NPASS Compound

Natural Product: NPC326082

Natural Product ID	NPC326082
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	[(2R,3S,5R)-5-(6-Aminopurin-9-Yl)-3-Hydroxyoxolan-2-Yl]Methyl [(2R,3S,5R)-5-(6-Aminopurin-9-Yl)-2-(Phosphonooxymethyl)Oxolan-3-Yl] Hydrogen Phosphate
IUPAC Name	[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-hydroxyoxolan-2-yl]methyl [(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] hydrogen phosphate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3144372
PubChem CID	11104208
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues [CHEMONTID:0003796] (3'->5')-dinucleotides and analogues [CHEMONTID:0003394] (3'->5')-dinucleotides

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 69 74 0 0 0 0 0 0 0 0999 V2000 4.7608 3.4655 0.6556 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2681 2.3757 -0.0919 C 0 0 1 0 0 0 0 0 0 0 0 0 5.4571 1.4201 -0.2302 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2017 0.4972 0.9390 C 0 0 1 0 0 0 0 0 0 0 0 0 3.8463 0.2759 0.8421 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3314 1.5678 0.7658 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9157 1.5580 0.2165 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4894 2.8958 0.1793 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0994 2.8778 -0.4218 P 0 0 0 0 0 0 0 0 0 0 0 0 -0.1162 2.7437 -1.9207 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8998 1.6088 0.3519 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2170 1.5030 -0.0025 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4550 0.0856 -0.5509 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7665 -0.6536 0.6905 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3251 0.2334 1.6033 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1771 1.5118 1.1396 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.5427 1.9516 0.5962 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4543 3.2658 0.1013 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0165 3.6405 -0.4774 P 0 0 0 0 0 0 0 0 0 0 0 0 -6.1309 3.2312 -1.9222 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2214 5.3056 -0.3040 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1602 2.8281 0.4699 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5747 -1.8175 0.5533 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.4864 -2.8966 1.3653 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3745 -3.8318 0.9874 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.0452 -3.3677 -0.0714 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5386 -2.1167 -0.3299 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0123 -1.3924 -1.3396 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.9940 -1.8760 -2.1207 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5122 -3.1100 -1.8866 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.0660 -3.8782 -0.8787 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5549 -5.1658 -0.5765 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.7998 4.3600 0.0669 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9986 -0.7074 0.9005 N 0 0 0 0 0 0 0 0 0 0 0 0 6.6547 -1.2713 1.9335 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2863 -2.3818 1.5153 N 0 0 0 0 0 0 0 0 0 0 0 0 7.0537 -2.5561 0.2178 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2470 -1.5044 -0.1609 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8675 -1.4557 -1.4482 N 0 0 0 0 0 0 0 0 0 0 0 0 6.2583 -2.3931 -2.3293 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0451 -3.4137 -1.9474 N 0 0 0 0 0 0 0 0 0 0 0 0 7.4770 -3.5425 -0.6645 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3026 -4.6098 -0.2548 N 0 0 0 0 0 0 0 0 0 0 0 0 4.0150 3.7260 1.2574 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8519 2.6720 -1.0547 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4063 1.9630 -0.1539 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3822 0.8570 -1.1843 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4481 1.0578 1.8656 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3225 1.9729 1.8002 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9094 1.1040 -0.7917 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3085 0.9345 0.8788 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5485 2.2611 -0.7380 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4809 -0.2756 -0.9938 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2444 0.1889 -1.2890 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7755 -0.9589 1.1427 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9256 2.2505 1.9248 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3247 1.8510 1.3658 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8247 1.3219 -0.2644 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9048 5.5291 0.6235 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5399 2.0547 -0.0185 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8227 -3.0472 2.2094 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4063 -1.3107 -2.9562 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5692 -5.3252 -0.5014 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8992 -5.9481 -0.4307 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0828 5.0374 -0.0720 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6543 -0.8674 2.9375 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9243 -2.3099 -3.3620 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9292 -5.3364 0.3755 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2772 -4.6635 -0.5849 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 7 8 1 0 8 9 1 0 9 10 2 0 9 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 1 0 17 18 1 0 18 19 1 0 19 20 2 0 19 21 1 0 19 22 1 0 14 23 1 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 27 28 1 0 28 29 2 0 29 30 1 0 30 31 2 0 31 32 1 0 9 33 1 0 4 34 1 0 34 35 1 0 35 36 2 0 36 37 1 0 37 38 2 0 38 39 1 0 39 40 2 0 40 41 1 0 41 42 2 0 42 43 1 0 6 2 1 0 16 12 1 0 27 23 1 0 38 34 1 0 31 26 1 0 42 37 1 0 1 44 1 0 2 45 1 6 3 46 1 0 3 47 1 0 4 48 1 1 6 49 1 1 7 50 1 0 7 51 1 0 12 52 1 6 13 53 1 0 13 54 1 0 14 55 1 1 16 56 1 1 17 57 1 0 17 58 1 0 21 59 1 0 22 60 1 0 24 61 1 0 29 62 1 0 32 63 1 0 32 64 1 0 33 65 1 0 35 66 1 0 40 67 1 0 43 68 1 0 43 69 1 0 M END

