Structure

Physi-Chem Properties

Molecular Weight:  499.93
Volume:  341.309
LogP:  -3.612
LogD:  -1.863
LogS:  0.296
# Rotatable Bonds:  8
TPSA:  294.86
# H-Bond Aceptor:  18
# H-Bond Donor:  6
# Rings:  1
# Heavy Atoms:  22

MedChem Properties

QED Drug-Likeness Score:  0.185
Synthetic Accessibility Score:  7.079
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:  -6.859
MDCK Permeability:  0.00019762491865549237
Pgp-inhibitor:  0.0
Pgp-substrate:  0.041
Human Intestinal Absorption (HIA):  0.955
20% Bioavailability (F20%):  0.998
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.225
Plasma Protein Binding (PPB):  13.635016441345215%
Volume Distribution (VD):  0.207
Pgp-substrate:  51.04435729980469%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.004
CYP2C19-inhibitor:  0.048
CYP2C19-substrate:  0.017
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.209
CYP2D6-inhibitor:  0.048
CYP2D6-substrate:  0.043
CYP3A4-inhibitor:  0.001
CYP3A4-substrate:  0.0

ADMET: Excretion

Clearance (CL):  1.232
Half-life (T1/2):  0.839

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.02
Drug-inuced Liver Injury (DILI):  0.001
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.95
Skin Sensitization:  0.356
Carcinogencity:  0.017
Eye Corrosion:  0.976
Eye Irritation:  0.672
Respiratory Toxicity:  0.198

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC325153

Natural Product ID:  NPC325153
Common Name*:   Phosphoric Acid Mono-(2,3-Dihydroxy-4,5,6-Tris-Phosphonooxy-Cyclohexyl) Ester
IUPAC Name:   [(1S,2R,3R,4R,5R,6R)-2,3-dihydroxy-4,5,6-triphosphonooxycyclohexyl] dihydrogen phosphate
Synonyms:  
Standard InCHIKey:  MRVYFOANPDTYBY-XCMZKKERSA-N
Standard InCHI:  InChI=1S/C6H16O18P4/c7-1-2(8)4(22-26(12,13)14)6(24-28(18,19)20)5(23-27(15,16)17)3(1)21-25(9,10)11/h1-8H,(H2,9,10,11)(H2,12,13,14)(H2,15,16,17)(H2,18,19,20)/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)OP(=O)(O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3351092
PubChem CID:   14033625
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
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. Wrocław, Poland 2004–2005 DOI[10.1016/J.FOODCHEM.2006.08.014]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf950732o]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10775096]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. root n.a. PMID[1622242]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16659156]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16668466]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. PMID[18270436]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[20963508]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. PMID[23793896]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds Tekirdag, Turkey PMID[24499198]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. seed n.a. PMID[24967651]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25053043]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25070365]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. PMID[25369450]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25369450]
NPO7635 Glycine max Species Fabaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Cotyledon n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Hypocotyl n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. Database[MetaboLights]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7635 Glycine max Species Fabaceae 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
NPT3526 Individual Protein Inositol-trisphosphate 3-kinase A Rattus norvegicus IC50 > 100000.0 nM PMID[487408]

