NPASS Compound

Natural Product: NPC537648

Natural Product ID	NPC537648
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	[(2~{R},3~{R},4~{R},5~{R},6~{R})-6-[2-(3,4-dihydroxyphenyl)ethoxy]-5-hydroxy-4-[(2~{S},3~{R},4~{R},5~{R},6~{S})-3,4,5-trihydroxy-6-methyl-tetrahydropyran-2-yl]oxy-2-[[(2~{S},3~{S},4~{R},5~{R})-3,4,5-trihydroxytetrahydropyran-2-yl]oxymethyl]tetrahydropyran-3-yl] (~{E})-3-(3,4-dihydroxyphenyl)prop-2-enoate
IUPAC Name	[(2~{R},3~{R},4~{R},5~{R},6~{R})-6-[2-(3,4-dihydroxyphenyl)ethoxy]-5-hydroxy-4-[(2~{S},3~{R},4~{R},5~{R},6~{S})-3,4,5-trihydroxy-6-methyl-tetrahydropyran-2-yl]oxy-2-[[(2~{S},3~{S},4~{R},5~{R})-3,4,5-trihydroxytetrahydropyran-2-yl]oxymethyl]tetrahydropyran-3-yl] (~{E})-3-(3,4-dihydroxyphenyl)prop-2-enoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 97101 0 0 0 0 0 0 0 0999 V2000 3.1557 5.0397 -0.3003 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7570 4.9142 -0.8358 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4097 3.6310 -1.1577 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1486 3.4038 -1.6022 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5224 2.5913 -0.7126 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8549 1.3499 -1.2293 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3229 1.0473 -1.2148 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8410 0.9683 -2.5130 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6227 -0.2298 -0.5282 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7798 -0.1570 0.8468 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0408 -0.4252 1.3022 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1897 -0.3463 2.7853 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5763 -0.6474 3.2037 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5424 0.3270 3.3306 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8436 0.0107 3.7275 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1793 -1.3009 4.0006 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4860 -1.6020 4.3968 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2309 -2.2732 3.8784 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5565 -3.6004 4.1516 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9403 -1.9447 3.4827 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8603 -1.3195 -0.8290 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5765 -1.0213 -1.1670 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3899 -2.1646 -0.9866 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0658 -3.1954 -1.8057 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7012 -4.3356 -1.7688 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1784 -4.5780 -3.0525 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2951 -5.3468 -3.8044 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4223 -6.7774 -3.3240 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7153 -7.2263 -3.5909 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1964 -6.7946 -1.8473 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2876 -7.3720 -1.1616 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1689 -5.4614 -1.2620 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4827 -5.1648 -1.5368 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1572 0.2319 -0.4810 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2493 0.4217 -0.4688 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8929 0.5697 0.7485 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1972 0.5274 1.7952 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3597 0.7733 0.8241 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9598 0.9148 1.9904 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3848 1.1191 2.1857 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8638 1.2508 3.4693 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1974 1.4465 3.7178 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1237 1.5210 2.6950 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4669 1.7206 2.9892 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6283 1.3876 1.4216 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5610 1.4622 0.3803 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2824 1.1883 1.1369 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5482 4.6519 -1.9747 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6867 4.4473 -2.7709 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4055 5.4860 -2.8479 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7289 4.8554 -4.0202 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6132 5.8684 -2.0097 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5206 7.1631 -1.5122 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2765 5.8657 0.4293 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8715 5.2716 -1.1357 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5206 4.1206 0.2027 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0589 5.2822 -0.0525 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2393 2.7916 -2.5500 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5160 1.2412 -2.2868 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7872 1.9324 -0.6724 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4800 1.6999 -2.7115 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6765 -0.5127 -0.8924 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8416 0.1716 0.8368 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2660 -1.4944 1.0129 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4791 -0.9837 3.3420 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9916 0.7126 3.1172 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3348 1.3638 3.1310 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6133 0.7677 3.8311 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.1955 -0.8871 4.3930 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0037 -4.0896 4.8386 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2296 -2.7458 3.4002 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5763 -0.8104 -2.2791 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4521 -2.5387 0.0350 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3777 -1.8068 -1.3937 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5730 -4.2748 -1.0953 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7425 -4.9880 -3.7564 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6346 -5.3070 -4.8567 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2786 -7.4572 -3.8804 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3618 -6.5028 -3.3480 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6627 -7.4818 -1.6471 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5321 -8.1732 -1.6652 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0540 -5.5245 -0.1598 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1363 -5.8053 -1.2146 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5576 0.2221 0.5533 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9609 0.8090 -0.0630 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3233 0.8727 2.8599 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1861 1.2008 4.2996 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5794 1.5500 4.7255 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7923 1.5374 3.9201 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2181 2.2424 0.4346 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9420 1.0896 0.1347 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7799 5.3197 -1.1107 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3969 3.8170 -3.4798 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1331 6.4251 -3.0834 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6995 4.7901 -4.2043 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5055 5.7701 -2.6348 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6107 7.5113 -1.4682 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 1 0 7 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 16 18 1 0 18 19 1 0 18 20 2 0 9 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 28 30 1 0 30 31 1 0 30 32 1 0 32 33 1 0 22 34 1 0 34 35 1 0 35 36 1 0 36 37 2 0 36 38 1 0 38 39 2 0 39 40 1 0 40 41 2 0 41 42 1 0 42 43 2 0 43 44 1 0 43 45 1 0 45 46 1 0 45 47 2 0 4 48 1 0 48 49 1 0 48 50 1 0 50 51 1 0 50 52 1 0 52 53 1 0 52 2 1 0 34 6 1 0 47 40 1 0 20 13 1 0 32 25 1 0 1 54 1 0 1 55 1 0 1 56 1 0 2 57 1 1 4 58 1 6 6 59 1 6 7 60 1 1 8 61 1 0 9 62 1 6 11 63 1 0 11 64 1 0 12 65 1 0 12 66 1 0 14 67 1 0 15 68 1 0 17 69 1 0 19 70 1 0 20 71 1 0 22 72 1 6 23 73 1 0 23 74 1 0 25 75 1 1 27 76 1 0 27 77 1 0 28 78 1 6 29 79 1 0 30 80 1 6 31 81 1 0 32 82 1 1 33 83 1 0 34 84 1 1 38 85 1 0 39 86 1 0 41 87 1 0 42 88 1 0 44 89 1 0 46 90 1 0 47 91 1 0 48 92 1 1 49 93 1 0 50 94 1 6 51 95 1 0 52 96 1 6 53 97 1 0 M END