Standard InCHIKey	JOUSLTRAASCXCM-PRSXHHODSA-N
Standard InCHI	InChI=1S/C20H26N10O11P2/c21-17-15-19(25-5-23-17)29(7-27-15)13-1-9(31)11(39-13)3-38-43(35,36)41-10-2-14(40-12(10)4-37-42(32,33)34)30-8-28-16-18(22)24-6-26-20(16)30/h5-14,31H,1-4H2,(H,35,36)(H2,21,23,25)(H2,22,24,26)(H2,32,33,34)/t9-,10-,11+,12+,13+,14+/m0/s1
SMILES	O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1cnc2c1ncnc2N)O)n1cnc2c1ncnc2N

Calculated Properties

Physi-Chem Properties

Molecular Weight:	644.13	Volume:	528.36 ? Van der Waals volume.
Dense:	1.219	LogP:	-2.363 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-0.17 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.252 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	10.0	Rigid Bonds:	32.0
TPSA:	300.45 ? Topological Polar Surface Area.	H-Bond Acceptor:	21.0
H-Bond Donor:	8.0	Rings:	6.0
Heavy Atoms:	23.0

MedChem Properties

QED Drug-Likeness Score:	0.117	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.858	Fsp³:	0.5
MCE-18:	134.267 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	1	PAINS Alert:	0
Colloidal aggregators:	0.132	Fluc inhibitor:	0.002 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.019 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.344 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.389	Promiscuous compounds:	0.42

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.74	MDCK Permeability:	-5.287
Pgp-inhibitor:	0.001	Pgp-substrate:	0.0
PAMPA:	0.912 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.0
20% Bioavailability (F20%):	0.0	30% Bioavailability (F30%):	0.0
50% Bioavailability (F50%):	0.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.106
Plasma Protein Binding (PPB):	28.774%	Volume Distribution (VD):	0.304
Fu:	55.076% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.002
BSEP inhibitor:	0.994

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
HLM stability:	0.743 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

1.993

Half-life (T1/2):

1.946

ADMET: Toxicity

hERG Blockers:	0.008	hERG Blockers (10um):	0.009
Human Hepatotoxicity (H-HT):	0.622	Drug-induced Liver Injury (DILI):	1.0
AMES Toxicity:	0.368	Rat Oral Acute Toxicity:	0.032
Maximum Recommended Daily Dose:	0.999	Skin Sensitization:	0.85
Carcinogencity:	0.977	Eye Corrosion:	0.0
Eye Irritation:	0.017	Respiratory Toxicity:	0.992
Drug-induced Neurotoxicity:	0.993	Ototoxicity:	0.768
Hematotoxicity:	0.217	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.316
A549 Cytotoxicity:	0.009	Hek293 Cytotoxicity:	0.74
BCF:	0.081 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	2.476 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.119 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.508 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO30193	Mycoplasma genitalium	Species	Mycoplasmataceae	Bacteria	n.a.	n.a.	n.a.	PMID[22817898]
NPO30193	Mycoplasma genitalium	Species	Mycoplasmataceae	Bacteria	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
Inhibition	3

Activity Type	# Activity
Nucleic acid	2
Others	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT317	Nucleic acid	Nucleic Acid	n.a.	Inhibition	=	3.0	%	PMID[6196481]
NPT317	Nucleic acid	Nucleic Acid	n.a.	Inhibition	=	18.0	%	PMID[6196481]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	n.a.	Inhibition	=	26.0	%	PMID[6196481]

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 NPC326082 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	32246
0.1-0.2	17441
0.2-0.3	72
0.3-0.4	48
0.4-0.5	32
0.5-0.6	14
0.6-0.7	2
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
0.8133	Intermediate Similarity	NPC161224
0.7671	Intermediate Similarity	NPC121222
0.6071	Remote Similarity	NPC174802
0.6	Remote Similarity	NPC606410
0.5904	Remote Similarity	NPC324198
0.5904	Remote Similarity	NPC326529
0.5904	Remote Similarity	NPC319100
0.5833	Remote Similarity	NPC130586
0.5814	Remote Similarity	NPC481375
0.5783	Remote Similarity	NPC302778
0.5783	Remote Similarity	NPC329404
0.5783	Remote Similarity	NPC212551
0.5663	Remote Similarity	NPC164952
0.5658	Remote Similarity	NPC209525
0.5658	Remote Similarity	NPC161659
0.561	Remote Similarity	NPC185991
0.561	Remote Similarity	NPC321814
0.5568	Remote Similarity	NPC323091

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC326082 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6063
0.1-0.2	2959
0.2-0.3	69
0.3-0.4	43
0.4-0.5	14
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
0.6071	Remote Similarity	NPD339	Phase 2
0.561	Remote Similarity	NPD283	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