NPASS Compound

Natural Product: NPC128362

Natural Product ID	NPC128362
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DRDZHMFYPWLHJH-SFTDATJTSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	643557
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids [CHEMONTID:0000356] Curcuminoids

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 65 66 0 0 0 0 0 0 0 0999 V2000 0.9457 -2.5216 -4.0482 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3507 -1.9415 -2.8234 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3110 -2.6763 -2.0655 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4913 -0.6339 -2.4800 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0018 0.0479 -1.3884 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0600 0.5833 -0.4502 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8875 -0.5751 0.0865 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9374 -0.1346 1.0059 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1792 0.1836 0.5113 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1760 0.5987 1.3608 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9820 0.7131 2.7196 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7271 0.3929 3.2298 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7349 -0.0234 2.3597 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5609 0.5158 4.5877 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3353 0.2217 5.2311 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0135 1.1363 3.5493 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9032 1.2196 -1.7445 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1148 0.8546 -2.5078 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0289 -0.0887 -1.8683 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7267 0.1686 -0.6128 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0154 0.4181 0.6289 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8219 1.6831 1.1287 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1546 1.9451 2.3079 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6434 0.8973 3.0454 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8156 -0.3894 2.5790 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4820 -0.6158 1.4062 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2893 -1.4201 3.3445 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4594 -2.7416 2.8772 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9635 1.1378 4.2434 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7715 0.3851 -3.8330 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0809 1.0652 -4.9803 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6994 2.1635 -4.8957 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7347 0.5948 -6.3434 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4710 -3.4918 -3.8288 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1629 -2.7626 -4.8168 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6496 -1.8122 -4.5349 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5989 -0.6535 -0.7776 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5188 1.0075 0.4227 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6635 1.3884 -0.8720 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2555 -1.2266 -0.7317 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1810 -1.2217 0.6814 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4095 0.1167 -0.5632 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1607 0.8504 0.9639 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7653 -0.2650 2.7991 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8662 -0.6803 4.7935 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6378 1.1028 5.1369 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5817 0.0350 6.2989 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9757 1.0208 3.2722 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1322 1.8855 -0.9137 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2327 1.9148 -2.4035 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6544 1.8445 -2.7221 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5330 -1.1235 -1.8763 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8731 -0.2943 -2.6398 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4712 1.0233 -0.8232 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4559 -0.7121 -0.4757 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1976 2.5743 0.6031 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0112 2.9477 2.6871 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6289 -1.6143 1.0216 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5055 -2.9504 2.5834 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8219 -2.9386 1.9838 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1696 -3.5002 3.6301 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2915 0.7741 5.1266 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5988 0.8614 -7.0128 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6312 -0.4955 -6.4073 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8587 1.1286 -6.7662 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 12 14 1 0 14 15 1 0 11 16 1 0 5 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 25 27 1 0 27 28 1 0 24 29 1 0 18 30 1 0 30 31 1 0 31 32 2 0 31 33 1 0 13 8 1 0 26 21 1 0 1 34 1 0 1 35 1 0 1 36 1 0 5 37 1 1 6 38 1 0 6 39 1 0 7 40 1 0 7 41 1 0 9 42 1 0 10 43 1 0 13 44 1 0 15 45 1 0 15 46 1 0 15 47 1 0 16 48 1 0 17 49 1 0 17 50 1 0 18 51 1 6 19 52 1 0 19 53 1 0 20 54 1 0 20 55 1 0 22 56 1 0 23 57 1 0 26 58 1 0 28 59 1 0 28 60 1 0 28 61 1 0 29 62 1 0 33 63 1 0 33 64 1 0 33 65 1 0 M END

