NPASS Compound

Natural Product: NPC472759

Natural Product ID	NPC472759
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NOBRZUCGXCJOPI-CZBHJNBTSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3582006
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0002875] Tigliane and ingenane diterpenoids

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 84 87 0 0 0 0 0 0 0 0999 V2000 8.6181 2.2862 1.0128 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1445 2.2283 -0.4034 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0495 1.8378 -1.3291 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8171 1.5872 -0.9434 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8236 1.2107 -1.9522 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5599 0.9487 -1.5933 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5754 0.5810 -2.5522 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3329 0.3143 -2.2707 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7823 0.3535 -0.9554 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4168 0.6413 0.0555 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4382 0.0485 -0.7886 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2271 0.0590 0.4846 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5307 -1.3463 0.8669 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0371 -1.6273 2.2999 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9786 -1.7524 0.8584 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4915 -1.3793 2.1262 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9946 -3.2246 0.8191 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3047 -3.8934 -0.2792 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7458 -5.1590 -0.2996 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7217 -5.3371 0.7686 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0605 -6.3206 1.4209 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2779 -3.9491 0.9222 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1362 -3.8275 -0.3402 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7879 -2.5173 -0.3121 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1749 -1.3489 -0.2347 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7079 -0.9898 -0.1543 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6822 0.4723 0.2290 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3399 1.0231 0.4612 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2882 2.0412 1.4477 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3236 2.9808 1.6100 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6404 3.0013 0.8371 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3833 3.9959 2.6926 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8910 5.3277 2.1860 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0084 5.8763 1.0992 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0765 1.4072 -0.7621 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7964 2.7736 -0.7637 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7109 1.0316 -2.1436 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2569 -2.4546 -0.3730 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7297 -3.0372 -1.5541 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3035 -6.2178 -1.2545 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1604 1.3041 1.2862 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4518 2.4337 1.7483 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9228 3.1239 1.1328 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5140 3.2589 -0.6655 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9798 1.5331 -0.5157 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2744 1.7506 -2.4021 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5580 1.6607 0.0854 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0664 1.1330 -2.9890 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3673 1.0394 -0.5500 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9185 0.5258 -3.6076 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6955 0.0435 -3.1388 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5679 0.3928 1.1954 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0687 -2.0949 0.2615 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3025 -2.6761 2.4168 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7788 -1.3376 3.0477 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9050 -1.0113 2.3954 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4774 -1.4449 2.0833 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4166 -3.5415 1.7521 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5640 -3.5381 -1.0028 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8442 -3.8278 1.8370 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4055 -3.8200 -1.1948 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8347 -4.6796 -0.4029 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8904 -0.5104 -0.2319 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3163 -1.1813 -1.1664 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5038 0.7940 0.9025 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0783 3.6558 3.4824 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6334 4.1838 3.1022 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9120 5.2126 1.7206 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9088 6.0311 3.0238 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4546 5.7343 0.0805 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1750 6.9625 1.2070 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9905 5.3680 1.0516 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2098 3.5170 -1.3102 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1060 3.0682 0.2399 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7285 2.5993 -1.3537 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5866 1.2004 -2.8387 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9602 1.7960 -2.5068 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2748 0.0697 -2.3365 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6413 -1.4204 -0.3596 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7490 -2.9653 0.4963 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5889 -2.4690 -2.3399 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1543 -5.7811 -2.2845 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3648 -6.7160 -0.9066 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0504 -7.0223 -1.3827 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 13 15 1 0 15 16 1 1 15 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 20 22 1 0 22 23 1 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 1 29 30 1 0 30 31 2 0 30 32 1 0 32 33 1 0 33 34 1 0 28 35 1 0 35 36 1 0 35 37 1 0 24 38 1 0 38 39 1 0 19 40 1 0 28 12 1 0 26 15 1 0 35 27 1 0 22 17 1 0 1 41 1 0 1 42 1 0 1 43 1 0 2 44 1 0 2 45 1 0 3 46 1 0 4 47 1 0 5 48 1 0 6 49 1 0 7 50 1 0 8 51 1 0 12 52 1 1 13 53 1 6 14 54 1 0 14 55 1 0 14 56 1 0 16 57 1 0 17 58 1 1 18 59 1 0 22 60 1 1 23 61 1 0 23 62 1 0 25 63 1 0 26 64 1 6 27 65 1 1 32 66 1 0 32 67 1 0 33 68 1 0 33 69 1 0 34 70 1 0 34 71 1 0 34 72 1 0 36 73 1 0 36 74 1 0 36 75 1 0 37 76 1 0 37 77 1 0 37 78 1 0 38 79 1 0 38 80 1 0 39 81 1 0 40 82 1 0 40 83 1 0 40 84 1 0 M END

