Structure

Physi-Chem Properties

Molecular Weight:  180.06
Volume:  162.437
LogP:  -2.301
LogD:  -2.465
LogS:  0.062
# Rotatable Bonds:  5
TPSA:  118.22
# H-Bond Aceptor:  6
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.301
Synthetic Accessibility Score:  3.801
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.303
MDCK Permeability:  0.004043754655867815
Pgp-inhibitor:  0.007
Pgp-substrate:  0.102
Human Intestinal Absorption (HIA):  0.192
20% Bioavailability (F20%):  0.715
30% Bioavailability (F30%):  0.884

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.532
Plasma Protein Binding (PPB):  10.912890434265137%
Volume Distribution (VD):  0.772
Pgp-substrate:  78.1568603515625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.032
CYP2C19-inhibitor:  0.008
CYP2C19-substrate:  0.055
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.075
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.099
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.011

ADMET: Excretion

Clearance (CL):  1.269
Half-life (T1/2):  0.903

ADMET: Toxicity

hERG Blockers:  0.087
Human Hepatotoxicity (H-HT):  0.155
Drug-inuced Liver Injury (DILI):  0.782
AMES Toxicity:  0.054
Rat Oral Acute Toxicity:  0.017
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.048
Carcinogencity:  0.004
Eye Corrosion:  0.003
Eye Irritation:  0.033
Respiratory Toxicity:  0.018

Download Data

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

  Natural Product: NPC247546

Natural Product ID:  NPC247546
Common Name*:   1,3,4,5,6-Pentahydroxyhexan-2-One
IUPAC Name:   1,3,4,5,6-pentahydroxyhexan-2-one
Synonyms:  
Standard InCHIKey:  BJHIKXHVCXFQLS-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H12O6/c7-1-3(9)5(11)6(12)4(10)2-8/h3,5-9,11-12H,1-2H2
SMILES:  OCC(C(C(C(=O)CO)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL23894
PubChem CID:   1101
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0001540] Monosaccharides

*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
NPO16850 Eucommia ulmoides Species Eucommiaceae Eukaryota n.a. n.a. n.a. PMID[26767291]
NPO16850 Eucommia ulmoides Species Eucommiaceae Eukaryota n.a. bark n.a. PMID[26767291]
NPO16850 Eucommia ulmoides Species Eucommiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16850 Eucommia ulmoides Species Eucommiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16850 Eucommia ulmoides Species Eucommiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16850 Eucommia ulmoides Species Eucommiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16850 Eucommia ulmoides Species Eucommiaceae 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
NPT1727 Individual Protein Acrosin Homo sapiens Inhibition = 18.0 % PMID[494327]
NPT56 Individual Protein Beta-lactamase AmpC Escherichia coli K-12 Potency = 8912.5 nM PMID[494328]
NPT532 Individual Protein Lysine-specific demethylase 4A Homo sapiens Potency n.a. 56234.1 nM PMID[494328]
NPT198 Individual Protein Vitamin D receptor Homo sapiens Potency n.a. 79432.8 nM PMID[494328]
NPT199 Individual Protein DNA polymerase kappa Homo sapiens Potency n.a. 21192.3 nM PMID[494329]
NPT100 Individual Protein Glutaminase kidney isoform, mitochondrial Homo sapiens Potency n.a. 35481.3 nM PMID[494328]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 23109.3 nM PMID[494328]
NPT50 Individual Protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency n.a. 25929.0 nM PMID[494328]
NPT50 Individual Protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency n.a. 29092.9 nM PMID[494328]
NPT803 Individual Protein Flap endonuclease 1 Homo sapiens Potency n.a. 89125.1 nM PMID[494328]
NPT698 Individual Protein Regulator of G-protein signaling 4 Homo sapiens Potency n.a. 50118.7 nM PMID[494328]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 13115.4 nM PMID[494328]
NPT755 Individual Protein Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 Homo sapiens Potency n.a. 35481.3 nM PMID[494328]
NPT831 Individual Protein Serine/threonine-protein kinase PLK1 Homo sapiens Potency n.a. 26679.5 nM PMID[494328]

