NPASS Compound

Natural Product: NPC22192

Natural Product ID	NPC22192
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Diplacol
IUPAC Name	(2R,3R)-2-(3,4-dihydroxyphenyl)-6-[(2E)-3,7-dimethylocta-2,6-dienyl]-3,5,7-trihydroxy-2,3-dihydrochromen-4-one
Synonyms	Diplacol
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL411385
PubChem CID	639466
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003646] 6-prenylated flavans [CHEMONTID:0003507] 6-prenylated flavanones

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 60 62 0 0 0 0 0 0 0 0999 V2000 -8.1687 -0.4795 1.8656 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8366 -0.3930 0.4309 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6880 0.2145 0.0699 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8000 0.7704 1.0729 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4825 0.1222 1.2554 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6434 0.1355 0.0364 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4732 0.8029 0.0364 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6514 0.8181 -1.1447 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2725 0.3709 -0.7965 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0910 -0.9227 -0.5569 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4050 -1.2711 -0.2404 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4005 -0.3218 -0.1545 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0534 0.9899 -0.3927 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7606 1.3148 -0.7020 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4318 2.6482 -0.9391 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1154 1.9897 -0.2966 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8259 3.2034 -0.3034 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5442 1.6091 -0.1900 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7461 0.1254 -0.4007 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0907 -0.2762 0.0868 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3568 -0.5247 1.4168 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6141 -0.8961 1.8517 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6659 -1.0359 0.9708 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4136 -0.7903 -0.3628 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1500 -0.4171 -0.7993 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4797 -0.9321 -1.2545 O 0 0 0 0 0 0 0 0 0 0 0 0 9.9400 -1.4092 1.3901 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7139 -0.6412 0.1578 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2469 2.3142 -1.1507 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8634 -1.9220 -0.6272 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0167 -0.5814 -1.1528 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7358 -0.9578 -0.6329 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3697 -0.9852 2.4781 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3368 0.5132 2.3173 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1270 -1.0612 2.0008 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4569 0.3082 -0.9913 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6475 1.8785 0.8551 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3302 0.7036 2.0802 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6358 -0.9702 1.5204 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9406 0.5681 2.1297 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1367 1.3339 0.9196 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5752 1.8819 -1.5277 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9469 0.2146 -2.0047 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6343 -2.3025 -0.0623 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4392 3.3198 -0.1727 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9348 1.8650 0.8021 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7337 -0.0379 -1.5048 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5156 -0.4109 2.1048 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8098 -1.0875 2.8938 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9781 -0.2324 -1.8347 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5269 -1.6596 -1.9552 H 0 0 0 0 0 0 0 0 0 0 0 0 10.7495 -1.1858 0.8227 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7843 2.1774 -2.0208 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6608 -2.8951 -0.4786 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3811 0.0637 -1.9708 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2544 -1.2338 -1.6150 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8507 -1.3050 -0.9043 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3089 -0.0641 -1.0192 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1675 -1.3525 -1.4835 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3931 -1.7011 -0.1610 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 0 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 13 16 1 0 16 17 2 0 16 18 1 0 18 19 1 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 24 26 1 0 23 27 1 0 19 28 1 0 18 29 1 0 10 30 1 0 6 31 1 0 2 32 1 0 14 9 1 0 25 20 1 0 28 12 1 0 1 33 1 0 1 34 1 0 1 35 1 0 3 36 1 0 4 37 1 0 4 38 1 0 5 39 1 0 5 40 1 0 7 41 1 0 8 42 1 0 8 43 1 0 11 44 1 0 15 45 1 0 18 46 1 1 19 47 1 6 21 48 1 0 22 49 1 0 25 50 1 0 26 51 1 0 27 52 1 0 29 53 1 0 30 54 1 0 31 55 1 0 31 56 1 0 31 57 1 0 32 58 1 0 32 59 1 0 32 60 1 0 M END

Standard InCHIKey	UESFDRVOHWXYIQ-PRANAVDNSA-N
Standard InCHI	InChI=1S/C25H28O7/c1-13(2)5-4-6-14(3)7-9-16-18(27)12-20-21(22(16)29)23(30)24(31)25(32-20)15-8-10-17(26)19(28)11-15/h5,7-8,10-12,24-29,31H,4,6,9H2,1-3H3/b14-7+/t24-,25+/m0/s1
SMILES	CC(=CCC/C(=C/Cc1c(cc2c(c1O)C(=O)[C@@H]([C@@H](c1ccc(c(c1)O)O)O2)O)O)/C)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
NPO27255	Macaranga alnifolia	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/0031-9422(92)80315-6]
NPO27255	Macaranga alnifolia	Species	Euphorbiaceae	Eukaryota	n.a.	Madagascar rainforest	n.a.	PMID[17326683]
NPO27255	Macaranga alnifolia	Species	Euphorbiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[17326683]
NPO27255	Macaranga alnifolia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27255	Macaranga alnifolia	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
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
NPT571	Cell line	A2780cisR	Homo sapiens	IC50	=	11500.0	nM	PMID[16413779]

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 NPC22192 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	11354
0.1-0.2	33225
0.2-0.3	4536
0.3-0.4	595
0.4-0.5	103
0.5-0.6	31
0.6-0.7	6
0.7-0.8	0
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8636	High Similarity	NPC262039
0.8143	Intermediate Similarity	NPC282009
0.7917	Intermediate Similarity	NPC287328
0.7857	Intermediate Similarity	NPC470326
0.7183	Intermediate Similarity	NPC213896
0.6456	Remote Similarity	NPC471499
0.6351	Remote Similarity	NPC228504
0.6234	Remote Similarity	NPC298692
0.6119	Remote Similarity	NPC611035
0.6104	Remote Similarity	NPC185276
0.6026	Remote Similarity	NPC321779
0.5921	Remote Similarity	NPC290133
0.5897	Remote Similarity	NPC261063
0.5875	Remote Similarity	NPC45849
0.5875	Remote Similarity	NPC195796
0.5844	Remote Similarity	NPC64915
0.5823	Remote Similarity	NPC278778
0.5769	Remote Similarity	NPC470328
0.5769	Remote Similarity	NPC209614
0.5769	Remote Similarity	NPC164272
0.5769	Remote Similarity	NPC470327
0.5714	Remote Similarity	NPC321399
0.5679	Remote Similarity	NPC210459
0.5658	Remote Similarity	NPC477242
0.5625	Remote Similarity	NPC226025
0.5513	Remote Similarity	NPC488440
0.5507	Remote Similarity	NPC36835
0.5507	Remote Similarity	NPC246162
0.5507	Remote Similarity	NPC9743
0.5507	Remote Similarity	NPC260491
0.5507	Remote Similarity	NPC61506
0.5507	Remote Similarity	NPC240476
0.5488	Remote Similarity	NPC472626
0.5443	Remote Similarity	NPC472629
0.5309	Remote Similarity	NPC472627
0.5309	Remote Similarity	NPC58805
0.525	Remote Similarity	NPC470802
0.5185	Remote Similarity	NPC488556
0.5181	Remote Similarity	NPC472628
0.5132	Remote Similarity	NPC264112
0.5067	Remote Similarity	NPC171651
0.5059	Remote Similarity	NPC472598

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC22192 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3246
0.1-0.2	5777
0.2-0.3	119
0.3-0.4	6
0.4-0.5	2
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