NPASS Compound

Natural Product: NPC349108

Natural Product ID	NPC349108
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	VILWYXXAYVMNPA-NFBGDUNESA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	38357467
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-3-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 57 60 0 0 0 0 0 0 0 0999 V2000 3.9778 -2.5885 2.0191 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4655 -2.7116 1.7104 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7961 -3.1875 2.9511 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5889 -2.4204 3.4013 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8367 -0.9664 2.9879 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0217 -0.8346 1.5263 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0881 -1.5722 1.1228 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1276 -1.0422 0.7187 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3676 -0.3216 -0.4398 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1719 -0.8277 -1.6234 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8381 -1.8985 -1.6020 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0217 -0.1756 -2.7952 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4712 -0.5927 -4.0077 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2528 0.1106 -5.1830 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4818 1.2692 -5.1406 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9826 1.6974 -3.9168 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7719 1.0010 -2.7345 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2562 1.4290 -1.6012 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0968 0.8218 -0.4265 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7133 1.4465 0.7466 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1091 2.7760 0.5932 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7510 3.4742 1.6029 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0094 2.8419 2.7803 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6325 1.5426 2.9405 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9814 0.8368 1.9227 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8825 0.8978 4.1158 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6593 3.5363 3.8078 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1396 4.8064 1.4473 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7275 2.8810 -3.9065 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7542 2.0418 -6.2928 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2710 1.6285 -7.5399 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2193 -1.7779 -4.0353 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0955 -0.6551 3.5583 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5197 -2.4151 4.7881 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4494 -4.5484 2.7526 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4581 -1.8494 1.3909 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4605 -3.5864 1.8069 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0794 -2.4554 3.1112 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4602 -3.5161 0.9097 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5249 -3.1469 3.8118 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3639 -2.8169 3.0254 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1552 -0.2472 3.4722 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3173 0.2332 1.2938 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6646 -0.2545 -6.1144 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9284 3.3324 -0.3124 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7222 -0.1946 2.0474 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3529 0.1247 4.5091 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0560 4.1185 4.3880 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0555 5.3040 0.5698 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1993 3.7464 -4.0359 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2946 0.5262 -7.6706 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9213 2.0265 -8.3789 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7470 2.0350 -7.7805 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6795 -2.6426 -3.9964 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9682 -0.2642 4.4542 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3118 -2.0844 5.2403 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0114 -4.8916 2.0098 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 2 0 10 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 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 22 28 1 0 16 29 1 0 15 30 1 0 30 31 1 0 13 32 1 0 5 33 1 0 4 34 1 0 3 35 1 0 7 2 1 0 19 9 2 0 25 20 1 0 17 12 1 0 1 36 1 0 1 37 1 0 1 38 1 0 2 39 1 6 3 40 1 1 4 41 1 6 5 42 1 1 6 43 1 1 14 44 1 0 21 45 1 0 25 46 1 0 26 47 1 0 27 48 1 0 28 49 1 0 29 50 1 0 31 51 1 0 31 52 1 0 31 53 1 0 32 54 1 0 33 55 1 0 34 56 1 0 35 57 1 0 M END

Standard InCHIKey	VILWYXXAYVMNPA-NFBGDUNESA-N
Standard InCHI	InChI=1S/C22H22O13/c1-6-13(26)17(30)18(31)22(33-6)35-21-16(29)12-8(23)5-11(32-2)15(28)20(12)34-19(21)7-3-9(24)14(27)10(25)4-7/h3-6,13,17-18,22-28,30-31H,1-2H3/t6-,13-,17+,18+,22-/m0/s1
SMILES	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)Oc1c(=O)c2c(cc(c(c2oc1c1cc(c(c(c1)O)O)O)O)OC)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
NPO17083	Atraphaxis frutescens	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28006914]
NPO17083	Atraphaxis frutescens	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17083	Atraphaxis frutescens	Species	Polygonaceae	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	2

Activity Type	# Activity
Others	2

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
NPT35	Others	n.a.	n.a.	IC50	=	9900.0	nM	PMID[28006914]
NPT2	Others	Unspecified	n.a.	IC50	=	1200000.0	nM	PMID[28006914]