Standard InCHIKey	NOBRZUCGXCJOPI-CZBHJNBTSA-N
Standard InCHI	InChI=1S/C33H44O7/c1-7-9-10-11-12-13-15-26(35)39-30-21(4)32(38)24-16-20(3)28(37)23(24)17-22(19-34)18-25(32)29-31(5,6)33(29,30)40-27(36)14-8-2/h9-13,15-16,18,21,23-25,29-30,34,38H,7-8,14,17,19H2,1-6H3/b10-9+,12-11+,15-13-/t21-,23-,24-,25+,29-,30-,32+,33-/m1/s1
SMILES	CC/C=C/C=C/C=CC(=O)O[C@@H]1[C@@H](C)[C@]2(O)[C@@H]3C=C(C(=O)[C@@H]3CC(=C[C@H]2[C@H]2[C@]1(OC(=O)CCC)C2(C)C)CO)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
NPO33329	stillingia lineata	Species	Euphorbiaceae	Eukaryota	Leaves	Langevin, La Reunion, France	2009-Nov	PMID[25946116]
NPO33329	stillingia lineata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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
EC50	5
Inhibition	3
Ratio CC50/EC50	4
CC50	2

Activity Type	# Activity
Cell line	5
Organism	4
Non-molecular	1
Others	4

Molecular-level activity

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

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT393	Cell line	HCT-116	Homo sapiens	Inhibition	<	40.0	%	PMID[17844994]
NPT83	Cell line	MCF7	Homo sapiens	Inhibition	<	40.0	%	PMID[23398362]
NPT306	Cell line	PC-3	Homo sapiens	Inhibition	<	40.0	%	PubChem BioAssay data set
NPT189	Cell line	Vero	Chlorocebus aethiops	CC50	=	7100.0	nM	DrugMatrix in vivo data: Biochemistry
NPT25	Cell line	MT4	Homo sapiens	CC50	=	8400.0	nM	PMID[20805391]
NPT856	Organism	Semliki forest virus	Semliki forest virus	EC50	>	177000.0	nM	PMID[17190442]
NPT332	Organism	Human immunodeficiency virus type 2 (ISOLATE ROD)	Human immunodeficiency virus type 2 (ISOLATE ROD)	EC50	=	174.0	nM	PMID[18302336]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	EC50	=	1400.0	nM	PMID[25946116]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	233.0	nM	PMID[18809945]
NPT338	Organism	Sindbis virus	Sindbis virus	EC50	=	5000.0	nM	PMID[19029333]
NPT2	Others	Unspecified	n.a.	Ratio CC50/EC50	=	36.0	n.a.	PMID[18500841]
NPT2	Others	Unspecified	n.a.	Ratio CC50/EC50	=	33.0	n.a.	PMID[17181158]
NPT2	Others	Unspecified	n.a.	Ratio CC50/EC50	=	5.1	n.a.	PMID[14738378]
NPT2	Others	Unspecified	n.a.	Ratio CC50/EC50	=	1.4	n.a.	PMID[23398362]

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 NPC472759 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	19566
0.1-0.2	29128
0.2-0.3	1014
0.3-0.4	64
0.4-0.5	43
0.5-0.6	17
0.6-0.7	16
0.7-0.8	0
0.8-0.85	2
0.85-0.9	2
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9104	High Similarity	NPC608501
0.8571	High Similarity	NPC236918
0.8571	High Similarity	NPC156745
0.8219	Intermediate Similarity	NPC482220
0.8082	Intermediate Similarity	NPC482221
0.7867	Intermediate Similarity	NPC482222
0.7763	Intermediate Similarity	NPC482219
0.7027	Intermediate Similarity	NPC485737
0.6883	Remote Similarity	NPC10721
0.6849	Remote Similarity	NPC154363
0.6806	Remote Similarity	NPC482406
0.6711	Remote Similarity	NPC476111
0.6622	Remote Similarity	NPC472757
0.6622	Remote Similarity	NPC481522
0.6533	Remote Similarity	NPC481520
0.6447	Remote Similarity	NPC234858
0.6447	Remote Similarity	NPC179207
0.641	Remote Similarity	NPC90814
0.641	Remote Similarity	NPC189393
0.6341	Remote Similarity	NPC329080
0.6296	Remote Similarity	NPC145238
0.6282	Remote Similarity	NPC471127
0.6282	Remote Similarity	NPC481525
0.6282	Remote Similarity	NPC481531
0.5949	Remote Similarity	NPC475885
0.575	Remote Similarity	NPC485734
0.5663	Remote Similarity	NPC478999
0.5632	Remote Similarity	NPC482199
0.5632	Remote Similarity	NPC482197
0.5568	Remote Similarity	NPC140021
0.5506	Remote Similarity	NPC482198
0.5465	Remote Similarity	NPC481523
0.5444	Remote Similarity	NPC479001
0.5444	Remote Similarity	NPC479002
0.5443	Remote Similarity	NPC171905
0.5412	Remote Similarity	NPC484333
0.5341	Remote Similarity	NPC611138
0.5275	Remote Similarity	NPC112752
0.5275	Remote Similarity	NPC311054
0.5244	Remote Similarity	NPC482405
0.5119	Remote Similarity	NPC481528

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC472759 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6787
0.1-0.2	2331
0.2-0.3	32
0.3-0.4	0
0.4-0.5	0
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