Standard InCHIKey	XPLMUADTACCMDJ-SLZARYJYSA-N
Standard InCHI	InChI=1S/C34H44O19/c1-14-24(41)26(43)28(45)34(50-14)53-31-29(46)33(47-9-8-16-3-6-18(36)20(38)11-16)51-22(13-49-32-27(44)25(42)21(39)12-48-32)30(31)52-23(40)7-4-15-2-5-17(35)19(37)10-15/h2-7,10-11,14,21-22,24-39,41-46H,8-9,12-13H2,1H3/b7-4+/t14-,21+,22+,24-,25+,26+,27-,28+,29+,30+,31+,32-,33+,34-/m0/s1
SMILES	C[C@@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@H](OCCC3=CC=C(O)C(O)=C3)O[C@H](CO[C@@H]3OC[C@@H](O)[C@@H](O)[C@@H]3O)[C@H]2OC(=O)/C=C/C2=CC=C(O)C(O)=C2)[C@H](O)[C@H](O)[C@H]1O

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
NPO52625	Scrophularia nodosa L.	Genus	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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 NPC537648 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	15321
0.1-0.2	30485
0.2-0.3	3515
0.3-0.4	424
0.4-0.5	44
0.5-0.6	24
0.6-0.7	25
0.7-0.8	1
0.8-0.85	2
0.85-0.9	3
0.9-0.95	1
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC205864
1.0	High Similarity	NPC247032
0.9114	High Similarity	NPC76406
0.8571	High Similarity	NPC298257
0.8571	High Similarity	NPC175214
0.8537	High Similarity	NPC611289
0.8391	Intermediate Similarity	NPC300894
0.8391	Intermediate Similarity	NPC23845
0.7849	Intermediate Similarity	NPC64195
0.7738	Intermediate Similarity	NPC472350
0.7738	Intermediate Similarity	NPC197316
0.7738	Intermediate Similarity	NPC89105
0.7609	Intermediate Similarity	NPC106818
0.7423	Intermediate Similarity	NPC229505
0.7381	Intermediate Similarity	NPC260425
0.7381	Intermediate Similarity	NPC81515
0.7292	Intermediate Similarity	NPC87403
0.7222	Intermediate Similarity	NPC269141
0.7053	Intermediate Similarity	NPC476384
0.7021	Intermediate Similarity	NPC259347
0.6915	Remote Similarity	NPC96795
0.6915	Remote Similarity	NPC264632
0.6882	Remote Similarity	NPC112
0.6827	Remote Similarity	NPC257970
0.6774	Remote Similarity	NPC252292
0.6735	Remote Similarity	NPC476380
0.6735	Remote Similarity	NPC476381
0.6705	Remote Similarity	NPC46137
0.6702	Remote Similarity	NPC119537
0.6667	Remote Similarity	NPC470933
0.6632	Remote Similarity	NPC100998
0.6629	Remote Similarity	NPC64141
0.66	Remote Similarity	NPC470934
0.6374	Remote Similarity	NPC483705
0.63	Remote Similarity	NPC196063
0.63	Remote Similarity	NPC604195
0.6277	Remote Similarity	NPC263829
0.6264	Remote Similarity	NPC483706
0.6204	Remote Similarity	NPC470927
0.6186	Remote Similarity	NPC476397
0.6132	Remote Similarity	NPC476386
0.6129	Remote Similarity	NPC68092
0.604	Remote Similarity	NPC476375
0.602	Remote Similarity	NPC296954
0.6	Remote Similarity	NPC94871
0.5979	Remote Similarity	NPC34587
0.596	Remote Similarity	NPC34927
0.59	Remote Similarity	NPC610636
0.5789	Remote Similarity	NPC134405
0.5784	Remote Similarity	NPC141455
0.5769	Remote Similarity	NPC476378
0.5747	Remote Similarity	NPC287597
0.5745	Remote Similarity	NPC205195
0.5699	Remote Similarity	NPC235294
0.5568	Remote Similarity	NPC886
0.5556	Remote Similarity	NPC473285
0.5446	Remote Similarity	NPC105005
0.5444	Remote Similarity	NPC34293
0.5421	Remote Similarity	NPC471062
0.5413	Remote Similarity	NPC473427
0.537	Remote Similarity	NPC476398
0.53	Remote Similarity	NPC106677
0.52	Remote Similarity	NPC476377
0.52	Remote Similarity	NPC476383
0.5149	Remote Similarity	NPC476376
0.5104	Remote Similarity	NPC475530
0.5096	Remote Similarity	NPC600370
0.5045	Remote Similarity	NPC306890
0.5044	Remote Similarity	NPC188393

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC537648 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5201
0.1-0.2	3892
0.2-0.3	55
0.3-0.4	1
0.4-0.5	0
0.5-0.6	0
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
0.7738	Intermediate Similarity	NPD7266	Phase 2

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