☑ 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 NPC247546 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 NPC172086
0.8864 High Similarity NPC259982
0.8864 High Similarity NPC228782
0.8864 High Similarity NPC313565
0.8776 High Similarity NPC277878
0.86 High Similarity NPC196612
0.8478 Intermediate Similarity NPC270088
0.8462 Intermediate Similarity NPC3547
0.8 Intermediate Similarity NPC320331
0.7963 Intermediate Similarity NPC220922
0.7963 Intermediate Similarity NPC293692
0.7857 Intermediate Similarity NPC320296
0.7708 Intermediate Similarity NPC38891
0.7708 Intermediate Similarity NPC242655
0.7679 Intermediate Similarity NPC323945
0.7547 Intermediate Similarity NPC19676
0.7547 Intermediate Similarity NPC323401
0.7447 Intermediate Similarity NPC35661
0.7407 Intermediate Similarity NPC6883
0.7288 Intermediate Similarity NPC317651
0.7288 Intermediate Similarity NPC258690
0.7273 Intermediate Similarity NPC66052
0.7273 Intermediate Similarity NPC325034
0.7273 Intermediate Similarity NPC293908
0.7273 Intermediate Similarity NPC86412
0.7273 Intermediate Similarity NPC192065
0.7115 Intermediate Similarity NPC46254
0.7083 Intermediate Similarity NPC19044
0.7083 Intermediate Similarity NPC100742
0.7083 Intermediate Similarity NPC192402
0.7083 Intermediate Similarity NPC121018
0.7083 Intermediate Similarity NPC97444
0.7083 Intermediate Similarity NPC24751
0.6825 Remote Similarity NPC32148
0.6792 Remote Similarity NPC293378
0.661 Remote Similarity NPC322855
0.6607 Remote Similarity NPC65985
0.6591 Remote Similarity NPC127074
0.6591 Remote Similarity NPC149070
0.6591 Remote Similarity NPC187058
0.6591 Remote Similarity NPC182541
0.6591 Remote Similarity NPC197207
0.6552 Remote Similarity NPC198377
0.6531 Remote Similarity NPC111882
0.6531 Remote Similarity NPC227707
0.6531 Remote Similarity NPC99573
0.6531 Remote Similarity NPC102981
0.6531 Remote Similarity NPC266553
0.6531 Remote Similarity NPC88278
0.65 Remote Similarity NPC17935
0.6481 Remote Similarity NPC328954
0.6441 Remote Similarity NPC61567
0.6379 Remote Similarity NPC68743
0.6379 Remote Similarity NPC60830
0.6333 Remote Similarity NPC179624
0.6308 Remote Similarity NPC57788
0.6308 Remote Similarity NPC53879
0.619 Remote Similarity NPC268243
0.6154 Remote Similarity NPC76051
0.6154 Remote Similarity NPC320240
0.6154 Remote Similarity NPC29721
0.6154 Remote Similarity NPC319680
0.6154 Remote Similarity NPC70756
0.6122 Remote Similarity NPC128713
0.6066 Remote Similarity NPC320032
0.6042 Remote Similarity NPC159089
0.6042 Remote Similarity NPC5505
0.6038 Remote Similarity NPC207656
0.6038 Remote Similarity NPC107091
0.6 Remote Similarity NPC131770
0.6 Remote Similarity NPC200618
0.5926 Remote Similarity NPC21209
0.5926 Remote Similarity NPC165846
0.5926 Remote Similarity NPC289758
0.5926 Remote Similarity NPC176017
0.5926 Remote Similarity NPC199857
0.5926 Remote Similarity NPC73906
0.5926 Remote Similarity NPC92246
0.5926 Remote Similarity NPC255377
0.5926 Remote Similarity NPC69445
0.5926 Remote Similarity NPC285364
0.5918 Remote Similarity NPC109026
0.5909 Remote Similarity NPC33415
0.5909 Remote Similarity NPC301586
0.587 Remote Similarity NPC261351
0.5833 Remote Similarity NPC317203
0.5833 Remote Similarity NPC168052
0.5833 Remote Similarity NPC250870
0.5833 Remote Similarity NPC191084
0.5818 Remote Similarity NPC314613
0.5818 Remote Similarity NPC277475
0.5818 Remote Similarity NPC88638
0.5818 Remote Similarity NPC230789
0.5818 Remote Similarity NPC321087
0.5818 Remote Similarity NPC252918
0.5789 Remote Similarity NPC90904
0.5781 Remote Similarity NPC10659
0.5778 Remote Similarity NPC270334
0.5775 Remote Similarity NPC125164
0.5769 Remote Similarity NPC474361
0.5741 Remote Similarity NPC469781
0.5714 Remote Similarity NPC14144
0.5714 Remote Similarity NPC1037
0.5714 Remote Similarity NPC112363
0.5692 Remote Similarity NPC88898
0.5692 Remote Similarity NPC106216
0.5692 Remote Similarity NPC325773
0.569 Remote Similarity NPC100096
0.5686 Remote Similarity NPC316217
0.5686 Remote Similarity NPC222792
0.5682 Remote Similarity NPC320326
0.5672 Remote Similarity NPC241949
0.5667 Remote Similarity NPC53463
0.5667 Remote Similarity NPC23155
0.5667 Remote Similarity NPC320588
0.5667 Remote Similarity NPC469937
0.566 Remote Similarity NPC310220
0.5658 Remote Similarity NPC159714
0.5658 Remote Similarity NPC221510
0.5658 Remote Similarity NPC67254
0.5625 Remote Similarity NPC127142
0.5614 Remote Similarity NPC157193
0.5614 Remote Similarity NPC282143
0.5614 Remote Similarity NPC82512
0.5614 Remote Similarity NPC325822
0.5614 Remote Similarity NPC299781
0.5614 Remote Similarity NPC42503
0.5614 Remote Similarity NPC61270
0.56 Remote Similarity NPC317945

