Structure

Physi-Chem Properties

Molecular Weight:  196.06
Volume:  171.228
LogP:  -2.551
LogD:  -2.566
LogS:  0.168
# Rotatable Bonds:  5
TPSA:  138.45
# H-Bond Aceptor:  7
# H-Bond Donor:  6
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.246
Synthetic Accessibility Score:  4.102
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.409
MDCK Permeability:  0.0023667176719754934
Pgp-inhibitor:  0.007
Pgp-substrate:  0.503
Human Intestinal Absorption (HIA):  0.253
20% Bioavailability (F20%):  0.81
30% Bioavailability (F30%):  0.97

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.603
Plasma Protein Binding (PPB):  14.905618667602539%
Volume Distribution (VD):  0.667
Pgp-substrate:  76.93225860595703%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.022
CYP2C19-inhibitor:  0.011
CYP2C19-substrate:  0.051
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.08
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.094
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.005

ADMET: Excretion

Clearance (CL):  1.3
Half-life (T1/2):  0.859

ADMET: Toxicity

hERG Blockers:  0.067
Human Hepatotoxicity (H-HT):  0.212
Drug-inuced Liver Injury (DILI):  0.834
AMES Toxicity:  0.055
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.008
Skin Sensitization:  0.158
Carcinogencity:  0.004
Eye Corrosion:  0.003
Eye Irritation:  0.02
Respiratory Toxicity:  0.037

Download Data

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

  Natural Product: NPC277878

Natural Product ID:  NPC277878
Common Name*:   Gluconic Acid
IUPAC Name:   (2R,3S,4R,5R)-2,3,4,5,6-pentahydroxyhexanoic acid
Synonyms:   E574
Standard InCHIKey:  RGHNJXZEOKUKBD-SQOUGZDYSA-N
Standard InCHI:  InChI=1S/C6H12O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-5,7-11H,1H2,(H,12,13)/t2-,3-,4+,5-/m1/s1
SMILES:  OC[C@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464345
PubChem CID:   10690
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0000215] Sugar acids and derivatives

*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
NPT35 Others n.a. Activity = 20.0 % PMID[500819]
NPT35 Others n.a. pKa n.a. 3.62 n.a. PMID[500820]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 24.98 % PMID[500821]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 14.91 % PMID[500822]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -0.03 % PMID[500823]
NPT2 Others Unspecified Potency n.a. 4888.2 nM PubChem BioAssay data set

