NPASS Compound

Natural Product: NPC269318

Natural Product ID	NPC269318
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Orizabin Viii
IUPAC Name	n.a.
Synonyms	Orizabin VIII
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL500529
PubChem CID	21635820
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003918] Saccharolipids

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

Chemical Representations

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33 1 0 33 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 39 40 1 0 39 41 1 0 38 42 1 0 42 43 1 0 43 44 1 0 44 45 1 0 45 46 1 0 46 47 1 0 47 48 1 0 47 49 1 0 46 50 1 0 45 51 1 0 44 52 1 0 37 53 1 0 36 54 1 0 54 55 1 0 55 56 2 0 55 57 1 0 57 58 1 0 57 59 1 0 59 60 1 0 32 61 1 0 61 62 1 0 62 63 1 0 63 64 1 0 64 65 1 0 65 66 1 0 65 67 1 0 67 68 1 0 68 69 1 0 64 70 1 0 63 71 1 0 20 72 1 0 69 6 1 0 33 19 1 0 41 35 1 0 49 43 1 0 68 62 1 0 1 73 1 0 1 74 1 0 1 75 1 0 2 76 1 0 2 77 1 0 3 78 1 0 3 79 1 0 4 80 1 0 4 81 1 0 5 82 1 0 5 83 1 0 6 84 1 1 7 85 1 0 7 86 1 0 8 87 1 0 8 88 1 0 9 89 1 0 9 90 1 0 10 91 1 0 10 92 1 0 11 93 1 0 11 94 1 0 12 95 1 0 12 96 1 0 13 97 1 0 13 98 1 0 14 99 1 0 14100 1 0 15101 1 0 15102 1 0 19103 1 1 20104 1 6 21105 1 1 22106 1 0 22107 1 0 26108 1 6 27109 1 0 27110 1 0 27111 1 0 28112 1 6 29113 1 0 29114 1 0 29115 1 0 30116 1 0 32117 1 1 33118 1 6 35119 1 1 36120 1 6 37121 1 6 38122 1 1 39123 1 6 40124 1 0 40125 1 0 40126 1 0 43127 1 6 44128 1 1 45129 1 6 46130 1 1 47131 1 6 48132 1 0 48133 1 0 48134 1 0 50135 1 0 51136 1 0 52137 1 0 53138 1 0 57139 1 6 58140 1 0 58141 1 0 58142 1 0 59143 1 0 59144 1 0 60145 1 0 60146 1 0 60147 1 0 62148 1 6 63149 1 1 64150 1 6 65151 1 1 66152 1 0 66153 1 0 66154 1 0 68155 1 1 70156 1 0 71157 1 0 72158 1 0 M END

Standard InCHIKey	MTNNYMSRZLOLMA-SUEAJDNPSA-N
Standard InCHI	InChI=1S/C50H86O22/c1-9-11-17-20-30-21-18-15-13-12-14-16-19-22-32(52)68-41-35(55)31(23-62-46(61)25(4)26(5)51)67-50(71-42-37(57)34(54)28(7)64-48(42)66-30)44(41)72-49-43(69-45(60)24(3)10-2)39(59)40(29(8)65-49)70-47-38(58)36(56)33(53)27(6)63-47/h24-31,33-44,47-51,53-59H,9-23H2,1-8H3/t24-,25+,26+,27+,28+,29-,30-,31+,33+,34+,35+,36-,37-,38+,39+,40-,41-,42+,43+,44+,47-,48-,49-,50-/m0/s1
SMILES	CCCCC[C@H]1CCCCCCCCCC(=O)O[C@H]2[C@@H]([C@@H](COC(=O)[C@H](C)[C@@H](C)O)O[C@H]([C@@H]2O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](C)O2)O)O)O)O)OC(=O)[C@@H](C)CC)O[C@@H]2[C@H]([C@@H]([C@@H](C)O[C@H]2O1)O)O)O

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
NPO19009	Ipomoea orizabensis	Species	Convolvulaceae	Eukaryota	Roots	Mexican	n.a.	PMID[10479311]
NPO19009	Ipomoea orizabensis	Species	Convolvulaceae	Eukaryota	crude resin	Mexican	n.a.	PMID[16562846]
NPO19009	Ipomoea orizabensis	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19009	Ipomoea orizabensis	Species	Convolvulaceae	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
ED50	4

Activity Type	# Activity
Cell line	3
Non-molecular	1

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
NPT91	Cell line	KB	Homo sapiens	ED50	=	7.0	ug ml-1	PMID[23972215]
NPT5198	Cell line	OVCAR	Homo sapiens	ED50	>	15.0	ug ml-1	PMID[21071520]
NPT148	Cell line	HCT-15	Homo sapiens	ED50	>	15.0	ug ml-1	PMID[26372073]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	ED50	>	15.0	ug ml-1	PMID[10479311]

