NPASS Compound

Natural Product: NPC295885

Natural Product ID	NPC295885
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Yadanzioside C
IUPAC Name	n.a.
Synonyms	Yadanzioside C
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL499465
PubChem CID	44584515
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0002119] Quassinoids

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

Chemical Representations

RDKit 2D 97102 0 0 0 0 0 0 0 0999 V2000 7.2346 -6.0905 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2704 -7.2395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3062 -8.3886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3420 -7.2395 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8648 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8648 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5658 -5.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5658 -3.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2668 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5658 -2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 -3.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 -5.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2668 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2668 -7.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5095 -4.9895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3313 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3313 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2668 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5863 -1.0950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0325 -2.5271 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6567 0.4034 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1200 0.0738 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3313 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6304 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9294 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6304 -0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3671 2.6491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8802 4.0586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3574 4.3191 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9160 5.2077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4290 6.6172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4648 7.7663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4993 8.9153 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6842 6.8021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6139 8.7305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9062 6.8777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2760 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 -1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8578 2.6401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1459 3.7548 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3250 2.9520 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7886 4.3786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3518 -8.9095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3160 -10.0586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7932 -9.7981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2704 -10.0586 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8290 -11.4681 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3876 -10.0586 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7216 -4.6809 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1213 -6.2753 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4195 -8.2037 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6053 -9.1386 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3876 -7.2395 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0077 -3.3366 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7316 -3.1939 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0544 -0.8318 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9466 -1.6639 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4131 -4.3361 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5453 -6.6595 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7700 -6.4667 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6142 -3.4932 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9867 -4.7291 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8293 -2.9215 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3155 -4.1320 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7121 -2.0861 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4647 -0.5972 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0397 -0.7242 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5252 -2.6758 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2353 1.7873 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1371 1.1763 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5192 2.1595 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2955 2.6491 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5820 5.1292 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9973 8.8369 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7813 7.8251 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0267 5.4539 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8333 5.8379 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6497 9.8795 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9259 8.0034 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7630 9.6946 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8278 8.3756 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1667 5.4005 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3834 7.1382 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6933 -1.9635 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1339 -2.6908 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2152 3.9150 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4291 5.0125 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2521 5.8051 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0528 -8.1595 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1181 -10.9614 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7932 -11.2981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7834 -11.4681 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8648 -12.6172 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7250 -11.5202 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 6 9 11 1 0 11 12 1 0 12 13 1 0 13 14 2 0 12 15 1 0 11 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 20 22 1 0 22 23 1 0 22 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 2 0 27 29 1 0 26 30 1 0 30 31 1 0 31 32 2 0 31 33 1 0 33 34 2 0 34 35 1 0 35 36 1 0 35 37 1 0 35 38 1 0 34 39 1 0 24 40 1 0 40 41 1 0 24 42 1 1 42 43 2 0 42 44 1 0 44 45 1 0 5 46 1 0 46 47 1 0 47 48 1 0 48 49 1 0 47 50 1 0 46 51 1 0 48 3 1 0 13 7 1 0 29 17 1 0 19 9 1 0 18 41 1 6 25 18 1 0 1 52 1 0 2 53 1 0 2 54 1 0 3 55 1 1 5 56 1 1 8 57 1 0 10 58 1 0 10 59 1 0 10 60 1 0 11 61 1 1 12 62 1 6 15 63 1 0 15 64 1 0 15 65 1 0 16 66 1 0 16 67 1 0 17 68 1 6 19 69 1 1 20 70 1 1 21 71 1 0 22 72 1 6 23 73 1 0 25 74 1 6 26 75 1 1 33 76 1 0 36 77 1 0 37 78 1 0 37 79 1 0 37 80 1 0 38 81 1 0 38 82 1 0 38 83 1 0 39 84 1 0 39 85 1 0 39 86 1 0 41 87 1 0 41 88 1 0 45 89 1 0 45 90 1 0 45 91 1 0 46 92 1 6 47 93 1 1 48 94 1 6 49 95 1 0 50 96 1 0 51 97 1 0 M END

