Structure

Physi-Chem Properties

Molecular Weight:  419.96
Volume:  295.111
LogP:  -3.067
LogD:  -1.847
LogS:  -0.036
# Rotatable Bonds:  6
TPSA:  251.49
# H-Bond Aceptor:  15
# H-Bond Donor:  6
# Rings:  1
# Heavy Atoms:  18

MedChem Properties

QED Drug-Likeness Score:  0.235
Synthetic Accessibility Score:  6.699
Fsp3:  1.0
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.634
MDCK Permeability:  0.0001711885561235249
Pgp-inhibitor:  0.0
Pgp-substrate:  0.012
Human Intestinal Absorption (HIA):  0.92
20% Bioavailability (F20%):  0.933
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.277
Plasma Protein Binding (PPB):  10.367180824279785%
Volume Distribution (VD):  0.244
Pgp-substrate:  55.397491455078125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.008
CYP2C19-inhibitor:  0.048
CYP2C19-substrate:  0.022
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.854
CYP2D6-inhibitor:  0.039
CYP2D6-substrate:  0.062
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.0

ADMET: Excretion

Clearance (CL):  1.412
Half-life (T1/2):  0.852

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.019
Drug-inuced Liver Injury (DILI):  0.002
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.933
Skin Sensitization:  0.247
Carcinogencity:  0.027
Eye Corrosion:  0.98
Eye Irritation:  0.674
Respiratory Toxicity:  0.26

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Similar NPs/Drugs  

  Natural Product: NPC325822

Natural Product ID:  NPC325822
Common Name*:   [(1S,2R,3R,4S,5S,6S)-2,3,5-Trihydroxy-4,6-Diphosphonooxycyclohexyl] Dihydrogen Phosphate
IUPAC Name:   [(1S,2R,3R,4S,5S,6S)-2,3,5-trihydroxy-4,6-diphosphonooxycyclohexyl] dihydrogen phosphate
Synonyms:  
Standard InCHIKey:  MMWCIQZXVOZEGG-MLQGYMEPSA-N
Standard InCHI:  InChI=1S/C6H15O15P3/c7-1-2(8)5(20-23(13,14)15)6(21-24(16,17)18)3(9)4(1)19-22(10,11)12/h1-9H,(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)/t1-,2-,3+,4+,5+,6+/m1/s1
SMILES:  O[C@H]1[C@H](OP(=O)(O)O)[C@@H](OP(=O)(O)O)[C@H]([C@H]([C@@H]1O)OP(=O)(O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL329137
PubChem CID:   439455
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001292] Cyclic alcohols and derivatives
            • [CHEMONTID:0002509] Cyclitols and derivatives
              • [CHEMONTID:0002511] Inositol phosphates

*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
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. DOI[10.1172/JCI16309]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. DOI[10.1371/journal.pone.0115359]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[10557354]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11034610]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11419736]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11530998]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1175644]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12391014]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12812989]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12840027]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12878451]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15084647]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1521032]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15230696]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15314235]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16112079]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16770722]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1687010]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17116739]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17190852]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17875433]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18311922]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18544912]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18799520]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19425150]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19961175]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20506249]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20601097]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. faeces n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. bile n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. urine n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20876113]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[21798258]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[2268561]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[22711758]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23315938]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23717534]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23752203]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23810710]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23811455]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23868375]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23919613]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24101735]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24399466]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24494566]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24558969]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24816727]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25114169]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25181601]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25293588]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25644343]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26236990]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[27471436]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[3179836]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[347637]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[4696527]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[5432584]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6121420]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6780563]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8600370]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8987136]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9192820]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9800648]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO20338 Mus musculus Species Muridae 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 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
NPT2 Others Unspecified IC50 n.a. 4000.0 nM PMID[548982]