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 NPC349108 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	19560
0.1-0.2	27032
0.2-0.3	2479
0.3-0.4	487
0.4-0.5	208
0.5-0.6	61
0.6-0.7	24
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8732	High Similarity	NPC59534
0.7703	Intermediate Similarity	NPC158674
0.7125	Intermediate Similarity	NPC355481
0.6974	Remote Similarity	NPC135599
0.6974	Remote Similarity	NPC73855
0.6974	Remote Similarity	NPC113968
0.6974	Remote Similarity	NPC328940
0.6974	Remote Similarity	NPC277174
0.6974	Remote Similarity	NPC606877
0.6951	Remote Similarity	NPC480463
0.6709	Remote Similarity	NPC271692
0.6341	Remote Similarity	NPC611303
0.6296	Remote Similarity	NPC305811
0.6296	Remote Similarity	NPC46420
0.6296	Remote Similarity	NPC27640
0.6235	Remote Similarity	NPC265115
0.6173	Remote Similarity	NPC265530
0.6125	Remote Similarity	NPC473043
0.6092	Remote Similarity	NPC480466
0.6049	Remote Similarity	NPC127546
0.6049	Remote Similarity	NPC249281
0.6049	Remote Similarity	NPC57625
0.6049	Remote Similarity	NPC173637
0.6049	Remote Similarity	NPC317489
0.6049	Remote Similarity	NPC223424
0.6049	Remote Similarity	NPC600591
0.6	Remote Similarity	NPC605784
0.5952	Remote Similarity	NPC219904
0.5854	Remote Similarity	NPC19388
0.5854	Remote Similarity	NPC240431
0.5854	Remote Similarity	NPC55786
0.5854	Remote Similarity	NPC476405
0.5843	Remote Similarity	NPC39834
0.5814	Remote Similarity	NPC223747
0.5747	Remote Similarity	NPC276377
0.5732	Remote Similarity	NPC111929
0.5732	Remote Similarity	NPC320283
0.5732	Remote Similarity	NPC41121
0.5632	Remote Similarity	NPC116458
0.5632	Remote Similarity	NPC246943
0.5618	Remote Similarity	NPC251417
0.5591	Remote Similarity	NPC483415
0.5532	Remote Similarity	NPC483416
0.5532	Remote Similarity	NPC606657
0.5488	Remote Similarity	NPC34531
0.5444	Remote Similarity	NPC278419
0.5444	Remote Similarity	NPC179198
0.5435	Remote Similarity	NPC150164
0.5426	Remote Similarity	NPC483414
0.5412	Remote Similarity	NPC136042
0.5402	Remote Similarity	NPC488071
0.5349	Remote Similarity	NPC84362
0.5319	Remote Similarity	NPC126784
0.5319	Remote Similarity	NPC241423
0.5312	Remote Similarity	NPC5319
0.5294	Remote Similarity	NPC19709
0.5294	Remote Similarity	NPC238376
0.5287	Remote Similarity	NPC42773
0.5287	Remote Similarity	NPC45522
0.5269	Remote Similarity	NPC293626
0.5263	Remote Similarity	NPC470443
0.5227	Remote Similarity	NPC182121
0.5222	Remote Similarity	NPC66087
0.5213	Remote Similarity	NPC186816
0.5208	Remote Similarity	NPC72016
0.5161	Remote Similarity	NPC267680
0.5155	Remote Similarity	NPC486577
0.5116	Remote Similarity	NPC289667
0.5114	Remote Similarity	NPC325555
0.5114	Remote Similarity	NPC226304
0.5114	Remote Similarity	NPC599850
0.5106	Remote Similarity	NPC203259
0.5106	Remote Similarity	NPC33054
0.5106	Remote Similarity	NPC176740
0.5106	Remote Similarity	NPC471725
0.5106	Remote Similarity	NPC134532
0.5106	Remote Similarity	NPC602582
0.5067	Remote Similarity	NPC480465
0.5057	Remote Similarity	NPC145038
0.5057	Remote Similarity	NPC56077
0.5057	Remote Similarity	NPC297987
0.5057	Remote Similarity	NPC281131
0.5057	Remote Similarity	NPC253662
0.5057	Remote Similarity	NPC179950
0.5057	Remote Similarity	NPC88789
0.5057	Remote Similarity	NPC491374
0.5056	Remote Similarity	NPC175107
0.5052	Remote Similarity	NPC473327

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC349108 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5321
0.1-0.2	3783
0.2-0.3	37
0.3-0.4	4
0.4-0.5	2
0.5-0.6	3
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
0.5312	Remote Similarity	NPD7804	Clinical (unspecified phase)
0.5106	Remote Similarity	NPD6797	Phase 2
0.5102	Remote Similarity	NPD7251	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