NPASS Compound

Natural Product: NPC276290

Natural Product ID	NPC276290
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Sarcophine
IUPAC Name	n.a.
Synonyms	(+)-Sarcophine; Sarcophine
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL518855
PubChem CID	6436805
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000147] Macrolides and analogues

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 51 53 0 0 0 0 0 0 0 0999 V2000 -0.7655 -4.1213 0.1112 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7179 -2.6632 -0.1953 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0672 -1.7908 0.3915 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0707 -2.0037 1.4587 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4598 -1.6969 1.0194 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7641 -0.3488 0.5075 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9005 -0.3221 -0.5505 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1351 0.5794 1.6388 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0251 0.7857 0.6769 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4050 1.9264 -0.2915 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6015 3.1514 -0.0172 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1485 2.9634 -0.2819 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2827 1.8341 -0.8020 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7513 1.6094 -1.0684 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1331 0.1798 -0.7545 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8978 0.1825 0.3133 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5012 -1.0134 0.9888 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1449 1.5708 0.6839 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8560 1.8990 1.6925 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5055 2.4042 -0.2047 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6299 -0.8343 -1.6876 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6477 -2.2411 -1.3132 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7589 4.1175 0.0694 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7996 -4.6588 -0.8803 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7495 -4.3952 0.5925 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0399 -4.4711 0.7484 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0145 -0.7320 0.0824 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0604 -3.0654 1.7805 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8561 -1.3772 2.3585 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7674 -2.4806 0.2603 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1193 -1.9590 1.9043 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4396 -1.2763 -0.5602 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5891 0.5136 -0.3810 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4022 -0.1429 -1.5262 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0942 0.9983 1.2135 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3115 1.6205 -1.3462 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4823 2.2108 -0.1681 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9972 4.0001 -0.6129 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6646 3.4685 1.0614 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4132 1.0601 -1.0866 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9672 1.8014 -2.1311 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1661 -1.5883 0.3220 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1980 -0.6606 1.8101 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7499 -1.6131 1.5350 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5949 -0.5380 -2.0085 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2681 -0.7133 -2.6196 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6108 -2.6952 -1.0835 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2462 -2.8325 -2.1961 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1366 5.0392 0.2626 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2849 3.9408 1.0276 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4352 4.3782 -0.7439 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 6 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 16 18 1 0 18 19 2 0 18 20 1 0 15 21 1 0 21 22 1 0 12 23 1 0 22 2 1 0 9 6 1 0 20 14 1 0 1 24 1 0 1 25 1 0 1 26 1 0 3 27 1 0 4 28 1 0 4 29 1 0 5 30 1 0 5 31 1 0 7 32 1 0 7 33 1 0 7 34 1 0 9 35 1 1 10 36 1 0 10 37 1 0 11 38 1 0 11 39 1 0 13 40 1 0 14 41 1 6 17 42 1 0 17 43 1 0 17 44 1 0 21 45 1 0 21 46 1 0 22 47 1 0 22 48 1 0 23 49 1 0 23 50 1 0 23 51 1 0 M END

Standard InCHIKey	CGAKBBMRMLAYMY-BUHUPKIQSA-N
Standard InCHI	InChI=1S/C20H28O3/c1-13-6-5-11-20(4)18(23-20)10-8-14(2)12-17-16(9-7-13)15(3)19(21)22-17/h6,12,17-18H,5,7-11H2,1-4H3/b13-6+,14-12+/t17-,18-,20-/m0/s1
SMILES	C/C/1=CCC[C@]2(C)O[C@H]2CC/C(=C/[C@H]2C(=C(C)C(=O)O2)CC1)/C

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO9888	Lobophytum laevigatum	Species	Alcyoniidae	Eukaryota	n.a.	Vietnamese	n.a.	PMID[21458279]
NPO9888	Lobophytum laevigatum	Species	Alcyoniidae	Eukaryota	n.a.	Vietnamese soft coral	n.a.	PMID[21507644]
NPO9888	Lobophytum laevigatum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9888	Lobophytum laevigatum	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	Organism Name	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
Activity	15
ED50	4
IC50	4
%PFU	3
FC	1

