NPASS Compound

Natural Product: NPC473071

Natural Product ID	NPC473071
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ARIBHQKYRYPXOK-NQEPOGRXSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3609096
PubChem CID	n.a.
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 75 80 0 0 0 0 0 0 0 0999 V2000 -3.5885 0.6379 4.2652 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5455 1.3341 2.9199 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9000 1.4742 2.3046 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3739 0.2476 1.6131 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2237 -0.6744 1.3421 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9738 0.1189 1.0326 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5553 0.8862 2.0853 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9681 -0.6901 0.5088 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6882 -0.3956 -0.7836 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0385 -1.6567 -1.6029 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0112 -1.2380 -3.0351 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7717 -0.4937 -3.3798 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3071 0.3854 -2.4451 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2605 -0.1044 -1.1393 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3864 0.8423 -0.3164 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6764 0.5015 0.1243 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8014 0.9522 -0.5021 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9590 0.5268 0.0149 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1088 -0.2424 1.0215 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3496 -0.6459 1.5068 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4576 -1.4880 2.6125 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3252 -1.9389 3.2479 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1085 -1.5334 2.7586 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9989 -0.7093 1.6772 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7490 -0.3455 1.2412 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7228 -0.7612 1.8284 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9675 -1.9775 3.3862 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6513 -2.7599 4.3178 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0516 -2.9264 4.2490 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5326 -2.0328 3.2905 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8315 1.8350 -1.6502 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8168 2.5984 -2.1382 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9308 3.3856 -3.2695 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1138 3.4300 -3.9678 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1610 2.6774 -3.5097 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0247 1.8989 -2.3794 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2132 4.2324 -5.1121 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8756 4.1544 -3.7449 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2948 -1.4577 -3.8603 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3611 -0.7405 -4.4429 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0397 -2.4167 -3.8159 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0072 -2.5588 -1.3665 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0882 -1.5588 2.3743 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9371 0.5723 0.3754 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8282 1.8864 3.2873 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5203 1.3666 5.1270 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8313 -0.1578 4.3669 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6285 0.2257 4.3744 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2326 2.4009 3.1769 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9329 2.3218 1.5566 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1420 -0.2896 2.2126 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5111 -1.2924 0.4388 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2732 0.8145 0.2167 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3006 0.4382 -1.2037 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0124 -2.0616 -1.2880 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9462 -0.6963 -3.3150 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0186 0.1298 -4.2913 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2841 -1.1000 -1.1353 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2278 -0.2876 1.0014 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7953 -2.9715 3.4474 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4807 -2.7412 5.2628 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2849 -3.9832 4.0124 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8774 2.6236 -1.6224 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0834 2.7253 -4.0718 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8820 1.3112 -2.0438 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3993 4.7162 -5.4534 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0450 4.1720 -3.3598 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7185 -1.9467 -2.9597 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1007 -2.2290 -4.5218 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2293 -1.1406 -4.2173 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8289 -3.2046 -3.2800 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2896 -3.3224 -0.7879 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8115 -2.4610 2.1550 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4996 1.3777 -0.0231 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7014 2.0306 2.8577 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 14 15 1 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 23 27 1 0 22 28 1 0 28 29 1 0 29 30 1 0 17 31 1 0 31 32 2 0 32 33 1 0 33 34 2 0 34 35 1 0 35 36 2 0 34 37 1 0 33 38 1 0 12 39 1 0 39 40 1 0 11 41 1 0 10 42 1 0 5 43 1 0 4 44 1 0 3 45 1 0 7 2 1 0 14 9 1 0 25 16 1 0 24 19 1 0 30 21 1 0 36 31 1 0 1 46 1 0 1 47 1 0 1 48 1 0 2 49 1 0 3 50 1 0 4 51 1 0 5 52 1 0 6 53 1 0 9 54 1 0 10 55 1 0 11 56 1 0 12 57 1 0 14 58 1 0 20 59 1 0 27 60 1 0 29 61 1 0 29 62 1 0 32 63 1 0 35 64 1 0 36 65 1 0 37 66 1 0 38 67 1 0 39 68 1 0 39 69 1 0 40 70 1 0 41 71 1 0 42 72 1 0 43 73 1 0 44 74 1 0 45 75 1 0 M END

