NPASS Compound

Natural Product: NPC81945

Natural Product ID	NPC81945
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	VCCNKWWXYVWTLT-CYZBKYQRSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	69964214
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-glycosides

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 75 79 0 0 0 0 0 0 0 0999 V2000 -1.5085 2.1903 1.8695 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8652 1.5921 2.2165 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.9794 2.5902 2.0283 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2690 1.7700 1.8913 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1559 1.0692 0.5392 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7431 0.5427 0.3454 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0636 0.4149 1.5365 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7618 -0.7407 -0.2441 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1409 -0.7378 -1.4895 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1416 -1.2483 -2.5035 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3158 -2.7354 -2.2774 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0318 -3.4263 -2.6212 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0520 -4.0428 -4.0116 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0322 -4.9941 -4.1616 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0004 -2.4910 -2.6166 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9974 -1.7363 -1.4386 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7524 -1.1204 -1.3566 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2199 -1.2773 -0.4194 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0913 -2.1208 0.6404 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1041 -2.2703 1.5975 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2624 -1.5303 1.4443 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3055 -1.6224 2.3453 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1917 -2.3972 3.3220 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4378 -0.8513 2.1302 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5693 0.0019 1.0593 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7448 0.8240 0.8065 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8362 1.6666 -0.2789 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9319 2.4476 -0.5347 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9977 2.3981 0.3240 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9573 1.5646 1.4346 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8139 0.7828 1.6560 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0407 1.5345 2.2796 O 0 0 0 0 0 0 0 0 0 0 0 0 9.1109 3.1914 0.0643 O 0 0 0 0 0 0 0 0 0 0 0 0 9.1091 4.0225 -1.0743 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5343 0.0423 0.2352 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4402 -0.6633 0.3889 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3949 -0.5568 -0.5334 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9768 -3.1247 2.6731 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5312 -2.9021 -0.8902 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6133 -1.0125 -3.7872 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4298 2.0723 -0.4187 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3064 2.6887 1.7991 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0710 3.5041 3.0625 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4269 3.2095 2.2907 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7333 1.5790 2.3613 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4186 2.1707 0.7735 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7900 1.3221 3.3107 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8386 3.0944 1.0341 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3955 1.0663 2.7207 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9230 0.2940 0.4332 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2173 1.2394 -0.3692 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7854 0.2833 -1.7062 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1078 -0.7090 -2.4574 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1759 -3.1388 -2.8578 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7575 -4.2249 -1.9000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0132 -4.4593 -4.1604 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1335 -3.2114 -4.7477 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3201 -5.3445 -3.2932 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1282 -2.4255 -0.5951 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7778 -2.7039 0.7935 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2506 -0.9367 2.8509 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0004 1.7133 -0.9629 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9816 3.1143 -1.4102 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8665 0.1654 2.5397 H 0 0 0 0 0 0 0 0 0 0 0 0 9.8075 0.9117 2.0318 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9960 3.3503 -1.9611 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2897 4.7664 -1.0507 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0850 4.5457 -1.1149 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5410 0.1270 -1.3615 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2067 -2.9982 3.2972 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8085 -3.8391 -0.6877 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2568 -0.0992 -3.7636 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3685 2.0597 -0.7044 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0259 2.4046 1.1951 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9306 3.3649 3.5491 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 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 12 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 22 24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 27 28 1 0 28 29 2 0 29 30 1 0 30 31 2 0 30 32 1 0 29 33 1 0 33 34 1 0 25 35 1 0 35 36 1 0 36 37 2 0 20 38 1 0 11 39 1 0 10 40 1 0 5 41 1 0 4 42 1 0 3 43 1 0 7 2 1 0 16 9 1 0 37 18 1 0 36 21 1 0 31 26 1 0 1 44 1 0 1 45 1 0 1 46 1 0 2 47 1 1 3 48 1 6 4 49 1 1 5 50 1 1 6 51 1 6 9 52 1 6 10 53 1 6 11 54 1 6 12 55 1 1 13 56 1 0 13 57 1 0 14 58 1 0 16 59 1 1 19 60 1 0 24 61 1 0 27 62 1 0 28 63 1 0 31 64 1 0 32 65 1 0 34 66 1 0 34 67 1 0 34 68 1 0 37 69 1 0 38 70 1 0 39 71 1 0 40 72 1 0 41 73 1 0 42 74 1 0 43 75 1 0 M END

Standard InCHIKey	VCCNKWWXYVWTLT-CYZBKYQRSA-N
Standard InCHI	InChI=1S/C28H32O15/c1-10-21(33)23(35)25(37)27(39-10)43-26-24(36)22(34)19(9-29)42-28(26)40-12-6-14(31)20-15(32)8-17(41-18(20)7-12)11-3-4-16(38-2)13(30)5-11/h3-8,10,19,21-31,33-37H,9H2,1-2H3/t10-,19+,21-,22+,23+,24-,25+,26+,27-,28+/m0/s1
SMILES	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@@H]([C@@H](CO)O[C@H]1Oc1cc(c2c(=O)cc(c3ccc(c(c3)O)OC)oc2c1)O)O)O)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
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0031-9422(99)00119-3]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37049761]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27288	Citrus maxima	Species	Rutaceae	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

