Structure

Physi-Chem Properties

Molecular Weight:  340.0
Volume:  254.833
LogP:  -3.156
LogD:  -1.727
LogS:  0.199
# Rotatable Bonds:  9
TPSA:  204.96
# H-Bond Aceptor:  12
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  14

MedChem Properties

QED Drug-Likeness Score:  0.27
Synthetic Accessibility Score:  6.139
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.341
MDCK Permeability:  0.0006170222768560052
Pgp-inhibitor:  0.001
Pgp-substrate:  0.082
Human Intestinal Absorption (HIA):  0.482
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.547
Plasma Protein Binding (PPB):  10.421062469482422%
Volume Distribution (VD):  0.266
Pgp-substrate:  78.74162292480469%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.016
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.027
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.837
CYP2D6-inhibitor:  0.023
CYP2D6-substrate:  0.086
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.001

ADMET: Excretion

Clearance (CL):  1.299
Half-life (T1/2):  0.901

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.052
Drug-inuced Liver Injury (DILI):  0.045
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.961
Skin Sensitization:  0.323
Carcinogencity:  0.02
Eye Corrosion:  0.049
Eye Irritation:  0.084
Respiratory Toxicity:  0.418

Download Data

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

  Natural Product: NPC3547

Natural Product ID:  NPC3547
Common Name*:   Fructose 1-6-Bisphosphate
IUPAC Name:   [(2R,3R,4S)-2,3,4-trihydroxy-5-oxo-6-phosphonooxyhexyl] dihydrogen phosphate
Synonyms:  
Standard InCHIKey:  XPYBSIWDXQFNMH-UYFOZJQFSA-N
Standard InCHI:  InChI=1S/C6H14O12P2/c7-3(1-17-19(11,12)13)5(9)6(10)4(8)2-18-20(14,15)16/h3,5-7,9-10H,1-2H2,(H2,11,12,13)(H2,14,15,16)/t3-,5-,6-/m1/s1
SMILES:  C([C@H]([C@H]([C@@H](C(=O)COP(=O)(O)O)O)O)O)OP(=O)(O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1235112
PubChem CID:   84951
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0001540] Monosaccharides
            • [CHEMONTID:0001498] Hexoses
              • [CHEMONTID:0002260] Hexose 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

☑ 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
NPT52 Individual Protein Pyruvate kinase isozymes M1/M2 Homo sapiens AC50 = 23.0 nM PMID[536115]
NPT714 Individual Protein Fructose-bisphosphate aldolase A Oryctolagus cuniculus Ki = 15000.0 nM PMID[536113]
NPT715 Individual Protein Fructose-bisphosphate aldolase Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacterpylori) Ki = 17000.0 nM PMID[536113]
NPT716 Individual Protein Fructose-bisphosphate aldolase Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast) Ki = 85000.0 nM PMID[536113]
NPT717 Individual Protein Fructose-bisphosphate aldolase Mycobacterium tuberculosis Ki = 21000.0 nM PMID[536113]
NPT718 Individual Protein Fructose-bisphosphate aldolase class II Yersinia pestis Ki = 55000.0 nM PMID[536113]
NPT719 Individual Protein Fructose-bisphosphate aldoloase, glycosomal Trypanosoma brucei brucei IC50 = 10000.0 nM PMID[536114]
NPT714 Individual Protein Fructose-bisphosphate aldolase A Oryctolagus cuniculus IC50 = 13000.0 nM PMID[536114]

☑ 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 NPC3547 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
0.8947 High Similarity NPC320296
0.8772 High Similarity NPC323945
0.8462 Intermediate Similarity NPC172086
0.8462 Intermediate Similarity NPC247546
0.7719 Intermediate Similarity NPC196612
0.7636 Intermediate Similarity NPC328954
0.7544 Intermediate Similarity NPC277878
0.75 Intermediate Similarity NPC228782
0.75 Intermediate Similarity NPC313565
0.75 Intermediate Similarity NPC259982
0.7222 Intermediate Similarity NPC270088
0.7018 Intermediate Similarity NPC325822
0.7018 Intermediate Similarity NPC61270
0.6935 Remote Similarity NPC293692
0.6935 Remote Similarity NPC220922
0.6792 Remote Similarity NPC320331
0.6727 Remote Similarity NPC318951
0.6727 Remote Similarity NPC320624
0.6721 Remote Similarity NPC6883
0.6667 Remote Similarity NPC321102
0.6667 Remote Similarity NPC320043
0.6667 Remote Similarity NPC103672
0.6667 Remote Similarity NPC325153
0.6667 Remote Similarity NPC322803
0.6667 Remote Similarity NPC278465
0.6667 Remote Similarity NPC317680
0.6607 Remote Similarity NPC38891
0.6607 Remote Similarity NPC242655
0.6557 Remote Similarity NPC19676
0.6557 Remote Similarity NPC323401
0.65 Remote Similarity NPC329095
0.6418 Remote Similarity NPC258690
0.6418 Remote Similarity NPC317651
0.6379 Remote Similarity NPC314613
0.6364 Remote Similarity NPC322956
0.6364 Remote Similarity NPC35661
0.6364 Remote Similarity NPC325307
0.629 Remote Similarity NPC317501
0.629 Remote Similarity NPC317626
0.629 Remote Similarity NPC314821
0.6286 Remote Similarity NPC32148
0.6167 Remote Similarity NPC46254
0.6154 Remote Similarity NPC293908
0.6154 Remote Similarity NPC66052
0.6154 Remote Similarity NPC86412
0.6154 Remote Similarity NPC325034
0.6154 Remote Similarity NPC192065
0.6111 Remote Similarity NPC328950
0.6071 Remote Similarity NPC192402
0.6071 Remote Similarity NPC24751
0.6071 Remote Similarity NPC100742
0.6071 Remote Similarity NPC121018
0.6071 Remote Similarity NPC97444
0.6071 Remote Similarity NPC19044
0.6027 Remote Similarity NPC321873
0.6 Remote Similarity NPC188428
0.6 Remote Similarity NPC318700
0.5902 Remote Similarity NPC293378
0.5821 Remote Similarity NPC322855
0.5806 Remote Similarity NPC322158
0.5806 Remote Similarity NPC329128
0.5781 Remote Similarity NPC65985
0.5758 Remote Similarity NPC198377
0.5735 Remote Similarity NPC174485
0.5735 Remote Similarity NPC17935
0.5714 Remote Similarity NPC268243
0.5672 Remote Similarity NPC61567
0.5616 Remote Similarity NPC53879
0.5616 Remote Similarity NPC57788
0.5614 Remote Similarity NPC266553
0.5614 Remote Similarity NPC102981
0.5614 Remote Similarity NPC88278
0.5614 Remote Similarity NPC111882
0.5614 Remote Similarity NPC227707
0.5614 Remote Similarity NPC99573
0.5606 Remote Similarity NPC60830
0.5606 Remote Similarity NPC68743

