NPASS Compound

Natural Product: NPC501224

Natural Product ID	NPC501224
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	7-hydroxy-3-(4-methoxyphenyl)-8-[(2~{S},3~{S},4~{S},5~{S},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chromen-4-one
IUPAC Name	7-hydroxy-3-(4-methoxyphenyl)-8-[(2~{S},3~{S},4~{S},5~{S},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chromen-4-one
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 54 57 0 0 0 0 0 0 0 0999 V2000 8.6621 1.2100 0.4487 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8974 0.8481 -0.6843 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5770 0.4484 -0.5064 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0034 0.4001 0.7585 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6801 -0.0049 0.8938 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9239 -0.3602 -0.2019 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5463 -0.7729 0.0240 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5620 -0.2729 -0.7960 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3040 -0.6287 -0.6156 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0846 -1.4563 0.3263 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4271 -1.7994 0.4735 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3076 -1.2196 -0.4237 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9560 0.0206 -0.1893 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2902 -0.2234 -0.1109 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1410 0.7938 -0.4314 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.3887 0.7958 0.4275 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2046 1.8660 0.0357 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4651 2.1580 -0.4338 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7827 2.3916 0.7434 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4538 2.0694 -1.5585 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1734 1.6786 -2.7020 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4949 0.9843 -1.2187 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1570 0.3253 -2.4193 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7930 -2.6613 1.4625 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1442 -2.9810 1.5791 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8907 -3.2153 2.3322 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4401 -2.8800 2.1922 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8356 -2.0103 1.1997 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1592 -1.6450 1.0212 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0400 -2.1186 1.7872 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4865 -0.3138 -1.4517 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8013 0.0880 -1.5923 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7331 1.3405 0.1584 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2255 2.1714 0.8233 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6068 0.4764 1.2605 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5906 0.6786 1.6344 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2965 -0.0197 1.9057 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7790 0.4197 -1.6065 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6018 0.3676 0.8100 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4910 0.6333 -1.4807 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1648 0.8013 1.5030 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9497 -0.1367 0.1512 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8031 2.1277 0.7685 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2537 2.9073 -0.6368 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2530 1.9774 1.5030 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9306 3.0308 -1.7240 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9328 0.7904 -3.0207 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5455 1.4658 -0.8780 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6021 0.9101 -2.9955 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5712 -3.7831 1.1610 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2116 -3.9079 3.1213 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1667 -3.3006 2.8610 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8954 -0.5904 -2.2974 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2531 0.1258 -2.5907 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 15 18 1 0 18 19 1 0 18 20 1 0 20 21 1 0 20 22 1 0 22 23 1 0 11 24 1 0 24 25 1 0 24 26 2 0 26 27 1 0 27 28 2 0 28 29 1 0 29 30 2 0 6 31 1 0 31 32 2 0 32 3 1 0 29 7 1 0 28 10 1 0 22 13 1 0 1 33 1 0 1 34 1 0 1 35 1 0 4 36 1 0 5 37 1 0 8 38 1 0 13 39 1 1 15 40 1 6 16 41 1 0 16 42 1 0 17 43 1 0 18 44 1 6 19 45 1 0 20 46 1 6 21 47 1 0 22 48 1 1 23 49 1 0 25 50 1 0 26 51 1 0 27 52 1 0 31 53 1 0 32 54 1 0 M END

Standard InCHIKey	MERHVPYVJWORNT-XGOKJXSNSA-N
Standard InCHI	InChI=1S/C22H22O10/c1-29-11-4-2-10(3-5-11)13-9-30-20-12(16(13)25)6-7-14(24)21(20)32-22-19(28)18(27)17(26)15(8-23)31-22/h2-7,9,15,17-19,22-24,26-28H,8H2,1H3/t15-,17+,18-,19-,22-/m0/s1
SMILES	COC1=CC=C(C2=COC3=C(O[C@@H]4O[C@@H](CO)[C@@H](O)[C@H](O)[C@@H]4O)C(O)=CC=C3C2=O)C=C1

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
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1016/S0031-9422(99)00103-X]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19969457]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21314138]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27553	Derris scandens	Species	Fabaceae	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 NPC501224 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	15624
0.1-0.2	29622
0.2-0.3	3462
0.3-0.4	900
0.4-0.5	209
0.5-0.6	30
0.6-0.7	7
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
0.75	Intermediate Similarity	NPC603782
0.7273	Intermediate Similarity	NPC258035
0.7013	Intermediate Similarity	NPC45165
0.6795	Remote Similarity	NPC135345
0.6667	Remote Similarity	NPC69430
0.6506	Remote Similarity	NPC229729
0.642	Remote Similarity	NPC161749
0.6341	Remote Similarity	NPC73511
0.622	Remote Similarity	NPC105511
0.622	Remote Similarity	NPC156457
0.5882	Remote Similarity	NPC100720
0.5698	Remote Similarity	NPC205076
0.5682	Remote Similarity	NPC307518
0.5647	Remote Similarity	NPC197896
0.5647	Remote Similarity	NPC313163
0.5632	Remote Similarity	NPC479401
0.5618	Remote Similarity	NPC479407
0.56	Remote Similarity	NPC264289
0.5568	Remote Similarity	NPC601607
0.5542	Remote Similarity	NPC474434
0.5506	Remote Similarity	NPC607201
0.5455	Remote Similarity	NPC479402
0.5444	Remote Similarity	NPC48773
0.5422	Remote Similarity	NPC25547
0.5349	Remote Similarity	NPC211014
0.5341	Remote Similarity	NPC138540
0.5287	Remote Similarity	NPC234739
0.5281	Remote Similarity	NPC481043
0.5281	Remote Similarity	NPC224462
0.5172	Remote Similarity	NPC259070
0.5165	Remote Similarity	NPC479406
0.5132	Remote Similarity	NPC209560
0.5132	Remote Similarity	NPC490700
0.5132	Remote Similarity	NPC610981
0.5114	Remote Similarity	NPC95090
0.5114	Remote Similarity	NPC27408
0.506	Remote Similarity	NPC94777
0.5057	Remote Similarity	NPC160515
0.5056	Remote Similarity	NPC186807
0.5055	Remote Similarity	NPC148710

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC501224 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3906
0.1-0.2	5093
0.2-0.3	136
0.3-0.4	10
0.4-0.5	3
0.5-0.6	1
0.6-0.7	1
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
0.642	Remote Similarity	NPD4381	Clinical (unspecified phase)
0.5412	Remote Similarity	NPD3818	Discontinued

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