☑ 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 NPC277878 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
0.9796 High Similarity NPC196612
0.9057 High Similarity NPC220922
0.9057 High Similarity NPC293692
0.8776 High Similarity NPC172086
0.8776 High Similarity NPC247546
0.8727 High Similarity NPC323945
0.8571 High Similarity NPC320296
0.8276 Intermediate Similarity NPC258690
0.8276 Intermediate Similarity NPC317651
0.8163 Intermediate Similarity NPC242655
0.8163 Intermediate Similarity NPC38891
0.7963 Intermediate Similarity NPC323401
0.7963 Intermediate Similarity NPC19676
0.7917 Intermediate Similarity NPC35661
0.7818 Intermediate Similarity NPC6883
0.78 Intermediate Similarity NPC270088
0.7755 Intermediate Similarity NPC228782
0.7755 Intermediate Similarity NPC259982
0.7755 Intermediate Similarity NPC313565
0.7742 Intermediate Similarity NPC32148
0.7551 Intermediate Similarity NPC97444
0.7551 Intermediate Similarity NPC100742
0.7551 Intermediate Similarity NPC19044
0.7551 Intermediate Similarity NPC192402
0.7551 Intermediate Similarity NPC24751
0.7551 Intermediate Similarity NPC121018
0.7547 Intermediate Similarity NPC46254
0.7544 Intermediate Similarity NPC3547
0.7222 Intermediate Similarity NPC293378
0.7188 Intermediate Similarity NPC53879
0.7188 Intermediate Similarity NPC57788
0.7018 Intermediate Similarity NPC65985
0.7 Intermediate Similarity NPC320331
0.6949 Remote Similarity NPC198377
0.6909 Remote Similarity NPC328954
0.6885 Remote Similarity NPC17935
0.6833 Remote Similarity NPC61567
0.678 Remote Similarity NPC68743
0.678 Remote Similarity NPC60830
0.6727 Remote Similarity NPC131770
0.6727 Remote Similarity NPC200618
0.6721 Remote Similarity NPC179624
0.6667 Remote Similarity NPC293908
0.6667 Remote Similarity NPC325034
0.6667 Remote Similarity NPC86412
0.6667 Remote Similarity NPC192065
0.6667 Remote Similarity NPC317203
0.6667 Remote Similarity NPC66052
0.6604 Remote Similarity NPC319680
0.6571 Remote Similarity NPC125164
0.6562 Remote Similarity NPC268243
0.6531 Remote Similarity NPC159089
0.6531 Remote Similarity NPC5505
0.6491 Remote Similarity NPC90904
0.6452 Remote Similarity NPC320032
0.64 Remote Similarity NPC109026
0.6379 Remote Similarity NPC100096
0.6333 Remote Similarity NPC469937
0.6333 Remote Similarity NPC23155
0.6333 Remote Similarity NPC320588
0.6333 Remote Similarity NPC53463
0.6327 Remote Similarity NPC168052
0.6327 Remote Similarity NPC191084
0.6327 Remote Similarity NPC250870
0.6308 Remote Similarity NPC325773
0.6275 Remote Similarity NPC128713
0.6269 Remote Similarity NPC241949
0.625 Remote Similarity NPC18224
0.625 Remote Similarity NPC328710
0.619 Remote Similarity NPC322855
0.6176 Remote Similarity NPC469925
0.6154 Remote Similarity NPC316217
0.6154 Remote Similarity NPC222792
0.6119 Remote Similarity NPC12040
0.6119 Remote Similarity NPC76881
0.6111 Remote Similarity NPC310220
0.6081 Remote Similarity NPC474003
0.6061 Remote Similarity NPC106216
0.6061 Remote Similarity NPC88898
0.6042 Remote Similarity NPC197207
0.6042 Remote Similarity NPC127074
0.6042 Remote Similarity NPC149070
0.6042 Remote Similarity NPC187058
0.6042 Remote Similarity NPC182541
0.6038 Remote Similarity NPC227707
0.6038 Remote Similarity NPC99573
0.6038 Remote Similarity NPC102981
0.6038 Remote Similarity NPC88278
0.6038 Remote Similarity NPC266553
0.6038 Remote Similarity NPC111882
0.6027 Remote Similarity NPC473948
0.6 Remote Similarity NPC320240
0.6 Remote Similarity NPC28526
0.6 Remote Similarity NPC29721
0.6 Remote Similarity NPC70756
0.5965 Remote Similarity NPC324004
0.5965 Remote Similarity NPC328497
0.5942 Remote Similarity NPC206601
0.5926 Remote Similarity NPC322956
0.5926 Remote Similarity NPC325307
0.5918 Remote Similarity NPC125575
0.5918 Remote Similarity NPC175342
0.5909 Remote Similarity NPC469923
0.5882 Remote Similarity NPC134782
0.5882 Remote Similarity NPC1037
0.5867 Remote Similarity NPC47844
0.5867 Remote Similarity NPC141195
0.5862 Remote Similarity NPC106872
0.5857 Remote Similarity NPC250619
0.5857 Remote Similarity NPC50228
0.5857 Remote Similarity NPC97736
0.5849 Remote Similarity NPC94368
0.5846 Remote Similarity NPC68974
0.5846 Remote Similarity NPC470363
0.5846 Remote Similarity NPC475821
0.5833 Remote Similarity NPC198126
0.5833 Remote Similarity NPC96322
0.5818 Remote Similarity NPC289686
0.5811 Remote Similarity NPC228411
0.58 Remote Similarity NPC127142
0.5789 Remote Similarity NPC289758
0.5789 Remote Similarity NPC255377
0.5789 Remote Similarity NPC69445
0.5789 Remote Similarity NPC73906
0.5789 Remote Similarity NPC165846
0.5789 Remote Similarity NPC199857
0.5789 Remote Similarity NPC470014
0.5789 Remote Similarity NPC285364
0.5789 Remote Similarity NPC92246
0.5789 Remote Similarity NPC21209
0.5789 Remote Similarity NPC176017
0.5789 Remote Similarity NPC133771
0.5781 Remote Similarity NPC112224
0.5781 Remote Similarity NPC327895
0.5781 Remote Similarity NPC93861
0.5781 Remote Similarity NPC43169
0.5775 Remote Similarity NPC241265
0.5775 Remote Similarity NPC211428
0.5775 Remote Similarity NPC285003
0.5769 Remote Similarity NPC317945
0.5769 Remote Similarity NPC206924
0.5769 Remote Similarity NPC297440
0.5763 Remote Similarity NPC304162
0.5758 Remote Similarity NPC469921
0.5753 Remote Similarity NPC474100
0.5753 Remote Similarity NPC475232
0.5753 Remote Similarity NPC51249
0.5753 Remote Similarity NPC326024
0.5753 Remote Similarity NPC475260
0.5753 Remote Similarity NPC473699
0.5753 Remote Similarity NPC473775
0.5741 Remote Similarity NPC240109
0.5738 Remote Similarity NPC317680
0.5714 Remote Similarity NPC65359
0.5714 Remote Similarity NPC320624
0.5714 Remote Similarity NPC76217
0.5714 Remote Similarity NPC318951
0.5714 Remote Similarity NPC307739
0.5714 Remote Similarity NPC76051
0.5714 Remote Similarity NPC286842
0.5694 Remote Similarity NPC321873
0.569 Remote Similarity NPC252918
0.569 Remote Similarity NPC321087
0.569 Remote Similarity NPC230789
0.569 Remote Similarity NPC277475
0.5686 Remote Similarity NPC325165
0.5676 Remote Similarity NPC317212
0.5672 Remote Similarity NPC10659
0.566 Remote Similarity NPC268826
0.5658 Remote Similarity NPC214030
0.5658 Remote Similarity NPC83108
0.5652 Remote Similarity NPC476330
0.5652 Remote Similarity NPC323477
0.5647 Remote Similarity NPC469627
0.5634 Remote Similarity NPC319007
0.5634 Remote Similarity NPC82315
0.5616 Remote Similarity NPC184550
0.5616 Remote Similarity NPC185419
0.5614 Remote Similarity NPC107091
0.5614 Remote Similarity NPC207656
0.56 Remote Similarity NPC217725
0.56 Remote Similarity NPC179922