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 NPC81945 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	18457
0.1-0.2	26524
0.2-0.3	3903
0.3-0.4	611
0.4-0.5	253
0.5-0.6	70
0.6-0.7	26
0.7-0.8	1
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8471	Intermediate Similarity	NPC115674
0.8409	Intermediate Similarity	NPC195257
0.8316	Intermediate Similarity	NPC198199
0.814	Intermediate Similarity	NPC65003
0.7879	Intermediate Similarity	NPC120952
0.7791	Intermediate Similarity	NPC8856
0.7529	Intermediate Similarity	NPC22832
0.7347	Intermediate Similarity	NPC311850
0.7234	Intermediate Similarity	NPC475382
0.7204	Intermediate Similarity	NPC209296
0.6961	Remote Similarity	NPC68592
0.6932	Remote Similarity	NPC80188
0.6809	Remote Similarity	NPC240306
0.6768	Remote Similarity	NPC11468
0.6571	Remote Similarity	NPC298666
0.6569	Remote Similarity	NPC473644
0.6566	Remote Similarity	NPC253685
0.6495	Remote Similarity	NPC32641
0.6495	Remote Similarity	NPC256188
0.6477	Remote Similarity	NPC95090
0.6477	Remote Similarity	NPC27408
0.6442	Remote Similarity	NPC488083
0.6422	Remote Similarity	NPC262222
0.6327	Remote Similarity	NPC35119
0.6277	Remote Similarity	NPC239549
0.625	Remote Similarity	NPC22062
0.625	Remote Similarity	NPC473634
0.625	Remote Similarity	NPC138811
0.6196	Remote Similarity	NPC243930
0.6186	Remote Similarity	NPC122809
0.618	Remote Similarity	NPC19709
0.6129	Remote Similarity	NPC311830
0.6111	Remote Similarity	NPC189142
0.6111	Remote Similarity	NPC77660
0.6087	Remote Similarity	NPC611303
0.6019	Remote Similarity	NPC488086
0.5957	Remote Similarity	NPC607707
0.5938	Remote Similarity	NPC251417
0.5926	Remote Similarity	NPC223579
0.5918	Remote Similarity	NPC210073
0.5889	Remote Similarity	NPC473043
0.5889	Remote Similarity	NPC331652
0.5882	Remote Similarity	NPC220173
0.5859	Remote Similarity	NPC257566
0.5851	Remote Similarity	NPC486578
0.5851	Remote Similarity	NPC601144
0.5851	Remote Similarity	NPC605067
0.5833	Remote Similarity	NPC488087
0.5824	Remote Similarity	NPC261866
0.5824	Remote Similarity	NPC39360
0.5824	Remote Similarity	NPC29763
0.5824	Remote Similarity	NPC210003
0.5773	Remote Similarity	NPC606546
0.5745	Remote Similarity	NPC191306
0.5745	Remote Similarity	NPC285197
0.57	Remote Similarity	NPC470444
0.5699	Remote Similarity	NPC181712
0.5657	Remote Similarity	NPC44931
0.5657	Remote Similarity	NPC163242
0.5657	Remote Similarity	NPC272068
0.5652	Remote Similarity	NPC199172
0.5648	Remote Similarity	NPC480441
0.5648	Remote Similarity	NPC25523
0.5631	Remote Similarity	NPC142142
0.5603	Remote Similarity	NPC35924
0.56	Remote Similarity	NPC155877
0.5566	Remote Similarity	NPC14187
0.5545	Remote Similarity	NPC255799
0.5514	Remote Similarity	NPC25724
0.5472	Remote Similarity	NPC135358
0.5464	Remote Similarity	NPC220169
0.5463	Remote Similarity	NPC473072
0.5408	Remote Similarity	NPC190003
0.5385	Remote Similarity	NPC606657
0.534	Remote Similarity	NPC64425
0.5319	Remote Similarity	NPC58053
0.5312	Remote Similarity	NPC27942
0.5306	Remote Similarity	NPC136761
0.5283	Remote Similarity	NPC473071
0.5238	Remote Similarity	NPC473623
0.5221	Remote Similarity	NPC488088
0.5217	Remote Similarity	NPC470719
0.5208	Remote Similarity	NPC186807
0.5192	Remote Similarity	NPC606547
0.5189	Remote Similarity	NPC479766
0.5189	Remote Similarity	NPC488089
0.5158	Remote Similarity	NPC289667
0.5158	Remote Similarity	NPC143851
0.5152	Remote Similarity	NPC116458
0.5152	Remote Similarity	NPC246943
0.5152	Remote Similarity	NPC605784
0.5149	Remote Similarity	NPC473682
0.514	Remote Similarity	NPC256760
0.5128	Remote Similarity	NPC209550
0.51	Remote Similarity	NPC170052
0.51	Remote Similarity	NPC135846
0.5096	Remote Similarity	NPC204693
0.5094	Remote Similarity	NPC482026
0.5052	Remote Similarity	NPC84362
0.5052	Remote Similarity	NPC45638
0.505	Remote Similarity	NPC254855
0.505	Remote Similarity	NPC94610
0.5049	Remote Similarity	NPC78734
0.5048	Remote Similarity	NPC46202
0.5043	Remote Similarity	NPC295625
0.5043	Remote Similarity	NPC470720

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC81945 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5014
0.1-0.2	4041
0.2-0.3	84
0.3-0.4	6
0.4-0.5	3
0.5-0.6	1
0.6-0.7	0
0.7-0.8	1
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
0.7204	Intermediate Similarity	NPD7054	Phase 4
0.5514	Remote Similarity	NPD7472	Pre-clinical

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