Structure

Physi-Chem Properties

Molecular Weight:  644.13
Volume:  528.36
LogP:  -3.537
LogD:  -1.467
LogS:  -2.077
# Rotatable Bonds:  10
TPSA:  295.59
# H-Bond Aceptor:  21
# H-Bond Donor:  6
# Rings:  6
# Heavy Atoms:  23

MedChem Properties

QED Drug-Likeness Score:  0.117
Synthetic Accessibility Score:  6.229
Fsp3:  0.5
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.481
MDCK Permeability:  5.706064712285297e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.997
Human Intestinal Absorption (HIA):  0.999
20% Bioavailability (F20%):  0.996
30% Bioavailability (F30%):  0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.644
Plasma Protein Binding (PPB):  19.3430118560791%
Volume Distribution (VD):  1.292
Pgp-substrate:  61.3983039855957%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.484
CYP2C19-inhibitor:  0.148
CYP2C19-substrate:  0.034
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.12
CYP2D6-inhibitor:  0.033
CYP2D6-substrate:  0.018
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.024

ADMET: Excretion

Clearance (CL):  1.763
Half-life (T1/2):  0.945

ADMET: Toxicity

hERG Blockers:  0.13
Human Hepatotoxicity (H-HT):  0.997
Drug-inuced Liver Injury (DILI):  0.995
AMES Toxicity:  0.9
Rat Oral Acute Toxicity:  0.081
Maximum Recommended Daily Dose:  0.99
Skin Sensitization:  0.924
Carcinogencity:  0.31
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.733

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General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC326082

Natural Product ID:  NPC326082
Common 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
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:  
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
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

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  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]