  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 NPC277878 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 NPD9007 Approved
1.0 High Similarity NPD65 Approved
1.0 High Similarity NPD64 Approved
1.0 High Similarity NPD9011 Approved
1.0 High Similarity NPD8960 Approved
1.0 High Similarity NPD9009 Approved
1.0 High Similarity NPD66 Approved
1.0 High Similarity NPD9008 Approved
1.0 High Similarity NPD72 Approved
1.0 High Similarity NPD9010 Approved
0.9231 High Similarity NPD73 Approved
0.9057 High Similarity NPD8959 Approved
0.9 High Similarity NPD9001 Clinical (unspecified phase)
0.9 High Similarity NPD9002 Approved
0.8776 High Similarity NPD9005 Phase 3
0.8776 High Similarity NPD9004 Approved
0.8776 High Similarity NPD9003 Clinical (unspecified phase)
0.8276 Intermediate Similarity NPD8961 Approved
0.7885 Intermediate Similarity NPD8964 Approved
0.7742 Intermediate Similarity NPD896 Approved
0.7742 Intermediate Similarity NPD898 Approved
0.7742 Intermediate Similarity NPD897 Approved
0.7551 Intermediate Similarity NPD8599 Approved
0.7551 Intermediate Similarity NPD8604 Approved
0.7551 Intermediate Similarity NPD8600 Approved
0.7551 Intermediate Similarity NPD8598 Approved
0.7551 Intermediate Similarity NPD8601 Approved
0.7551 Intermediate Similarity NPD8605 Approved
0.7551 Intermediate Similarity NPD8603 Approved
0.7551 Intermediate Similarity NPD8602 Approved
0.7222 Intermediate Similarity NPD71 Approved
0.7222 Intermediate Similarity NPD9126 Approved
0.7222 Intermediate Similarity NPD9129 Approved
0.7037 Intermediate Similarity NPD109 Approved
0.7037 Intermediate Similarity NPD9128 Approved
0.7037 Intermediate Similarity NPD9130 Phase 3
0.7037 Intermediate Similarity NPD9125 Approved
0.7037 Intermediate Similarity NPD70 Approved
0.7037 Intermediate Similarity NPD9123 Approved
0.7037 Intermediate Similarity NPD9124 Approved
0.7037 Intermediate Similarity NPD108 Approved
0.7037 Intermediate Similarity NPD9121 Approved
0.7037 Intermediate Similarity NPD9127 Approved
0.7037 Intermediate Similarity NPD9122 Approved
0.6957 Remote Similarity NPD376 Approved
0.6957 Remote Similarity NPD11 Approved
0.6667 Remote Similarity NPD3181 Approved
0.6667 Remote Similarity NPD9052 Approved
0.6667 Remote Similarity NPD9051 Approved
0.6667 Remote Similarity NPD9053 Approved
0.6575 Remote Similarity NPD7329 Approved
0.6333 Remote Similarity NPD3730 Approved
0.6333 Remote Similarity NPD3728 Approved
0.6076 Remote Similarity NPD619 Phase 3
0.6042 Remote Similarity NPD8814 Phase 3
0.6038 Remote Similarity NPD8995 Clinical (unspecified phase)
0.6038 Remote Similarity NPD8996 Phase 3
0.6 Remote Similarity NPD9120 Clinical (unspecified phase)
0.6 Remote Similarity NPD9006 Approved
0.5833 Remote Similarity NPD8618 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 NPD8999 Phase 3
0.5789 Remote Similarity NPD8997 Approved
0.5789 Remote Similarity NPD8998 Phase 2
0.5789 Remote Similarity NPD9000 Phase 3
0.5735 Remote Similarity NPD7909 Approved
0.5714 Remote Similarity NPD8205 Approved
0.5714 Remote Similarity NPD8202 Approved
0.5694 Remote Similarity NPD9446 Approved
0.5625 Remote Similarity NPD8617 Approved
0.5625 Remote Similarity NPD8619 Approved
0.5614 Remote Similarity NPD9218 Clinical (unspecified phase)
0.5614 Remote Similarity NPD9219 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