NPASS Compound

Natural Product: NPC228674

Natural Product ID	NPC228674
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	GSKSGARIFBGQBN-FTXQXWJMSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
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:0002877] Jatrophane and cyclojatrophane 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 85 87 0 0 0 0 0 0 0 0999 V2000 0.5957 -3.4084 1.8899 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1095 -3.2524 0.5420 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1820 -2.2370 0.6215 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3455 -1.4115 1.6098 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2827 -0.3598 1.9185 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6529 0.6585 2.8144 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3365 -1.0797 2.8273 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1530 0.2836 0.9113 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5773 0.8425 -0.3002 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1729 1.2710 -0.3923 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3530 0.4805 -1.3296 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6636 -0.2559 -0.8922 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5382 -1.0874 -1.6817 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8898 -0.5116 -1.8724 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6641 -1.7063 -2.4059 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3086 -1.8027 -3.8951 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0370 -2.8677 -1.6771 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9411 -2.3210 -0.8257 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8131 -3.2020 -0.5758 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6170 -4.0474 -1.4716 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5111 -1.7962 0.3287 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4395 -0.1578 -0.6258 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9437 1.1092 -0.3877 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8954 1.9411 -1.3249 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5188 1.5134 0.8827 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0034 2.7925 1.0561 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5596 3.2309 2.2396 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6510 2.3811 3.3154 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1739 1.1011 3.1644 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6181 0.6666 1.9782 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6771 0.4965 -2.7750 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8710 2.6053 -0.4560 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1573 3.3796 0.4115 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3171 2.8313 1.4381 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0235 4.8235 0.1031 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4374 1.5586 -1.1048 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0674 1.2342 -2.2578 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8814 0.1068 -2.7238 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9627 2.1722 -2.9739 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2531 -0.5393 0.5330 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5614 -0.2912 0.8302 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7601 0.7459 1.4840 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6174 -1.2155 0.3853 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1818 -2.5041 2.1533 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1716 -3.5238 2.6838 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1878 -4.3330 1.8838 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7076 -4.2261 0.4813 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8410 -2.2432 -0.2304 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5914 -1.5363 2.4294 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9337 1.7129 2.5146 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0459 0.6244 3.8803 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5598 0.5370 2.9659 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9415 -1.7655 2.2338 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8189 -1.6649 3.6009 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9800 -0.3532 3.3132 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6597 1.0907 1.4591 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5468 -0.1588 -0.9948 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6624 0.9651 0.6435 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8397 -0.2007 0.2053 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1018 -1.4931 -2.6165 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9204 0.3371 -2.5940 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7438 -1.6183 -2.2530 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1770 -2.0331 -4.5158 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8635 -0.8622 -4.2674 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5713 -2.6413 -4.0617 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8198 -3.4115 -1.0858 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6596 -3.6098 -2.4235 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1552 -2.3979 0.7566 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9413 3.4886 0.2117 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9338 4.2508 2.3425 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0874 2.7093 4.2592 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2222 0.3946 3.9790 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2469 -0.3468 1.8764 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2711 0.5971 -3.3796 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3022 1.3354 -3.0891 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2178 -0.4405 -3.0634 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8612 5.2739 0.6700 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9438 5.3499 0.3476 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2753 4.9804 -0.9790 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9717 2.2252 -2.5198 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1106 1.8624 -4.0376 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5684 3.2154 -2.9809 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5721 -2.1993 0.9032 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6271 -1.3133 -0.7111 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5983 -0.7484 0.6735 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 1 0 5 7 1 0 5 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 15 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 18 21 1 1 14 22 1 0 22 23 1 0 23 24 2 0 23 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 28 29 1 0 29 30 2 0 11 31 1 0 10 32 1 0 32 33 1 0 33 34 2 0 33 35 1 0 9 36 1 0 36 37 1 0 37 38 2 0 37 39 1 0 8 40 1 0 40 41 1 0 41 42 2 0 41 43 1 0 19 2 1 0 30 25 1 0 18 13 1 0 1 44 1 0 1 45 1 0 1 46 1 0 2 47 1 6 3 48 1 0 4 49 1 0 6 50 1 0 6 51 1 0 6 52 1 0 7 53 1 0 7 54 1 0 7 55 1 0 8 56 1 1 9 57 1 6 10 58 1 1 12 59 1 0 13 60 1 6 14 61 1 6 15 62 1 6 16 63 1 0 16 64 1 0 16 65 1 0 17 66 1 0 17 67 1 0 21 68 1 0 26 69 1 0 27 70 1 0 28 71 1 0 29 72 1 0 30 73 1 0 31 74 1 0 31 75 1 0 31 76 1 0 35 77 1 0 35 78 1 0 35 79 1 0 39 80 1 0 39 81 1 0 39 82 1 0 43 83 1 0 43 84 1 0 43 85 1 0 M END