Activity Type	# Activity
Individual protein	4
Cell line	19
Others	4

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT540	Individual protein	Bile acid receptor FXR	Homo sapiens	Activity	=	1.18	%	DOI[10.6019/CHEMBL1201861]
NPT540	Individual protein	Bile acid receptor FXR	Homo sapiens	Activity	=	86.0	%	PubChem BioAssay data set
NPT545	Individual protein	Phospholipase A2 group 1B	Homo sapiens	Activity	=	95.0	%	DOI[10.6019/CHEMBL1201861]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT80	Cell line	Raji	Homo sapiens	Activity	=	60.0	%	PMID[20112996]
NPT80	Cell line	Raji	Homo sapiens	Activity	>	80.0	%	PubChem BioAssay data set
NPT81	Cell line	A549	Homo sapiens	ED50	=	10.38	ug ml-1	PMID[19702283]
NPT139	Cell line	HT-29	Homo sapiens	ED50	=	10.46	ug ml-1	PMID[15332869]
NPT91	Cell line	KB	Homo sapiens	ED50	>	50.0	ug ml-1	PMID[9322358]
NPT168	Cell line	P388	Mus musculus	ED50	=	2.42	ug ml-1	PMID[22620987]
NPT116	Cell line	HL-60	Homo sapiens	IC50	=	34700.0	nM	Open TG-GATES in vivo data: Biochemistry
NPT81	Cell line	A549	Homo sapiens	IC50	>	40000.0	nM	PMID[23517371]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	>	40000.0	nM	PMID[23517371]
NPT83	Cell line	MCF7	Homo sapiens	IC50	>	40000.0	nM	PubChem BioAssay data set
NPT83	Cell line	MCF7	Homo sapiens	%PFU	=	24.0	%	DOI[10.1007/s00044-004-0054-2]
NPT83	Cell line	MCF7	Homo sapiens	%PFU	=	38.0	%	DOI[10.1007/s00044-004-0054-2]
NPT83	Cell line	MCF7	Homo sapiens	%PFU	=	69.0	%	DOI[10.1007/s00044-004-0054-2]
NPT83	Cell line	MCF7	Homo sapiens	Activity	=	96.0	%	PMID[15921441]
NPT83	Cell line	MCF7	Homo sapiens	Activity	=	120.0	%	PMID[22413887]
NPT83	Cell line	MCF7	Homo sapiens	Activity	=	90.0	%	PMID[22620677]
NPT83	Cell line	MCF7	Homo sapiens	FC	=	2.0	n.a.	PMID[22620677]
NPT2	Others	Unspecified	n.a.	Activity	=	19.6	%	PMID[19848432]
NPT2	Others	Unspecified	n.a.	Activity	=	67.5	%	PMID[19114678]
NPT2	Others	Unspecified	n.a.	Activity	=	84.0	%	PMID[25760525]
NPT2	Others	Unspecified	n.a.	Activity	=	100.0	%	PMID[20112996]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC276290 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	23548
0.1-0.2	24443
0.2-0.3	1632
0.3-0.4	158
0.4-0.5	55
0.5-0.6	14
0.6-0.7	2
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8261	Intermediate Similarity	NPC609651
0.7872	Intermediate Similarity	NPC605688
0.7	Intermediate Similarity	NPC143810
0.7	Intermediate Similarity	NPC83838
0.7	Intermediate Similarity	NPC605986
0.7	Intermediate Similarity	NPC609177
0.6591	Remote Similarity	NPC606552
0.6111	Remote Similarity	NPC601849
0.5455	Remote Similarity	NPC475310
0.5385	Remote Similarity	NPC127824
0.537	Remote Similarity	NPC485573
0.537	Remote Similarity	NPC480697
0.537	Remote Similarity	NPC603728
0.5357	Remote Similarity	NPC603424
0.5263	Remote Similarity	NPC489677
0.5254	Remote Similarity	NPC606888
0.5179	Remote Similarity	NPC601974
0.5094	Remote Similarity	NPC56419
0.5091	Remote Similarity	NPC607547
0.5085	Remote Similarity	NPC269841
0.5085	Remote Similarity	NPC129630
0.5082	Remote Similarity	NPC485432

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC276290 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7411
0.1-0.2	1714
0.2-0.3	23
0.3-0.4	0
0.4-0.5	2
0.5-0.6	0
0.6-0.7	0
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
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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