Standard InCHIKey	ARIBHQKYRYPXOK-NQEPOGRXSA-N
Standard InCHI	InChI=1S/C28H30O17/c1-8-16(32)20(36)22(38)27(41-8)45-26-21(37)17(33)14(6-29)43-28(26)44-25-19(35)15-12(5-13-24(18(15)34)40-7-39-13)42-23(25)9-2-3-10(30)11(31)4-9/h2-5,8,14,16-17,20-22,26-34,36-38H,6-7H2,1H3/t8-,14+,16-,17+,20+,21-,22+,26+,27-,28-/m0/s1
SMILES	CC1C(C(C(C(O1)OC2C(C(C(OC2OC3=C(OC4=CC5=C(C(=C4C3=O)O)OCO5)C6=CC(=C(C=C6)O)O)CO)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
NPO33494	atriplex littoralis	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26290401]
NPO33494	atriplex littoralis	Species	Chenopodiaceae	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

Activity Type	# Activity
Activity	15

Activity Type	# Activity
Cell line	15

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
NPT885	Cell line	PBL	n.a.	Activity	=	178.8	n.a.	PMID[21910504]
NPT885	Cell line	PBL	n.a.	Activity	=	181.0	n.a.	PMID[21910504]
NPT885	Cell line	PBL	n.a.	Activity	=	15.3	%	DrugMatrix in vitro pharmacology data
NPT885	Cell line	PBL	n.a.	Activity	=	14.1	%	PMID[8410974]
NPT885	Cell line	PBL	n.a.	Activity	=	15.1	%	DrugMatrix in vitro pharmacology data
NPT885	Cell line	PBL	n.a.	Activity	=	1.7	n.a.	PMID[24269513]
NPT885	Cell line	PBL	n.a.	Activity	=	1.2	n.a.	PubChem BioAssay data set
NPT885	Cell line	PBL	n.a.	Activity	=	1.3	n.a.	PubChem BioAssay data set
NPT885	Cell line	PBL	n.a.	Activity	=	187.0	n.a.	PubChem BioAssay data set
NPT885	Cell line	PBL	n.a.	Activity	=	98.9	%	PMID[17371812]
NPT885	Cell line	PBL	n.a.	Activity	=	97.7	%	PMID[17371812]
NPT885	Cell line	PBL	n.a.	Activity	=	102.2	%	PMID[21377877]