☑ 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT317 Uncleic Acid Nucleic Acid Inhibition = 3.0 % PMID[524839]
NPT317 Uncleic Acid Nucleic Acid Inhibition = 18.0 % PMID[524839]
NPT2 Others Unspecified Inhibition = 26.0 % PMID[524839]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  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>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9744 High Similarity NPC326529
0.9682 High Similarity NPC319100
0.9682 High Similarity NPC324198
0.9079 High Similarity NPC161224
0.8903 High Similarity NPC174802
0.8882 High Similarity NPC121222
0.8839 High Similarity NPC212551
0.8839 High Similarity NPC302778
0.8839 High Similarity NPC164952
0.8839 High Similarity NPC130586
0.879 High Similarity NPC226245
0.875 High Similarity NPC323091
0.8726 High Similarity NPC224076
0.871 High Similarity NPC85689
0.871 High Similarity NPC185991
0.871 High Similarity NPC211025
0.8654 High Similarity NPC321814
0.8553 High Similarity NPC316618
0.8421 Intermediate Similarity NPC209525
0.8421 Intermediate Similarity NPC161659
0.8323 Intermediate Similarity NPC107374
0.8323 Intermediate Similarity NPC21448
0.8323 Intermediate Similarity NPC156461
0.8312 Intermediate Similarity NPC314152
0.8269 Intermediate Similarity NPC189068
0.8269 Intermediate Similarity NPC164665
0.8217 Intermediate Similarity NPC309832
0.8217 Intermediate Similarity NPC269827
0.8217 Intermediate Similarity NPC219313
0.8194 Intermediate Similarity NPC229974
0.8176 Intermediate Similarity NPC189261
0.8065 Intermediate Similarity NPC317821
0.8036 Intermediate Similarity NPC324033
0.8036 Intermediate Similarity NPC321458
0.7976 Intermediate Similarity NPC261595
0.7963 Intermediate Similarity NPC472816
0.7904 Intermediate Similarity NPC14590
0.7879 Intermediate Similarity NPC239737
0.7744 Intermediate Similarity NPC207633
0.7669 Intermediate Similarity NPC136349
0.7658 Intermediate Similarity NPC129756
0.7636 Intermediate Similarity NPC328479
0.7622 Intermediate Similarity NPC150853
0.7619 Intermediate Similarity NPC195140
0.7605 Intermediate Similarity NPC52238
0.7595 Intermediate Similarity NPC33996
0.756 Intermediate Similarity NPC313754
0.756 Intermediate Similarity NPC311197
0.756 Intermediate Similarity NPC54320
0.7531 Intermediate Similarity NPC317746
0.7485 Intermediate Similarity NPC232408
0.7485 Intermediate Similarity NPC64705
0.7484 Intermediate Similarity NPC30326
0.7469 Intermediate Similarity NPC318590
0.7423 Intermediate Similarity NPC89147
0.7423 Intermediate Similarity NPC274384
0.7423 Intermediate Similarity NPC177169
0.7362 Intermediate Similarity NPC251233
0.7362 Intermediate Similarity NPC211820
0.7358 Intermediate Similarity NPC320818
0.7346 Intermediate Similarity NPC186619
0.7299 Intermediate Similarity NPC324484
0.7273 Intermediate Similarity NPC290959
0.7257 Intermediate Similarity NPC325906
0.7207 Intermediate Similarity NPC313897
0.7202 Intermediate Similarity NPC326694
0.7151 Intermediate Similarity NPC93365
0.712 Intermediate Similarity NPC24589
0.7097 Intermediate Similarity NPC282458
0.7097 Intermediate Similarity NPC78941
0.7053 Intermediate Similarity NPC107160
0.6975 Remote Similarity NPC262926
0.6952 Remote Similarity NPC21461
0.6933 Remote Similarity NPC61198
0.6825 Remote Similarity NPC313514
0.6821 Remote Similarity NPC321052
0.6748 Remote Similarity NPC324009
0.6707 Remote Similarity NPC319221
0.6686 Remote Similarity NPC315642
0.6686 Remote Similarity NPC74306
0.6667 Remote Similarity NPC276373
0.6633 Remote Similarity NPC5802
0.66 Remote Similarity NPC157821
0.6544 Remote Similarity NPC158055
0.6413 Remote Similarity NPC33382
0.6378 Remote Similarity NPC168702
0.6378 Remote Similarity NPC125659
0.631 Remote Similarity NPC222174
0.6244 Remote Similarity NPC250178
0.6196 Remote Similarity NPC321393
0.6154 Remote Similarity NPC57279
0.6131 Remote Similarity NPC104011
0.6131 Remote Similarity NPC246193
0.6111 Remote Similarity NPC327579
0.6104 Remote Similarity NPC476564
0.6013 Remote Similarity NPC87981
0.6013 Remote Similarity NPC174114
0.6011 Remote Similarity NPC472834
0.5964 Remote Similarity NPC160666
0.5912 Remote Similarity NPC4837
0.5912 Remote Similarity NPC312187
0.5833 Remote Similarity NPC248007
0.581 Remote Similarity NPC103388
0.5722 Remote Similarity NPC217656
0.5696 Remote Similarity NPC18335
0.5691 Remote Similarity NPC89139
0.5685 Remote Similarity NPC164845
0.5674 Remote Similarity NPC296437
0.5665 Remote Similarity NPC287876
0.5655 Remote Similarity NPC139776
0.5642 Remote Similarity NPC470266
0.5607 Remote Similarity NPC14330