☑ 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 NPC325153 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 NPC278465
1.0 High Similarity NPC321102
1.0 High Similarity NPC322803
0.9375 High Similarity NPC61270
0.9375 High Similarity NPC325822
0.9167 High Similarity NPC188428
0.9167 High Similarity NPC318700
0.8571 High Similarity NPC314613
0.7759 Intermediate Similarity NPC174485
0.7708 Intermediate Similarity NPC227707
0.7708 Intermediate Similarity NPC99573
0.7708 Intermediate Similarity NPC88278
0.7708 Intermediate Similarity NPC102981
0.7708 Intermediate Similarity NPC111882
0.7143 Intermediate Similarity NPC320043
0.7143 Intermediate Similarity NPC103672
0.7115 Intermediate Similarity NPC107091
0.7115 Intermediate Similarity NPC207656
0.7018 Intermediate Similarity NPC314821
0.7018 Intermediate Similarity NPC317501
0.7018 Intermediate Similarity NPC317626
0.6964 Remote Similarity NPC329095
0.6852 Remote Similarity NPC88638
0.6667 Remote Similarity NPC3547
0.6667 Remote Similarity NPC86412
0.6667 Remote Similarity NPC192065
0.6667 Remote Similarity NPC66052
0.6667 Remote Similarity NPC293908
0.6667 Remote Similarity NPC325034
0.6618 Remote Similarity NPC321873
0.6346 Remote Similarity NPC266553
0.6207 Remote Similarity NPC322158
0.6207 Remote Similarity NPC329128
0.6094 Remote Similarity NPC323945
0.6042 Remote Similarity NPC149070
0.6042 Remote Similarity NPC266566
0.6042 Remote Similarity NPC127074
0.6042 Remote Similarity NPC197207
0.6042 Remote Similarity NPC182541
0.6042 Remote Similarity NPC321170
0.6042 Remote Similarity NPC31433
0.6042 Remote Similarity NPC187058
0.6 Remote Similarity NPC320296
0.6 Remote Similarity NPC476149
0.6 Remote Similarity NPC476136
0.6 Remote Similarity NPC320240
0.6 Remote Similarity NPC317263
0.6 Remote Similarity NPC70756
0.6 Remote Similarity NPC300235
0.6 Remote Similarity NPC244869
0.5833 Remote Similarity NPC326533
0.5789 Remote Similarity NPC73906
0.5789 Remote Similarity NPC255377
0.5789 Remote Similarity NPC21209
0.5789 Remote Similarity NPC199857
0.5789 Remote Similarity NPC92246
0.5789 Remote Similarity NPC176017
0.5789 Remote Similarity NPC285364
0.5789 Remote Similarity NPC289758
0.5789 Remote Similarity NPC165846
0.5789 Remote Similarity NPC69445
0.5714 Remote Similarity NPC29721
0.5692 Remote Similarity NPC182903
0.569 Remote Similarity NPC277475
0.569 Remote Similarity NPC321087
0.5645 Remote Similarity NPC67660
0.5645 Remote Similarity NPC246558
0.5645 Remote Similarity NPC165198
0.5645 Remote Similarity NPC107914
0.5645 Remote Similarity NPC130683
0.5645 Remote Similarity NPC58629
0.5645 Remote Similarity NPC89145
0.5645 Remote Similarity NPC145112
0.5645 Remote Similarity NPC157514
0.5645 Remote Similarity NPC242073
0.5645 Remote Similarity NPC323361
0.5645 Remote Similarity NPC269166

  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 NPC325153 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
0.9375 High Similarity NPD9061 Clinical (unspecified phase)
0.9167 High Similarity NPD9065 Phase 3
0.8269 Intermediate Similarity NPD8991 Phase 1
0.7708 Intermediate Similarity NPD8996 Phase 3
0.7708 Intermediate Similarity NPD8995 Clinical (unspecified phase)
0.7143 Intermediate Similarity NPD9049 Discontinued
0.7143 Intermediate Similarity NPD9050 Approved
0.7115 Intermediate Similarity NPD9218 Clinical (unspecified phase)
0.7115 Intermediate Similarity NPD9219 Approved
0.7018 Intermediate Similarity NPD9035 Clinical (unspecified phase)
0.7018 Intermediate Similarity NPD9036 Phase 3
0.6667 Remote Similarity NPD9052 Approved
0.6667 Remote Similarity NPD9051 Approved
0.6667 Remote Similarity NPD9053 Approved
0.6042 Remote Similarity NPD8814 Phase 3
0.6042 Remote Similarity NPD8237 Approved
0.5833 Remote Similarity NPD8234 Approved
0.5833 Remote Similarity NPD8235 Approved
0.5833 Remote Similarity NPD904 Phase 3
0.5833 Remote Similarity NPD8236 Phase 1
0.5833 Remote Similarity NPD905 Approved
0.5818 Remote Similarity NPD8958 Phase 2
0.5818 Remote Similarity NPD8957 Approved
0.5789 Remote Similarity NPD8993 Phase 1
0.5789 Remote Similarity NPD9000 Phase 3
0.5789 Remote Similarity NPD8994 Approved
0.5789 Remote Similarity NPD8997 Approved
0.5789 Remote Similarity NPD8999 Phase 3
0.5789 Remote Similarity NPD8998 Phase 2
0.5714 Remote Similarity NPD9006 Approved
0.5645 Remote Similarity NPD892 Phase 3
0.5645 Remote Similarity NPD894 Approved
0.5645 Remote Similarity NPD890 Clinical (unspecified phase)
0.5645 Remote Similarity NPD887 Approved
0.5645 Remote Similarity NPD889 Approved
0.5645 Remote Similarity NPD893 Approved
0.5645 Remote Similarity NPD895 Approved
0.5645 Remote Similarity NPD891 Phase 3
0.5645 Remote Similarity NPD888 Phase 3

  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