  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 NPC247546 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 NPD9003 Clinical (unspecified phase)
1.0 High Similarity NPD9004 Approved
1.0 High Similarity NPD9005 Phase 3
0.8958 High Similarity NPD9002 Approved
0.8958 High Similarity NPD9001 Clinical (unspecified phase)
0.8776 High Similarity NPD72 Approved
0.8776 High Similarity NPD64 Approved
0.8776 High Similarity NPD9009 Approved
0.8776 High Similarity NPD9007 Approved
0.8776 High Similarity NPD8960 Approved
0.8776 High Similarity NPD9010 Approved
0.8776 High Similarity NPD9008 Approved
0.8776 High Similarity NPD66 Approved
0.8776 High Similarity NPD65 Approved
0.8776 High Similarity NPD9011 Approved
0.8113 Intermediate Similarity NPD73 Approved
0.7963 Intermediate Similarity NPD8959 Approved
0.78 Intermediate Similarity NPD8964 Approved
0.7288 Intermediate Similarity NPD8961 Approved
0.7273 Intermediate Similarity NPD9053 Approved
0.7273 Intermediate Similarity NPD9052 Approved
0.7273 Intermediate Similarity NPD9051 Approved
0.7083 Intermediate Similarity NPD8599 Approved
0.7083 Intermediate Similarity NPD8605 Approved
0.7083 Intermediate Similarity NPD8598 Approved
0.7083 Intermediate Similarity NPD8603 Approved
0.7083 Intermediate Similarity NPD8602 Approved
0.7083 Intermediate Similarity NPD8604 Approved
0.7083 Intermediate Similarity NPD8601 Approved
0.7083 Intermediate Similarity NPD8600 Approved
0.6825 Remote Similarity NPD898 Approved
0.6825 Remote Similarity NPD897 Approved
0.6825 Remote Similarity NPD896 Approved
0.6792 Remote Similarity NPD71 Approved
0.6792 Remote Similarity NPD9126 Approved
0.6792 Remote Similarity NPD9129 Approved
0.6604 Remote Similarity NPD9121 Approved
0.6604 Remote Similarity NPD9127 Approved
0.6604 Remote Similarity NPD9122 Approved
0.6604 Remote Similarity NPD9130 Phase 3
0.6604 Remote Similarity NPD70 Approved
0.6604 Remote Similarity NPD9128 Approved
0.6604 Remote Similarity NPD109 Approved
0.6604 Remote Similarity NPD108 Approved
0.6604 Remote Similarity NPD9124 Approved
0.6604 Remote Similarity NPD9123 Approved
0.6604 Remote Similarity NPD9125 Approved
0.6591 Remote Similarity NPD8814 Phase 3
0.6531 Remote Similarity NPD8995 Clinical (unspecified phase)
0.6531 Remote Similarity NPD8996 Phase 3
0.6393 Remote Similarity NPD9120 Clinical (unspecified phase)
0.6324 Remote Similarity NPD3181 Approved
0.6275 Remote Similarity NPD8958 Phase 2
0.6275 Remote Similarity NPD8957 Approved
0.6154 Remote Similarity NPD9006 Approved
0.6143 Remote Similarity NPD11 Approved
0.6143 Remote Similarity NPD376 Approved
0.6038 Remote Similarity NPD9219 Approved
0.6038 Remote Similarity NPD9218 Clinical (unspecified phase)
0.5926 Remote Similarity NPD8998 Phase 2
0.5926 Remote Similarity NPD9000 Phase 3
0.5926 Remote Similarity NPD8999 Phase 3
0.5926 Remote Similarity NPD8997 Approved
0.5926 Remote Similarity NPD8994 Approved
0.5926 Remote Similarity NPD8993 Phase 1
0.5909 Remote Similarity NPD8549 Clinical (unspecified phase)
0.5811 Remote Similarity NPD7329 Approved
0.58 Remote Similarity NPD8977 Phase 3
0.58 Remote Similarity NPD8976 Approved
0.5714 Remote Similarity NPD8966 Approved
0.5714 Remote Similarity NPD9139 Approved
0.5714 Remote Similarity NPD8965 Approved
0.5667 Remote Similarity NPD3730 Approved
0.5667 Remote Similarity NPD3728 Approved
0.5614 Remote Similarity NPD9061 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