NPASS Compound

Natural Product: NPC226137

Natural Product ID	NPC226137
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	MJQQYLKJAGVSNG-HOTMZDKISA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	15385692
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002207] O-glycosyl 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 36 36 0 0 0 0 0 0 0 0999 V2000 3.6278 -1.4246 0.2201 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4205 -0.0118 -0.2829 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4245 0.9517 0.2953 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0058 0.4214 0.0244 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0689 -0.4081 -0.5881 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1947 0.0667 -0.2494 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9794 0.4835 -1.4832 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4610 0.1892 -1.3229 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8681 0.4983 0.1043 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9803 -0.2160 1.0673 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.7434 -1.1240 2.0067 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3110 -2.1553 1.2630 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9653 -0.8991 0.3992 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7485 1.8755 0.2826 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7085 -1.1431 -1.6390 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8532 1.8543 -1.7108 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3209 -2.1584 -0.5565 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6873 -1.6045 0.4580 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0204 -1.6213 1.1170 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5504 0.0145 -1.3872 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3143 1.9181 -0.2147 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4362 0.5076 0.0929 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3223 1.0826 1.3899 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8341 1.4610 -0.3126 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8243 0.3306 1.1314 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1568 0.9624 0.4055 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5812 -0.0274 -2.3868 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0111 0.8270 -2.0423 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9291 0.1961 0.2407 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4496 0.5291 1.7293 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5021 -0.4977 2.5091 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0447 -1.4819 2.7718 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6147 -2.8641 1.1301 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4458 2.3512 -0.2542 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5745 -1.1920 -2.1257 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7348 2.3085 -0.8314 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 10 13 1 0 9 14 1 0 8 15 1 0 7 16 1 0 13 6 1 0 1 17 1 0 1 18 1 0 1 19 1 0 2 20 1 0 3 21 1 0 3 22 1 0 3 23 1 0 4 24 1 0 4 25 1 0 6 26 1 1 7 27 1 6 8 28 1 6 9 29 1 6 10 30 1 1 11 31 1 0 11 32 1 0 12 33 1 0 14 34 1 0 15 35 1 0 16 36 1 0 M END

Standard InCHIKey	MJQQYLKJAGVSNG-HOTMZDKISA-N
Standard InCHI	InChI=1S/C10H20O6/c1-5(2)4-15-10-9(14)8(13)7(12)6(3-11)16-10/h5-14H,3-4H2,1-2H3/t6-,7-,8+,9-,10-/m1/s1
SMILES	CC(C)CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)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
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24813739]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8874	Glehnia littoralis	Species	Apiaceae	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 NPC226137 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	23833
0.1-0.2	21580
0.2-0.3	3453
0.3-0.4	772
0.4-0.5	179
0.5-0.6	24
0.6-0.7	15
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
0.7742	Intermediate Similarity	NPC124963
0.697	Remote Similarity	NPC326533
0.6667	Remote Similarity	NPC233726
0.6562	Remote Similarity	NPC23134
0.6316	Remote Similarity	NPC155457
0.625	Remote Similarity	NPC42503
0.625	Remote Similarity	NPC282143
0.625	Remote Similarity	NPC107914
0.625	Remote Similarity	NPC242073
0.625	Remote Similarity	NPC299781
0.625	Remote Similarity	NPC157193
0.625	Remote Similarity	NPC608193
0.6	Remote Similarity	NPC13143
0.6	Remote Similarity	NPC294813
0.6	Remote Similarity	NPC606861
0.6	Remote Similarity	NPC607126
0.575	Remote Similarity	NPC145112
0.5745	Remote Similarity	NPC71381
0.5745	Remote Similarity	NPC263407
0.5676	Remote Similarity	NPC143326
0.5581	Remote Similarity	NPC100204
0.5526	Remote Similarity	NPC31496
0.55	Remote Similarity	NPC268243
0.5405	Remote Similarity	NPC317501
0.5405	Remote Similarity	NPC605930
0.5349	Remote Similarity	NPC89145
0.5349	Remote Similarity	NPC157514
0.5349	Remote Similarity	NPC322314
0.5349	Remote Similarity	NPC269166
0.5333	Remote Similarity	NPC147292
0.5217	Remote Similarity	NPC277570
0.5217	Remote Similarity	NPC63058
0.5192	Remote Similarity	NPC37866
0.5111	Remote Similarity	NPC36927
0.5111	Remote Similarity	NPC262826
0.5111	Remote Similarity	NPC271772
0.5111	Remote Similarity	NPC166250
0.5106	Remote Similarity	NPC206601
0.5102	Remote Similarity	NPC9447
0.5094	Remote Similarity	NPC235051

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC226137 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7050
0.1-0.2	1925
0.2-0.3	141
0.3-0.4	14
0.4-0.5	17
0.5-0.6	2
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
0.6216	Remote Similarity	NPD904	Phase 3
0.5294	Remote Similarity	NPD8994	Approved
0.5263	Remote Similarity	NPD905	Phase 4

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