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 NPC269318 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	25034
0.1-0.2	21757
0.2-0.3	2790
0.3-0.4	152
0.4-0.5	16
0.5-0.6	58
0.6-0.7	47
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
0.7701	Intermediate Similarity	NPC173328
0.7416	Intermediate Similarity	NPC186992
0.7241	Intermediate Similarity	NPC89843
0.7065	Intermediate Similarity	NPC238056
0.6966	Remote Similarity	NPC158302
0.6957	Remote Similarity	NPC483170
0.6957	Remote Similarity	NPC476087
0.6957	Remote Similarity	NPC475667
0.6882	Remote Similarity	NPC478732
0.6848	Remote Similarity	NPC119583
0.6813	Remote Similarity	NPC146992
0.6813	Remote Similarity	NPC85759
0.6809	Remote Similarity	NPC475270
0.6809	Remote Similarity	NPC475327
0.6739	Remote Similarity	NPC44682
0.6702	Remote Similarity	NPC169345
0.6702	Remote Similarity	NPC115013
0.6667	Remote Similarity	NPC294748
0.6598	Remote Similarity	NPC475164
0.6526	Remote Similarity	NPC477317
0.6526	Remote Similarity	NPC477318
0.6484	Remote Similarity	NPC477331
0.6481	Remote Similarity	NPC472352
0.6452	Remote Similarity	NPC478722
0.6364	Remote Similarity	NPC473605
0.6364	Remote Similarity	NPC475375
0.6316	Remote Similarity	NPC478730
0.6304	Remote Similarity	NPC477332
0.6289	Remote Similarity	NPC184915
0.6289	Remote Similarity	NPC224953
0.6264	Remote Similarity	NPC22742
0.6264	Remote Similarity	NPC477346
0.625	Remote Similarity	NPC478726
0.6211	Remote Similarity	NPC477319
0.6186	Remote Similarity	NPC478731
0.6162	Remote Similarity	NPC44782
0.6146	Remote Similarity	NPC143421
0.6146	Remote Similarity	NPC307400
0.6146	Remote Similarity	NPC27289
0.6122	Remote Similarity	NPC479057
0.6105	Remote Similarity	NPC479061
0.6105	Remote Similarity	NPC60849
0.6091	Remote Similarity	NPC600940
0.6061	Remote Similarity	NPC475525
0.6061	Remote Similarity	NPC475540
0.6044	Remote Similarity	NPC477329
0.6042	Remote Similarity	NPC479060
0.6023	Remote Similarity	NPC478729
0.602	Remote Similarity	NPC290012
0.6019	Remote Similarity	NPC610996
0.6	Remote Similarity	NPC476066
0.5979	Remote Similarity	NPC472204
0.5941	Remote Similarity	NPC478728
0.5934	Remote Similarity	NPC477330
0.59	Remote Similarity	NPC163409
0.59	Remote Similarity	NPC123204
0.5882	Remote Similarity	NPC478727
0.5876	Remote Similarity	NPC479058
0.5876	Remote Similarity	NPC297768
0.5876	Remote Similarity	NPC478724
0.5833	Remote Similarity	NPC109887
0.5824	Remote Similarity	NPC475425
0.578	Remote Similarity	NPC10883
0.578	Remote Similarity	NPC611287
0.5773	Remote Similarity	NPC478725
0.5761	Remote Similarity	NPC477328
0.5743	Remote Similarity	NPC472200
0.5729	Remote Similarity	NPC479059
0.5714	Remote Similarity	NPC478723
0.5664	Remote Similarity	NPC610997
0.5652	Remote Similarity	NPC146380
0.5644	Remote Similarity	NPC183888
0.5644	Remote Similarity	NPC259294
0.5644	Remote Similarity	NPC126685
0.5636	Remote Similarity	NPC10121
0.5636	Remote Similarity	NPC198918
0.5625	Remote Similarity	NPC478734
0.5625	Remote Similarity	NPC600721
0.5625	Remote Similarity	NPC605872
0.5619	Remote Similarity	NPC475241
0.5612	Remote Similarity	NPC267592
0.5586	Remote Similarity	NPC600672
0.5579	Remote Similarity	NPC113745
0.5579	Remote Similarity	NPC477320
0.5579	Remote Similarity	NPC477323
0.5579	Remote Similarity	NPC477325
0.5579	Remote Similarity	NPC609436
0.5567	Remote Similarity	NPC477344
0.5543	Remote Similarity	NPC477350
0.5534	Remote Similarity	NPC477347
0.5532	Remote Similarity	NPC281563
0.551	Remote Similarity	NPC478733
0.5495	Remote Similarity	NPC290276
0.5495	Remote Similarity	NPC606819
0.5446	Remote Similarity	NPC238264
0.5446	Remote Similarity	NPC477345
0.5417	Remote Similarity	NPC477349
0.5361	Remote Similarity	NPC604005
0.5361	Remote Similarity	NPC605014
0.5273	Remote Similarity	NPC35338
0.5273	Remote Similarity	NPC204214
0.5273	Remote Similarity	NPC63404
0.5273	Remote Similarity	NPC92283
0.5253	Remote Similarity	NPC600446
0.5253	Remote Similarity	NPC605013
0.5248	Remote Similarity	NPC472205
0.5234	Remote Similarity	NPC477348
0.5225	Remote Similarity	NPC28069
0.51	Remote Similarity	NPC477326

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC269318 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7453
0.1-0.2	1623
0.2-0.3	73
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