☑ 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 NPC325822 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
1.0 High Similarity NPC61270
0.9375 High Similarity NPC325153
0.9375 High Similarity NPC278465
0.9375 High Similarity NPC322803
0.9375 High Similarity NPC321102
0.913 High Similarity NPC314613
0.8542 High Similarity NPC188428
0.8542 High Similarity NPC318700
0.8222 Intermediate Similarity NPC88278
0.8222 Intermediate Similarity NPC227707
0.8222 Intermediate Similarity NPC99573
0.8222 Intermediate Similarity NPC111882
0.8222 Intermediate Similarity NPC102981
0.7857 Intermediate Similarity NPC174485
0.7551 Intermediate Similarity NPC207656
0.7551 Intermediate Similarity NPC107091
0.7547 Intermediate Similarity NPC103672
0.7547 Intermediate Similarity NPC320043
0.7407 Intermediate Similarity NPC314821
0.7407 Intermediate Similarity NPC317626
0.7407 Intermediate Similarity NPC317501
0.7358 Intermediate Similarity NPC329095
0.7255 Intermediate Similarity NPC88638
0.7111 Intermediate Similarity NPC192065
0.7111 Intermediate Similarity NPC86412
0.7111 Intermediate Similarity NPC325034
0.7111 Intermediate Similarity NPC293908
0.7111 Intermediate Similarity NPC66052
0.7018 Intermediate Similarity NPC3547
0.6735 Remote Similarity NPC266553
0.6667 Remote Similarity NPC321873
0.6545 Remote Similarity NPC322158
0.6545 Remote Similarity NPC329128
0.6444 Remote Similarity NPC197207
0.6444 Remote Similarity NPC321170
0.6444 Remote Similarity NPC149070
0.6444 Remote Similarity NPC127074
0.6444 Remote Similarity NPC31433
0.6444 Remote Similarity NPC187058
0.6444 Remote Similarity NPC182541
0.6444 Remote Similarity NPC266566
0.6393 Remote Similarity NPC323945
0.6346 Remote Similarity NPC320240
0.6346 Remote Similarity NPC70756
0.6316 Remote Similarity NPC300235
0.6316 Remote Similarity NPC476136
0.6316 Remote Similarity NPC476149
0.6316 Remote Similarity NPC244869
0.629 Remote Similarity NPC320296
0.6111 Remote Similarity NPC165846
0.6111 Remote Similarity NPC21209
0.6111 Remote Similarity NPC289758
0.6111 Remote Similarity NPC199857
0.6111 Remote Similarity NPC285364
0.6111 Remote Similarity NPC176017
0.6111 Remote Similarity NPC73906
0.6111 Remote Similarity NPC92246
0.6111 Remote Similarity NPC69445
0.6111 Remote Similarity NPC255377
0.6038 Remote Similarity NPC29721
0.6027 Remote Similarity NPC317263
0.6 Remote Similarity NPC321087
0.6 Remote Similarity NPC277475
0.5968 Remote Similarity NPC182903
0.5893 Remote Similarity NPC14144
0.5862 Remote Similarity NPC326533
0.5789 Remote Similarity NPC42503
0.5789 Remote Similarity NPC282143
0.5789 Remote Similarity NPC299781
0.5789 Remote Similarity NPC157193
0.5789 Remote Similarity NPC328954
0.5778 Remote Similarity NPC301586
0.5778 Remote Similarity NPC325345
0.5778 Remote Similarity NPC33415
0.5714 Remote Similarity NPC252918
0.5714 Remote Similarity NPC476209
0.5714 Remote Similarity NPC230789
0.569 Remote Similarity NPC323574
0.5667 Remote Similarity NPC246558
0.5667 Remote Similarity NPC242073
0.5667 Remote Similarity NPC323361
0.5667 Remote Similarity NPC157514
0.5667 Remote Similarity NPC165198
0.5667 Remote Similarity NPC67660
0.5667 Remote Similarity NPC89145
0.5667 Remote Similarity NPC269166
0.5667 Remote Similarity NPC130683
0.5667 Remote Similarity NPC107914
0.5667 Remote Similarity NPC145112
0.5667 Remote Similarity NPC58629
0.5614 Remote Similarity NPC247546
0.5614 Remote Similarity NPC172086
0.5614 Remote Similarity NPC112363

  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 NPC325822 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
1.0 High Similarity NPD9061 Clinical (unspecified phase)
0.8542 High Similarity NPD9065 Phase 3
0.8222 Intermediate Similarity NPD8996 Phase 3
0.8222 Intermediate Similarity NPD8995 Clinical (unspecified phase)
0.8039 Intermediate Similarity NPD8991 Phase 1
0.7551 Intermediate Similarity NPD9218 Clinical (unspecified phase)
0.7551 Intermediate Similarity NPD9219 Approved
0.7547 Intermediate Similarity NPD9050 Approved
0.7547 Intermediate Similarity NPD9049 Discontinued
0.7407 Intermediate Similarity NPD9035 Clinical (unspecified phase)
0.7407 Intermediate Similarity NPD9036 Phase 3
0.7111 Intermediate Similarity NPD9053 Approved
0.7111 Intermediate Similarity NPD9052 Approved
0.7111 Intermediate Similarity NPD9051 Approved
0.6444 Remote Similarity NPD8814 Phase 3
0.6444 Remote Similarity NPD8237 Approved
0.6222 Remote Similarity NPD8236 Phase 1
0.6222 Remote Similarity NPD8234 Approved
0.6222 Remote Similarity NPD8235 Approved
0.6154 Remote Similarity NPD8958 Phase 2
0.6154 Remote Similarity NPD8957 Approved
0.6111 Remote Similarity NPD8993 Phase 1
0.6111 Remote Similarity NPD9000 Phase 3
0.6111 Remote Similarity NPD8997 Approved
0.6111 Remote Similarity NPD8994 Approved
0.6111 Remote Similarity NPD8999 Phase 3
0.6111 Remote Similarity NPD8998 Phase 2
0.6038 Remote Similarity NPD9006 Approved
0.5893 Remote Similarity NPD8965 Approved
0.5893 Remote Similarity NPD8966 Approved
0.5862 Remote Similarity NPD905 Approved
0.5862 Remote Similarity NPD904 Phase 3
0.5778 Remote Similarity NPD8549 Clinical (unspecified phase)
0.5778 Remote Similarity NPD8988 Clinical (unspecified phase)
0.5686 Remote Similarity NPD8976 Approved
0.5686 Remote Similarity NPD8977 Phase 3
0.5667 Remote Similarity NPD892 Phase 3
0.5667 Remote Similarity NPD890 Clinical (unspecified phase)
0.5667 Remote Similarity NPD894 Approved
0.5667 Remote Similarity NPD889 Approved
0.5667 Remote Similarity NPD893 Approved
0.5667 Remote Similarity NPD888 Phase 3
0.5667 Remote Similarity NPD895 Approved
0.5667 Remote Similarity NPD891 Phase 3
0.5667 Remote Similarity NPD887 Approved
0.5614 Remote Similarity NPD9005 Phase 3
0.5614 Remote Similarity NPD9139 Approved
0.5614 Remote Similarity NPD9003 Clinical (unspecified phase)
0.5614 Remote Similarity NPD9004 Approved

  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