  Chemically structural similarity: II. 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>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.9682 High Similarity NPD4171 Clinical (unspecified phase)
0.8903 High Similarity NPD339 Approved
0.8839 High Similarity NPD338 Approved
0.8726 High Similarity NPD169 Phase 2
0.871 High Similarity NPD283 Approved
0.8599 High Similarity NPD242 Approved
0.8415 Intermediate Similarity NPD7988 Suspended
0.8353 Intermediate Similarity NPD4716 Approved
0.8323 Intermediate Similarity NPD250 Approved
0.8323 Intermediate Similarity NPD249 Approved
0.8312 Intermediate Similarity NPD185 Approved
0.8304 Intermediate Similarity NPD4744 Clinical (unspecified phase)
0.825 Intermediate Similarity NPD1369 Phase 2
0.8217 Intermediate Similarity NPD195 Approved
0.8217 Intermediate Similarity NPD186 Discovery
0.8205 Intermediate Similarity NPD166 Approved
0.8182 Intermediate Similarity NPD193 Suspended
0.8137 Intermediate Similarity NPD1750 Clinical (unspecified phase)
0.8137 Intermediate Similarity NPD3107 Discontinued
0.8121 Intermediate Similarity NPD3083 Approved
0.8098 Intermediate Similarity NPD2646 Discontinued
0.8098 Intermediate Similarity NPD2624 Phase 2
0.8023 Intermediate Similarity NPD1412 Clinical (unspecified phase)
0.7988 Intermediate Similarity NPD1732 Phase 3
0.7976 Intermediate Similarity NPD247 Clinical (unspecified phase)
0.7939 Intermediate Similarity NPD4074 Clinical (unspecified phase)
0.7809 Intermediate Similarity NPD6417 Clinical (unspecified phase)
0.773 Intermediate Similarity NPD3085 Phase 1
0.7722 Intermediate Similarity NPD2632 Approved
0.7722 Intermediate Similarity NPD2631 Clinical (unspecified phase)
0.7722 Intermediate Similarity NPD2630 Approved
0.7719 Intermediate Similarity NPD2647 Phase 3
0.7701 Intermediate Similarity NPD5666 Phase 2
0.7683 Intermediate Similarity NPD3086 Phase 3
0.7669 Intermediate Similarity NPD548 Clinical (unspecified phase)
0.7598 Intermediate Similarity NPD1692 Approved
0.756 Intermediate Similarity NPD219 Phase 3
0.756 Intermediate Similarity NPD220 Clinical (unspecified phase)
0.756 Intermediate Similarity NPD218 Approved
0.756 Intermediate Similarity NPD216 Approved
0.756 Intermediate Similarity NPD217 Approved
0.7486 Intermediate Similarity NPD4054 Clinical (unspecified phase)
0.7485 Intermediate Similarity NPD213 Clinical (unspecified phase)
0.7485 Intermediate Similarity NPD214 Approved
0.7484 Intermediate Similarity NPD248 Discontinued
0.7423 Intermediate Similarity NPD7158 Phase 1
0.7355 Intermediate Similarity NPD870 Clinical (unspecified phase)
0.7257 Intermediate Similarity NPD1776 Approved
0.7257 Intermediate Similarity NPD1777 Approved
0.7197 Intermediate Similarity NPD9633 Phase 3
0.7151 Intermediate Similarity NPD546 Clinical (unspecified phase)
0.7135 Intermediate Similarity NPD5683 Clinical (unspecified phase)
0.7135 Intermediate Similarity NPD5684 Clinical (unspecified phase)
0.7135 Intermediate Similarity NPD5682 Phase 3
0.7115 Intermediate Similarity NPD9408 Phase 3
0.7073 Intermediate Similarity NPD3696 Approved
0.7073 Intermediate Similarity NPD3695 Approved
0.7044 Intermediate Similarity NPD9632 Phase 3
0.6933 Remote Similarity NPD252 Clinical (unspecified phase)
0.6901 Remote Similarity NPD3708 Phase 2
0.6836 Remote Similarity NPD516 Clinical (unspecified phase)
0.6825 Remote Similarity NPD7138 Phase 2
0.678 Remote Similarity NPD5080 Phase 2
0.6772 Remote Similarity NPD1063 Phase 2
