
0.6933	Remote Similarity	NPC472014
0.6912	Remote Similarity	NPC470325
0.6912	Remote Similarity	NPC53642
0.6901	Remote Similarity	NPC67608
0.6892	Remote Similarity	NPC114236
0.6892	Remote Similarity	NPC89374
0.6892	Remote Similarity	NPC77501
0.6892	Remote Similarity	NPC251435
0.6892	Remote Similarity	NPC39362
0.6885	Remote Similarity	NPC236623
0.6857	Remote Similarity	NPC469868
0.6857	Remote Similarity	NPC33583
0.6857	Remote Similarity	NPC60120
0.6857	Remote Similarity	NPC161612
0.6849	Remote Similarity	NPC275098
0.6849	Remote Similarity	NPC470237
0.6849	Remote Similarity	NPC472813
0.6842	Remote Similarity	NPC207772
0.6842	Remote Similarity	NPC275494
0.6842	Remote Similarity	NPC19443
0.6842	Remote Similarity	NPC471409
0.6825	Remote Similarity	NPC63396
0.6825	Remote Similarity	NPC202850
0.6818	Remote Similarity	NPC96551
0.6818	Remote Similarity	NPC285594
0.6806	Remote Similarity	NPC91369
0.6806	Remote Similarity	NPC235586
0.68	Remote Similarity	NPC470525
0.68	Remote Similarity	NPC474527
0.68	Remote Similarity	NPC215481
0.68	Remote Similarity	NPC151622
0.68	Remote Similarity	NPC7629
0.68	Remote Similarity	NPC471726
0.68	Remote Similarity	NPC263582
0.68	Remote Similarity	NPC271070
0.68	Remote Similarity	NPC20466
0.6795	Remote Similarity	NPC478262
0.6769	Remote Similarity	NPC65786
0.6769	Remote Similarity	NPC101285
0.6769	Remote Similarity	NPC7491
0.6769	Remote Similarity	NPC27853
0.6769	Remote Similarity	NPC13789
0.6757	Remote Similarity	NPC470299
0.6757	Remote Similarity	NPC38426
0.6757	Remote Similarity	NPC199316
0.6757	Remote Similarity	NPC102313
0.6757	Remote Similarity	NPC55527
0.6757	Remote Similarity	NPC162164
0.6757	Remote Similarity	NPC472966
0.6753	Remote Similarity	NPC472013
0.6753	Remote Similarity	NPC215843
0.6753	Remote Similarity	NPC476624
0.6712	Remote Similarity	NPC84790
0.6712	Remote Similarity	NPC72343
0.6712	Remote Similarity	NPC288667
0.6712	Remote Similarity	NPC144627
0.6711	Remote Similarity	NPC97377
0.6711	Remote Similarity	NPC471035
0.6711	Remote Similarity	NPC74995
0.6711	Remote Similarity	NPC122847
0.6711	Remote Similarity	NPC469867
0.6711	Remote Similarity	NPC197659
0.6711	Remote Similarity	NPC106078
0.6711	Remote Similarity	NPC66105
0.6711	Remote Similarity	NPC165711
0.6711	Remote Similarity	NPC212661
0.6711	Remote Similarity	NPC137547
0.6667	Remote Similarity	NPC233352
0.6667	Remote Similarity	NPC476809
0.6667	Remote Similarity	NPC250928
0.6667	Remote Similarity	NPC138492
0.6667	Remote Similarity	NPC10758
0.6667	Remote Similarity	NPC824
0.6667	Remote Similarity	NPC475861
0.6667	Remote Similarity	NPC474141
0.6667	Remote Similarity	NPC100445
0.6667	Remote Similarity	NPC201263
0.6623	Remote Similarity	NPC476627
0.6623	Remote Similarity	NPC470905
0.6623	Remote Similarity	NPC297996
0.6623	Remote Similarity	NPC321690
0.6623	Remote Similarity	NPC80088
0.6623	Remote Similarity	NPC62336
0.6623	Remote Similarity	NPC74410
0.6623	Remote Similarity	NPC476986
0.6623	Remote Similarity	NPC321514
0.6623	Remote Similarity	NPC179028
0.6623	Remote Similarity	NPC253561
0.6622	Remote Similarity	NPC92909
0.6622	Remote Similarity	NPC107783
0.6622	Remote Similarity	NPC177826
0.6622	Remote Similarity	NPC244708
0.6622	Remote Similarity	NPC161187
0.6622	Remote Similarity	NPC330659
0.6622	Remote Similarity	NPC247586