Standard InCHIKey	HOEZNQMKHRGGTI-HLPBMULKSA-N
Standard InCHI	InChI=1S/C34H46O17/c1-12(31(3,4)45)7-18(36)51-24-26-33-11-47-34(26,30(44)46-6)27(42)23(41)25(33)32(5)9-15(19(37)13(2)14(32)8-17(33)50-28(24)43)48-29-22(40)21(39)20(38)16(10-35)49-29/h7,9,13-14,16-17,20-27,29,35,38-42,45H,8,10-11H2,1-6H3/b12-7+/t13-,14-,16+,17+,20+,21-,22+,23+,24+,25+,26+,27-,29+,32-,33+,34+/m0/s1
SMILES	OC[C@H]1O[C@@H](OC2=C[C@@]3(C)[C@H]([C@@H](C2=O)C)C[C@@H]2[C@@]45[C@@H]3[C@@H](O)[C@H](O)[C@@]([C@@H]5[C@H](C(=O)O2)OC(=O)/C=C(/C(O)(C)C)C)(OC4)C(=O)OC)[C@@H]([C@H]([C@@H]1O)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
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/0031-9422(96)00258-0]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1016/S1383-5769(99)00023-9]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10086989]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1512598]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[15165151]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	fruit	Indonesia	n.a.	PMID[17896817]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	Vietnam	n.a.	PMID[19026551]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	seeds	n.a.	n.a.	PMID[20050684]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[22506620]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6481366]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561896]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14948	Brucea javanica	Species	Simaroubaceae	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
IC50	1

Activity Type	# Activity
Cell line	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
NPT759	Cell line	H9	Homo sapiens	IC50	=	55000.0	nM	DOI[10.1016/0960-894X(96)00096-0]

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 NPC295885 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	18898
0.1-0.2	27403
0.2-0.3	3417
0.3-0.4	90
0.4-0.5	12
0.5-0.6	17
0.6-0.7	7
0.7-0.8	0
0.8-0.85	1
0.85-0.9	4
0.9-0.95	3
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9294	High Similarity	NPC190065
0.9205	High Similarity	NPC140045
0.908	High Similarity	NPC141215
0.8977	High Similarity	NPC479019
0.8706	High Similarity	NPC475636
0.8587	High Similarity	NPC471089
0.8523	High Similarity	NPC602216
0.8065	Intermediate Similarity	NPC54614
0.73	Intermediate Similarity	NPC102465
0.7172	Intermediate Similarity	NPC251998
0.7143	Intermediate Similarity	NPC480779
0.6863	Remote Similarity	NPC480778
0.6837	Remote Similarity	NPC596
0.6735	Remote Similarity	NPC309096
0.66	Remote Similarity	NPC262813
0.6471	Remote Similarity	NPC480789
0.6147	Remote Similarity	NPC480790
0.61	Remote Similarity	NPC87662
0.5905	Remote Similarity	NPC295220
0.5714	Remote Similarity	NPC476729
0.5684	Remote Similarity	NPC476008
0.567	Remote Similarity	NPC67251
0.5521	Remote Similarity	NPC146432
0.5521	Remote Similarity	NPC470778
0.5484	Remote Similarity	NPC213084
0.5474	Remote Similarity	NPC479018
0.5354	Remote Similarity	NPC480787
0.5312	Remote Similarity	NPC89929
0.52	Remote Similarity	NPC480785
0.52	Remote Similarity	NPC480784
0.5152	Remote Similarity	NPC18945
0.5152	Remote Similarity	NPC152301
0.5149	Remote Similarity	NPC94509
0.5146	Remote Similarity	NPC470779
0.51	Remote Similarity	NPC190185

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC295885 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7065
0.1-0.2	2015
0.2-0.3	69
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