NPASS Compound

Natural Product: NPC309832

Natural Product ID	NPC309832
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	5-(6-Amino-Purin-9-Yl)-2-Hydroxymethyl-4-Methoxy-Tetrahydro-Furan-3-Ol
IUPAC Name	(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-2-(hydroxymethyl)-4-methoxyoxolan-3-ol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL73237
PubChem CID	102213
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues [CHEMONTID:0000479] Purine nucleosides

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 35 37 0 0 0 0 0 0 0 0999 V2000 -1.2522 -3.0294 0.8322 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2307 -2.2281 -0.3248 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4474 -0.9074 0.0404 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7214 -0.3598 -0.6091 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8238 -0.8879 -1.8837 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3828 1.1018 -0.7308 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0869 1.2782 -0.3298 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4354 0.0384 -0.5233 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8249 0.0288 0.1429 N 0 0 0 0 0 0 0 0 0 0 0 0 1.0708 -0.2752 1.4295 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3914 -0.1572 1.6373 N 0 0 0 0 0 0 0 0 0 0 0 0 2.9830 0.2220 0.4814 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9927 0.3352 -0.4462 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3431 0.7107 -1.7084 N 0 0 0 0 0 0 0 0 0 0 0 0 3.6005 0.9693 -2.0703 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5670 0.8534 -1.1441 N 0 0 0 0 0 0 0 0 0 0 0 0 4.2920 0.4877 0.1185 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2949 0.3593 1.1107 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.3738 1.8831 0.1028 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3173 1.5046 1.4509 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0775 -4.0943 0.5382 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2071 -2.9928 1.3559 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3950 -2.7762 1.5077 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5781 -0.8264 1.1200 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6048 -0.5487 0.0153 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3260 -0.3656 -2.5608 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4873 1.4772 -1.7749 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3697 -0.0992 -1.6120 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3752 -0.5692 2.2071 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8855 1.2688 -3.0744 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1792 -0.1212 0.8570 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1821 0.7240 2.0749 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4092 1.6665 -0.2294 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2330 2.9841 0.0006 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2230 2.3455 1.9988 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 4 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 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 6 19 1 0 19 20 1 0 8 3 1 0 13 9 1 0 17 12 1 0 1 21 1 0 1 22 1 0 1 23 1 0 3 24 1 1 4 25 1 1 5 26 1 0 6 27 1 6 8 28 1 6 10 29 1 0 15 30 1 0 18 31 1 0 18 32 1 0 19 33 1 0 19 34 1 0 20 35 1 0 M END

Standard InCHIKey	FPUGCISOLXNPPC-IOSLPCCCSA-N
Standard InCHI	InChI=1S/C11H15N5O4/c1-19-8-7(18)5(2-17)20-11(8)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
SMILES	CO[C@@H]1[C@H](O)[C@H](O[C@H]1n1cnc2c1ncnc2N)CO

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
NPO30270	Cordyceps sinensis	Species	Cordycipitaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[10423860]
NPO30270	Cordyceps sinensis	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15863936]
NPO30270	Cordyceps sinensis	Species	Cordycipitaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[21848266]
NPO30270	Cordyceps sinensis	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21848266]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO30270	Cordyceps sinensis	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO30270	Cordyceps sinensis	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO30270	Cordyceps sinensis	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	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	3
EC50	3
Displacement	3
Imax	1

Activity Type	# Activity
Individual protein	10

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1758	Individual protein	Hepatitis C virus NS5B RNA-dependent RNA polymerase	Hepatitis C virus	IC50	=	47000.0	nM	PMID[15084127]
NPT1758	Individual protein	Hepatitis C virus NS5B RNA-dependent RNA polymerase	Hepatitis C virus	EC50	>	50000.0	nM	PMID[15084127]
NPT1315	Individual protein	Adenosine A1 receptor	Rattus norvegicus	Displacement	=	29.0	%	PMID[7707320]
NPT1316	Individual protein	Adenosine A2a receptor	Rattus norvegicus	Displacement	=	49.0	%	PMID[7707320]
NPT1760	Individual protein	Adenosine A3 receptor	Rattus norvegicus	Displacement	=	43.0	%	PMID[7707320]
NPT218	Individual protein	Adenosine A3 receptor	Homo sapiens	EC50	>	100000.0	nM	PMID[17560111]
NPT218	Individual protein	Adenosine A3 receptor	Homo sapiens	IC50	=	15.0	nM	PMID[17560111]
NPT218	Individual protein	Adenosine A3 receptor	Homo sapiens	Imax	=	100.0	%	PMID[17560111]
NPT216	Individual protein	Adenosine A1 receptor	Homo sapiens	EC50	>	3000.0	nM	PMID[17560111]
NPT216	Individual protein	Adenosine A1 receptor	Homo sapiens	IC50	>	3000.0	nM	PMID[17560111]

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 NPC309832 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	34559
0.1-0.2	15098
0.2-0.3	97
0.3-0.4	37
0.4-0.5	35
0.5-0.6	17
0.6-0.7	10
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
0.807	Intermediate Similarity	NPC211025
0.6667	Remote Similarity	NPC156461
0.6667	Remote Similarity	NPC107374
0.6667	Remote Similarity	NPC600382
0.6667	Remote Similarity	NPC612067
0.6552	Remote Similarity	NPC209525
0.6552	Remote Similarity	NPC161659
0.6441	Remote Similarity	NPC609472
0.6316	Remote Similarity	NPC317821
0.6271	Remote Similarity	NPC229974
0.6102	Remote Similarity	NPC33996
0.5873	Remote Similarity	NPC136349
0.5873	Remote Similarity	NPC219313
0.5606	Remote Similarity	NPC85689
0.5484	Remote Similarity	NPC604998
0.5217	Remote Similarity	NPC185991
0.5217	Remote Similarity	NPC321814
0.5143	Remote Similarity	NPC328479
0.5143	Remote Similarity	NPC121222
0.5139	Remote Similarity	NPC324198
0.5139	Remote Similarity	NPC326529
0.5139	Remote Similarity	NPC319100
0.5132	Remote Similarity	NPC607463
0.507	Remote Similarity	NPC164952
0.5068	Remote Similarity	NPC130586
0.5063	Remote Similarity	NPC78941
0.5063	Remote Similarity	NPC282458
0.5057	Remote Similarity	NPC157821

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC309832 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6825
0.1-0.2	2162
0.2-0.3	95
0.3-0.4	40
0.4-0.5	21
0.5-0.6	4
0.6-0.7	3
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
0.6769	Remote Similarity	NPD2646	Discontinued
0.6667	Remote Similarity	NPD249	Phase 4
0.6667	Remote Similarity	NPD250	Phase 4
0.5873	Remote Similarity	NPD548	Clinical (unspecified phase)
0.5806	Remote Similarity	NPD193	Phase 2
0.5217	Remote Similarity	NPD283	Phase 4
0.507	Remote Similarity	NPD4171	Clinical (unspecified phase)

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