Standard InCHIKey	DRDZHMFYPWLHJH-SFTDATJTSA-N
Standard InCHI	InChI=1S/C25H32O8/c1-16(26)32-20(9-5-18-7-11-22(28)24(13-18)30-3)15-21(33-17(2)27)10-6-19-8-12-23(29)25(14-19)31-4/h7-8,11-14,20-21,28-29H,5-6,9-10,15H2,1-4H3/t20-,21-/m0/s1
SMILES	CC(=O)O[C@@H](CCc1ccc(c(c1)OC)O)C[C@H](CCc1ccc(c(c1)OC)O)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
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[18177011]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19271742]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20590154]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32872604]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36352904]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39679248]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39680258]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[8064299]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8064299]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Resin, Exudate, Sap	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Rhizome	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

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

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

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 NPC128362 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	10309
0.1-0.2	30362
0.2-0.3	8185
0.3-0.4	762
0.4-0.5	168
0.5-0.6	58
0.6-0.7	5
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
0.7045	Intermediate Similarity	NPC299406
0.6512	Remote Similarity	NPC8547
0.6383	Remote Similarity	NPC70084
0.6383	Remote Similarity	NPC177291
0.6383	Remote Similarity	NPC127937
0.6078	Remote Similarity	NPC114298
0.5962	Remote Similarity	NPC4181
0.5962	Remote Similarity	NPC201777
0.5962	Remote Similarity	NPC604524
0.5882	Remote Similarity	NPC5018
0.5882	Remote Similarity	NPC481914
0.5882	Remote Similarity	NPC86198
0.5814	Remote Similarity	NPC156840
0.5769	Remote Similarity	NPC53305
0.5745	Remote Similarity	NPC603326
0.5741	Remote Similarity	NPC164778
0.5741	Remote Similarity	NPC163083
0.569	Remote Similarity	NPC252307
0.569	Remote Similarity	NPC245826
0.566	Remote Similarity	NPC303680
0.5636	Remote Similarity	NPC257976
0.5636	Remote Similarity	NPC273686
0.5636	Remote Similarity	NPC242372
0.5636	Remote Similarity	NPC312404
0.5625	Remote Similarity	NPC17943
0.5556	Remote Similarity	NPC137427
0.549	Remote Similarity	NPC51840
0.5455	Remote Similarity	NPC481913
0.5455	Remote Similarity	NPC123228
0.5455	Remote Similarity	NPC123722
0.5439	Remote Similarity	NPC20287
0.5439	Remote Similarity	NPC20404
0.54	Remote Similarity	NPC312675
0.54	Remote Similarity	NPC262156
0.54	Remote Similarity	NPC184651
0.54	Remote Similarity	NPC113865
0.5357	Remote Similarity	NPC179777
0.5357	Remote Similarity	NPC257589
0.5345	Remote Similarity	NPC12022
0.5345	Remote Similarity	NPC280767
0.5345	Remote Similarity	NPC278308
0.5319	Remote Similarity	NPC165133
0.5319	Remote Similarity	NPC242885
0.5319	Remote Similarity	NPC95614
0.5319	Remote Similarity	NPC232316
0.5283	Remote Similarity	NPC74817
0.5273	Remote Similarity	NPC487680
0.5263	Remote Similarity	NPC276466
0.5263	Remote Similarity	NPC229497
0.5217	Remote Similarity	NPC257124
0.5192	Remote Similarity	NPC82679
0.5185	Remote Similarity	NPC159968
0.5172	Remote Similarity	NPC304622
0.5172	Remote Similarity	NPC215941
0.5172	Remote Similarity	NPC123196
0.5172	Remote Similarity	NPC311419
0.5106	Remote Similarity	NPC221049
0.5106	Remote Similarity	NPC140359
0.5091	Remote Similarity	NPC282000
0.5091	Remote Similarity	NPC164386
0.5085	Remote Similarity	NPC84076
0.5085	Remote Similarity	NPC275724
0.5085	Remote Similarity	NPC244246
0.5085	Remote Similarity	NPC611247

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC128362 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2474
0.1-0.2	6070
0.2-0.3	590
0.3-0.4	13
0.4-0.5	2
0.5-0.6	1
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
0.5217	Remote Similarity	NPD228	Phase 0

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