0.6622	Remote Similarity	NPC36310
0.6622	Remote Similarity	NPC35656
0.662	Remote Similarity	NPC472875
0.6618	Remote Similarity	NPC174560
0.6618	Remote Similarity	NPC15152
0.6618	Remote Similarity	NPC253204
0.6618	Remote Similarity	NPC125312
0.6615	Remote Similarity	NPC264779
0.6615	Remote Similarity	NPC39068
0.6613	Remote Similarity	NPC27438
0.661	Remote Similarity	NPC87439
0.661	Remote Similarity	NPC314679
0.6582	Remote Similarity	NPC226068
0.6582	Remote Similarity	NPC473217
0.6579	Remote Similarity	NPC142759
0.6579	Remote Similarity	NPC473437
0.6579	Remote Similarity	NPC180886
0.6579	Remote Similarity	NPC469646
0.6579	Remote Similarity	NPC182848
0.6579	Remote Similarity	NPC124289
0.6579	Remote Similarity	NPC141346
0.6579	Remote Similarity	NPC25908
0.6579	Remote Similarity	NPC115719
0.6567	Remote Similarity	NPC310228
0.6567	Remote Similarity	NPC52431
0.6552	Remote Similarity	NPC15162
0.6538	Remote Similarity	NPC7232
0.6538	Remote Similarity	NPC308038
0.6538	Remote Similarity	NPC477371
0.6538	Remote Similarity	NPC231431
0.6538	Remote Similarity	NPC263951
0.6538	Remote Similarity	NPC308545
0.6538	Remote Similarity	NPC84185
0.6538	Remote Similarity	NPC201459
0.6538	Remote Similarity	NPC82488
0.6538	Remote Similarity	NPC229204
0.6538	Remote Similarity	NPC66677
0.6538	Remote Similarity	NPC152061
0.6538	Remote Similarity	NPC192744
0.6538	Remote Similarity	NPC471890
0.6533	Remote Similarity	NPC301065
0.6533	Remote Similarity	NPC183503
0.6533	Remote Similarity	NPC161923
0.6533	Remote Similarity	NPC3753
0.6533	Remote Similarity	NPC167049
0.6533	Remote Similarity	NPC469691
0.6533	Remote Similarity	NPC237591
0.6533	Remote Similarity	NPC103958
0.6533	Remote Similarity	NPC283908
0.6515	Remote Similarity	NPC278550
0.6515	Remote Similarity	NPC193695
0.6508	Remote Similarity	NPC306195
0.6508	Remote Similarity	NPC181255
0.6508	Remote Similarity	NPC157781
0.6508	Remote Similarity	NPC179169
0.6508	Remote Similarity	NPC35519
0.65	Remote Similarity	NPC256750
0.65	Remote Similarity	NPC145143
0.65	Remote Similarity	NPC133844
0.65	Remote Similarity	NPC193347
0.65	Remote Similarity	NPC20262
0.6494	Remote Similarity	NPC476811
0.6494	Remote Similarity	NPC107668
0.6494	Remote Similarity	NPC149249

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 NPC40206 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	270
0.1-0.2	3399
0.2-0.3	3885
0.3-0.4	1116
0.4-0.5	388
0.5-0.6	88
0.6-0.7	4
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
0.7313	Intermediate Similarity	NPD7341	Phase 2
0.7206	Intermediate Similarity	NPD7331	Phase 2
0.661	Remote Similarity	NPD634	Phase 3
0.6562	Remote Similarity	NPD615	Clinical (unspecified phase)
0.65	Remote Similarity	NPD4221	Approved
0.65	Remote Similarity	NPD4223	Phase 3
0.6456	Remote Similarity	NPD4695	Discontinued
0.642	Remote Similarity	NPD4788	Approved
0.6393	Remote Similarity	NPD622	Approved
0.6375	Remote Similarity	NPD857	Phase 3
0.6341	Remote Similarity	NPD4197	Approved
0.6296	Remote Similarity	NPD3667	Approved
0.6265	Remote Similarity	NPD5329	Approved
0.6203	Remote Similarity	NPD3617	Approved
0.619	Remote Similarity	NPD5280	Approved
0.619	Remote Similarity	NPD5690	Phase 2
0.619	Remote Similarity	NPD4690	Approved
0.619	Remote Similarity	NPD4693	Phase 3
0.619	Remote Similarity	NPD4688	Approved