Standard InCHIKey	GSKSGARIFBGQBN-FTXQXWJMSA-N
Standard InCHI	InChI=1S/C33H42O10/c1-18-14-15-32(7,8)30(42-23(6)36)28(41-22(5)35)27(40-21(4)34)19(2)16-25-26(20(3)17-33(25,39)29(18)37)43-31(38)24-12-10-9-11-13-24/h9-16,18,20,25-28,30,39H,17H2,1-8H3/b15-14+,19-16+/t18-,20+,25-,26-,27+,28-,30+,33+/m0/s1
SMILES	C[C@H]1/C=C/C(C)(C)[C@@H]([C@H]([C@@H](/C(=C/[C@H]2[C@H]([C@H](C)C[C@@]2(C1=O)O)OC(=O)c1ccccc1)/C)OC(=O)C)OC(=O)C)OC(=O)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
NPO17435	Euphorbia mellifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23098168]
NPO17435	Euphorbia mellifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17435	Euphorbia mellifera	Species	Euphorbiaceae	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
Ratio	6
Activity	3

Activity Type	# Activity
Cell line	2
Individual protein	6
Non-molecular	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	Ratio	=	5.1	n.a.	PMID[23098168]
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	Ratio	=	1.1	n.a.	PMID[23098168]
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	Ratio	=	72.9	n.a.	PMID[23098168]
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	Ratio	=	12.1	n.a.	PMID[23098168]
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	Ratio	=	2.9	n.a.	PMID[23098168]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2641	Cell line	COLO 320	Homo sapiens	Activity	=	4.97	%	PMID[23098168]
NPT2641	Cell line	COLO 320	Homo sapiens	Activity	=	6.72	%	PMID[23098168]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Activity	=	0.74	%	PMID[23098168]

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 NPC228674 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	9106
0.1-0.2	37118
0.2-0.3	3014
0.3-0.4	505
0.4-0.5	79
0.5-0.6	24
0.6-0.7	6
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	Natural Product ID
0.7397	Intermediate Similarity	NPC482358
0.7397	Intermediate Similarity	NPC482232
0.6974	Remote Similarity	NPC482266
0.6709	Remote Similarity	NPC482224
0.6709	Remote Similarity	NPC482225
0.6543	Remote Similarity	NPC482201
0.6049	Remote Similarity	NPC482231
0.6	Remote Similarity	NPC482360
0.5854	Remote Similarity	NPC482247
0.5679	Remote Similarity	NPC473497
0.5667	Remote Similarity	NPC482259
0.5632	Remote Similarity	NPC482202
0.5568	Remote Similarity	NPC482155
0.5506	Remote Similarity	NPC482204
0.5476	Remote Similarity	NPC475262
0.5412	Remote Similarity	NPC482248
0.5349	Remote Similarity	NPC482268
0.5349	Remote Similarity	NPC482269
0.5301	Remote Similarity	NPC482313
0.5301	Remote Similarity	NPC482227
0.5294	Remote Similarity	NPC290833
0.5294	Remote Similarity	NPC482304
0.5233	Remote Similarity	NPC482316
0.5233	Remote Similarity	NPC482251
0.5181	Remote Similarity	NPC233860
0.5172	Remote Similarity	NPC482267
0.5119	Remote Similarity	NPC482228
0.5116	Remote Similarity	NPC265459
0.5116	Remote Similarity	NPC482249
0.5116	Remote Similarity	NPC482265
0.5109	Remote Similarity	NPC482154
0.506	Remote Similarity	NPC601473

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC228674 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3149
0.1-0.2	5826
0.2-0.3	174
0.3-0.4	1
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