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 NPC473071 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	24047
0.1-0.2	22076
0.2-0.3	3036
0.3-0.4	382
0.4-0.5	208
0.5-0.6	78
0.6-0.7	22
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.837	Intermediate Similarity	NPC473072
0.7363	Intermediate Similarity	NPC155877
0.7083	Intermediate Similarity	NPC473073
0.7033	Intermediate Similarity	NPC473682
0.6842	Remote Similarity	NPC240306
0.6739	Remote Similarity	NPC254855
0.6739	Remote Similarity	NPC94610
0.6737	Remote Similarity	NPC470444
0.6702	Remote Similarity	NPC163242
0.6702	Remote Similarity	NPC272068
0.6701	Remote Similarity	NPC32641
0.6701	Remote Similarity	NPC256188
0.6559	Remote Similarity	NPC95866
0.6531	Remote Similarity	NPC35119
0.6442	Remote Similarity	NPC480441
0.6373	Remote Similarity	NPC14187
0.6264	Remote Similarity	NPC27640
0.6238	Remote Similarity	NPC220173
0.6224	Remote Similarity	NPC115674
0.6129	Remote Similarity	NPC488071
0.6105	Remote Similarity	NPC170052
0.6105	Remote Similarity	NPC135846
0.61	Remote Similarity	NPC483414
0.6061	Remote Similarity	NPC255157
0.6061	Remote Similarity	NPC259896
0.604	Remote Similarity	NPC122467
0.5938	Remote Similarity	NPC476215
0.5833	Remote Similarity	NPC25523
0.5833	Remote Similarity	NPC605784
0.581	Remote Similarity	NPC602448
0.5794	Remote Similarity	NPC488075
0.5784	Remote Similarity	NPC480471
0.5784	Remote Similarity	NPC488076
0.5673	Remote Similarity	NPC142142
0.5657	Remote Similarity	NPC8856
0.5644	Remote Similarity	NPC65003
0.5545	Remote Similarity	NPC303694
0.549	Remote Similarity	NPC304741
0.549	Remote Similarity	NPC605592
0.5481	Remote Similarity	NPC12013
0.5481	Remote Similarity	NPC11432
0.5481	Remote Similarity	NPC483415
0.5481	Remote Similarity	NPC477613
0.5478	Remote Similarity	NPC480444
0.5474	Remote Similarity	NPC136042
0.5472	Remote Similarity	NPC483412
0.5472	Remote Similarity	NPC89127
0.5429	Remote Similarity	NPC483416
0.5417	Remote Similarity	NPC305811
0.5417	Remote Similarity	NPC24043
0.5417	Remote Similarity	NPC271692
0.5385	Remote Similarity	NPC64425
0.5361	Remote Similarity	NPC42773
0.5361	Remote Similarity	NPC45522
0.5327	Remote Similarity	NPC195257
0.5258	Remote Similarity	NPC84362
0.5253	Remote Similarity	NPC21666
0.5243	Remote Similarity	NPC470405
0.5243	Remote Similarity	NPC471748
0.5238	Remote Similarity	NPC126784
0.5238	Remote Similarity	NPC241423
0.5208	Remote Similarity	NPC127546
0.5208	Remote Similarity	NPC57625
0.5208	Remote Similarity	NPC173637
0.5208	Remote Similarity	NPC317489
0.5208	Remote Similarity	NPC223424
0.5208	Remote Similarity	NPC600591
0.52	Remote Similarity	NPC116458
0.52	Remote Similarity	NPC246943
0.5189	Remote Similarity	NPC470443
0.5169	Remote Similarity	NPC209550
0.5155	Remote Similarity	NPC145038
0.5155	Remote Similarity	NPC56077
0.5155	Remote Similarity	NPC281131
0.5155	Remote Similarity	NPC253662
0.5155	Remote Similarity	NPC179950
0.5155	Remote Similarity	NPC88789
0.5155	Remote Similarity	NPC491374
0.5149	Remote Similarity	NPC488072
0.5146	Remote Similarity	NPC480466
0.5146	Remote Similarity	NPC29958
0.514	Remote Similarity	NPC482026
0.5138	Remote Similarity	NPC221342
0.5138	Remote Similarity	NPC476470
0.5135	Remote Similarity	NPC89052
0.5126	Remote Similarity	NPC175429
0.5124	Remote Similarity	NPC21359
0.5124	Remote Similarity	NPC460984
0.51	Remote Similarity	NPC224530
0.5094	Remote Similarity	NPC253521
0.5094	Remote Similarity	NPC488073
0.5094	Remote Similarity	NPC113836
0.5091	Remote Similarity	NPC253685
0.5051	Remote Similarity	NPC59534
0.5049	Remote Similarity	NPC251417
0.5048	Remote Similarity	NPC203259
0.5048	Remote Similarity	NPC33054
0.5048	Remote Similarity	NPC176740
0.5048	Remote Similarity	NPC471725
0.5048	Remote Similarity	NPC134532
0.5048	Remote Similarity	NPC602582
0.5046	Remote Similarity	NPC76831
0.5044	Remote Similarity	NPC219043
0.5043	Remote Similarity	NPC480445

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC473071 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6113
0.1-0.2	2979
0.2-0.3	50
0.3-0.4	5
0.4-0.5	1
0.5-0.6	2
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
0.5185	Remote Similarity	NPD7251	Phase 2
0.5048	Remote Similarity	NPD6797	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