0.619	Remote Similarity	NPD4519	Discontinued
0.619	Remote Similarity	NPD4689	Approved
0.619	Remote Similarity	NPD4694	Approved
0.619	Remote Similarity	NPD4623	Approved
0.619	Remote Similarity	NPD4138	Approved
0.619	Remote Similarity	NPD5205	Approved
0.6173	Remote Similarity	NPD4139	Approved
0.6173	Remote Similarity	NPD5369	Approved
0.6173	Remote Similarity	NPD4692	Approved
0.6154	Remote Similarity	NPD3172	Approved
0.6145	Remote Similarity	NPD3666	Approved
0.6145	Remote Similarity	NPD4786	Approved
0.6145	Remote Similarity	NPD3665	Phase 1
0.6145	Remote Similarity	NPD3133	Approved
0.6098	Remote Similarity	NPD4800	Clinical (unspecified phase)
0.6061	Remote Similarity	NPD3194	Approved
0.6061	Remote Similarity	NPD3195	Phase 2
0.6061	Remote Similarity	NPD3196	Approved
0.6061	Remote Similarity	NPD4266	Approved
0.6056	Remote Similarity	NPD2664	Clinical (unspecified phase)
0.6049	Remote Similarity	NPD5368	Approved
0.6047	Remote Similarity	NPD4518	Approved
0.6	Remote Similarity	NPD5279	Phase 3
0.6	Remote Similarity	NPD3574	Clinical (unspecified phase)
0.6	Remote Similarity	NPD3186	Phase 1
0.6	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6	Remote Similarity	NPD3618	Phase 1
0.5977	Remote Similarity	NPD4753	Phase 2
0.5942	Remote Similarity	NPD287	Approved
0.5909	Remote Similarity	NPD4096	Approved
0.5904	Remote Similarity	NPD4270	Approved
0.5904	Remote Similarity	NPD4269	Approved
0.5904	Remote Similarity	NPD6435	Approved
0.589	Remote Similarity	NPD3171	Clinical (unspecified phase)
0.5882	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.5867	Remote Similarity	NPD5360	Phase 3
0.5867	Remote Similarity	NPD5361	Clinical (unspecified phase)
0.5857	Remote Similarity	NPD3198	Approved
0.5843	Remote Similarity	NPD5284	Approved
0.5843	Remote Similarity	NPD5281	Approved
0.5833	Remote Similarity	NPD5362	Discontinued
0.5811	Remote Similarity	NPD4224	Phase 2
0.5806	Remote Similarity	NPD388	Approved
0.5806	Remote Similarity	NPD386	Approved
0.5795	Remote Similarity	NPD5328	Approved
0.5778	Remote Similarity	NPD4202	Approved
0.5765	Remote Similarity	NPD3668	Phase 3
0.5732	Remote Similarity	NPD4195	Approved
0.5714	Remote Similarity	NPD5282	Discontinued
0.5698	Remote Similarity	NPD5363	Approved
0.5694	Remote Similarity	NPD368	Approved
0.5667	Remote Similarity	NPD6079	Approved
0.5667	Remote Similarity	NPD7515	Phase 2
0.5663	Remote Similarity	NPD4252	Approved
0.5663	Remote Similarity	NPD4820	Approved
0.5663	Remote Similarity	NPD4822	Approved
0.5663	Remote Similarity	NPD4821	Approved
0.5663	Remote Similarity	NPD4819	Approved
0.5652	Remote Similarity	NPD4629	Approved
0.5652	Remote Similarity	NPD5210	Approved
0.5652	Remote Similarity	NPD5695	Phase 3
0.5647	Remote Similarity	NPD7154	Phase 3
0.5641	Remote Similarity	NPD4758	Discontinued
0.5632	Remote Similarity	NPD6098	Approved
0.5632	Remote Similarity	NPD5786	Approved
0.5618	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.5618	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.5618	Remote Similarity	NPD6101	Approved
0.5606	Remote Similarity	NPD28	Approved
0.5606	Remote Similarity	NPD29	Approved
0.5604	Remote Similarity	NPD6399	Phase 3
0.5604	Remote Similarity	NPD5133	Approved
0.56	Remote Similarity	NPD3704	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