  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 NPC3547 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
0.8462 Intermediate Similarity NPD9004 Approved
0.8462 Intermediate Similarity NPD9005 Phase 3
0.8462 Intermediate Similarity NPD9003 Clinical (unspecified phase)
0.7679 Intermediate Similarity NPD9001 Clinical (unspecified phase)
0.7679 Intermediate Similarity NPD9002 Approved
0.7544 Intermediate Similarity NPD64 Approved
0.7544 Intermediate Similarity NPD66 Approved
0.7544 Intermediate Similarity NPD72 Approved
0.7544 Intermediate Similarity NPD9009 Approved
0.7544 Intermediate Similarity NPD9008 Approved
0.7544 Intermediate Similarity NPD9010 Approved
0.7544 Intermediate Similarity NPD9011 Approved
0.7544 Intermediate Similarity NPD65 Approved
0.7544 Intermediate Similarity NPD8960 Approved
0.7544 Intermediate Similarity NPD9007 Approved
0.7333 Intermediate Similarity NPD73 Approved
0.7018 Intermediate Similarity NPD9061 Clinical (unspecified phase)
0.6935 Remote Similarity NPD8959 Approved
0.6724 Remote Similarity NPD8964 Approved
0.6667 Remote Similarity NPD9050 Approved
0.6667 Remote Similarity NPD9049 Discontinued
0.6418 Remote Similarity NPD8961 Approved
0.629 Remote Similarity NPD9035 Clinical (unspecified phase)
0.629 Remote Similarity NPD9036 Phase 3
0.6286 Remote Similarity NPD896 Approved
0.6286 Remote Similarity NPD898 Approved
0.6286 Remote Similarity NPD897 Approved
0.6154 Remote Similarity NPD9053 Approved
0.6154 Remote Similarity NPD9052 Approved
0.6154 Remote Similarity NPD9051 Approved
0.6071 Remote Similarity NPD8602 Approved
0.6071 Remote Similarity NPD8598 Approved
0.6071 Remote Similarity NPD8605 Approved
0.6071 Remote Similarity NPD8600 Approved
0.6071 Remote Similarity NPD8604 Approved
0.6071 Remote Similarity NPD8601 Approved
0.6071 Remote Similarity NPD8599 Approved
0.6071 Remote Similarity NPD8603 Approved
0.6 Remote Similarity NPD9065 Phase 3
0.5902 Remote Similarity NPD9129 Approved
0.5902 Remote Similarity NPD71 Approved
0.5902 Remote Similarity NPD9126 Approved
0.5867 Remote Similarity NPD3181 Approved
0.5738 Remote Similarity NPD9128 Approved
0.5738 Remote Similarity NPD70 Approved
0.5738 Remote Similarity NPD9125 Approved
0.5738 Remote Similarity NPD9122 Approved
0.5738 Remote Similarity NPD9121 Approved
0.5738 Remote Similarity NPD108 Approved
0.5738 Remote Similarity NPD9124 Approved
0.5738 Remote Similarity NPD9127 Approved
0.5738 Remote Similarity NPD109 Approved
0.5738 Remote Similarity NPD9123 Approved
0.5738 Remote Similarity NPD9130 Phase 3
0.5714 Remote Similarity NPD11 Approved
0.5714 Remote Similarity NPD376 Approved
0.5714 Remote Similarity NPD8991 Phase 1
0.5652 Remote Similarity NPD9120 Clinical (unspecified phase)
0.5614 Remote Similarity NPD8995 Clinical (unspecified phase)
0.5614 Remote Similarity NPD8996 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