0.6768 Remote Similarity NPD194 Clinical (unspecified phase)
0.6766 Remote Similarity NPD549 Approved
0.6746 Remote Similarity NPD4240 Approved
0.6732 Remote Similarity NPD5079 Phase 2
0.6706 Remote Similarity NPD171 Discontinued
0.6686 Remote Similarity NPD582 Approved
0.665 Remote Similarity NPD2965 Clinical (unspecified phase)
0.6629 Remote Similarity NPD536 Clinical (unspecified phase)
0.6617 Remote Similarity NPD2876 Phase 3
0.6617 Remote Similarity NPD2877 Clinical (unspecified phase)
0.6552 Remote Similarity NPD2824 Phase 2
0.6544 Remote Similarity NPD6840 Approved
0.6488 Remote Similarity NPD4495 Phase 1
0.6477 Remote Similarity NPD353 Discontinued
0.6455 Remote Similarity NPD1046 Clinical (unspecified phase)
0.6425 Remote Similarity NPD2903 Clinical (unspecified phase)
0.6425 Remote Similarity NPD2902 Phase 2
0.6348 Remote Similarity NPD231 Clinical (unspecified phase)
0.6171 Remote Similarity NPD7502 Clinical (unspecified phase)
0.6167 Remote Similarity NPD9605 Phase 3
0.6163 Remote Similarity NPD799 Phase 1
0.6149 Remote Similarity NPD9606 Approved
0.6111 Remote Similarity NPD9607 Approved
0.6102 Remote Similarity NPD1730 Discontinued
0.6082 Remote Similarity NPD1119 Phase 2
0.6057 Remote Similarity NPD2253 Discontinued
0.6023 Remote Similarity NPD209 Clinical (unspecified phase)
0.6023 Remote Similarity NPD1058 Discontinued
0.6019 Remote Similarity NPD4459 Clinical (unspecified phase)
0.6019 Remote Similarity NPD4458 Phase 2
0.6012 Remote Similarity NPD6112 Approved
0.5976 Remote Similarity NPD9409 Discontinued
0.5974 Remote Similarity NPD8250 Phase 2
0.5957 Remote Similarity NPD527 Clinical (unspecified phase)
0.595 Remote Similarity NPD2152 Clinical (unspecified phase)
0.5904 Remote Similarity NPD2593 Clinical (unspecified phase)
0.5872 Remote Similarity NPD545 Clinical (unspecified phase)
0.5864 Remote Similarity NPD9374 Approved
0.5839 Remote Similarity NPD9373 Approved
0.5837 Remote Similarity NPD5486 Discontinued
0.5833 Remote Similarity NPD9084 Phase 2
0.5818 Remote Similarity NPD307 Approved
0.5814 Remote Similarity NPD282 Approved
0.5801 Remote Similarity NPD7531 Clinical (unspecified phase)
0.5787 Remote Similarity NPD1431 Approved
0.5787 Remote Similarity NPD1430 Approved
0.578 Remote Similarity NPD547 Clinical (unspecified phase)
0.5769 Remote Similarity NPD775 Approved
0.5755 Remote Similarity NPD5458 Discontinued
0.5747 Remote Similarity NPD6381 Phase 2
0.5744 Remote Similarity NPD4089 Clinical (unspecified phase)
0.5735 Remote Similarity NPD4715 Clinical (unspecified phase)
0.5735 Remote Similarity NPD4713 Clinical (unspecified phase)
0.5735 Remote Similarity NPD4714 Approved
0.5735 Remote Similarity NPD34 Approved
0.573 Remote Similarity NPD1118 Discontinued
0.5728 Remote Similarity NPD2452 Phase 2
0.5728 Remote Similarity NPD2453 Phase 2
0.5728 Remote Similarity NPD2450 Phase 2
0.5728 Remote Similarity NPD2451 Phase 2
0.5714 Remote Similarity NPD207 Discontinued
0.5696 Remote Similarity NPD8836 Approved
0.5667 Remote Similarity NPD4599 Clinical (unspecified phase)
0.5665 Remote Similarity NPD8829 Clinical (unspecified phase)
0.5657 Remote Similarity NPD9083 Clinical (unspecified phase)
0.564 Remote Similarity NPD1127 Approved
0.564 Remote Similarity NPD1128 Approved
0.5616 Remote Similarity NPD3913 Clinical (unspecified phase)

  Bioactivity similarity: Similar Natural Products in NPASS

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