Structure

Physi-Chem Properties

Molecular Weight:  150.05
Volume:  130.431
LogP:  -2.086
LogD:  -2.042
LogS:  0.05
# Rotatable Bonds:  0
TPSA:  90.15
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.304
Synthetic Accessibility Score:  3.803
Fsp3:  1.0
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:  -5.264
MDCK Permeability:  0.0004930837312713265
Pgp-inhibitor:  0.001
Pgp-substrate:  0.064
Human Intestinal Absorption (HIA):  0.625
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.319

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.393
Plasma Protein Binding (PPB):  11.556318283081055%
Volume Distribution (VD):  0.461
Pgp-substrate:  80.6225357055664%

ADMET: Metabolism

CYP1A2-inhibitor:  0.015
CYP1A2-substrate:  0.074
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.172
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.152
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.164
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.021

ADMET: Excretion

Clearance (CL):  1.427
Half-life (T1/2):  0.747

ADMET: Toxicity

hERG Blockers:  0.056
Human Hepatotoxicity (H-HT):  0.036
Drug-inuced Liver Injury (DILI):  0.032
AMES Toxicity:  0.207
Rat Oral Acute Toxicity:  0.095
Maximum Recommended Daily Dose:  0.004
Skin Sensitization:  0.207
Carcinogencity:  0.033
Eye Corrosion:  0.005
Eye Irritation:  0.785
Respiratory Toxicity:  0.065

Download Data

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

  Natural Product: NPC298699

Natural Product ID:  NPC298699
Common Name*:   (3S,4S,5R)-Oxane-2,3,4,5-Tetrol
IUPAC Name:   (3S,4S,5R)-oxane-2,3,4,5-tetrol
Synonyms:  
Standard InCHIKey:  SRBFZHDQGSBBOR-AGQMPKSLSA-N
Standard InCHI:  InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4+,5?/m1/s1
SMILES:  O[C@@H]1COC([C@H]([C@H]1O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1222248
PubChem CID:   439240
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:0001497] Pentoses

*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
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. leaf n.a. PMID[12575075]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. stem n.a. PMID[12575075]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[15577255]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30188125]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29463 Pogostemon cablin Species Lamiaceae 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 Potency n.a. 7497.8 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 NPC298699 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 NPC134252
1.0 High Similarity NPC291502
1.0 High Similarity NPC86191
1.0 High Similarity NPC317182
1.0 High Similarity NPC213159
0.9286 High Similarity NPC176017
0.9286 High Similarity NPC255377
0.9286 High Similarity NPC69445
0.9286 High Similarity NPC165846
0.9286 High Similarity NPC21209
0.9286 High Similarity NPC289758
0.9286 High Similarity NPC199857
0.9286 High Similarity NPC285364
0.9286 High Similarity NPC92246
0.9286 High Similarity NPC73906
0.907 High Similarity NPC321087
0.907 High Similarity NPC277475
0.9024 High Similarity NPC320189
0.8864 High Similarity NPC14144
0.881 High Similarity NPC70756
0.881 High Similarity NPC320240
0.8667 High Similarity NPC299781
0.8667 High Similarity NPC42503
0.8667 High Similarity NPC157193
0.8667 High Similarity NPC282143
0.8478 Intermediate Similarity NPC323574
0.8298 Intermediate Similarity NPC124963
0.8298 Intermediate Similarity NPC233726
0.8298 Intermediate Similarity NPC23134
0.8298 Intermediate Similarity NPC326533
0.8095 Intermediate Similarity NPC266553
0.7959 Intermediate Similarity NPC323361
0.7959 Intermediate Similarity NPC67660
0.7959 Intermediate Similarity NPC317626
0.7959 Intermediate Similarity NPC242073
0.7959 Intermediate Similarity NPC314821
0.7959 Intermediate Similarity NPC89145
0.7959 Intermediate Similarity NPC107914
0.7959 Intermediate Similarity NPC58629
0.7959 Intermediate Similarity NPC246558
0.7959 Intermediate Similarity NPC157514
0.7959 Intermediate Similarity NPC317501
0.7959 Intermediate Similarity NPC269166
0.7959 Intermediate Similarity NPC165198
0.7959 Intermediate Similarity NPC130683
0.7959 Intermediate Similarity NPC145112
0.7955 Intermediate Similarity NPC29721
0.78 Intermediate Similarity NPC303727
0.7708 Intermediate Similarity NPC329128
0.7708 Intermediate Similarity NPC322158
0.75 Intermediate Similarity NPC148424
0.7447 Intermediate Similarity NPC252918
0.7447 Intermediate Similarity NPC230789
0.7436 Intermediate Similarity NPC127074
0.7436 Intermediate Similarity NPC182541
0.7436 Intermediate Similarity NPC187058
0.7436 Intermediate Similarity NPC149070
0.7436 Intermediate Similarity NPC197207
0.7358 Intermediate Similarity NPC219040
0.7358 Intermediate Similarity NPC472025
0.7222 Intermediate Similarity NPC322855
0.7222 Intermediate Similarity NPC320032
0.7222 Intermediate Similarity NPC317023
0.7222 Intermediate Similarity NPC290179
0.7222 Intermediate Similarity NPC34877
0.7143 Intermediate Similarity NPC82512
0.7091 Intermediate Similarity NPC143326
0.7073 Intermediate Similarity NPC227267
0.6964 Remote Similarity NPC477763
0.6964 Remote Similarity NPC477762
0.6964 Remote Similarity NPC155457
0.6964 Remote Similarity NPC477750
0.6964 Remote Similarity NPC477755
0.6964 Remote Similarity NPC477753
0.6964 Remote Similarity NPC477757
0.6964 Remote Similarity NPC472026
0.6905 Remote Similarity NPC325034
0.6905 Remote Similarity NPC293908
0.6905 Remote Similarity NPC192065
0.6905 Remote Similarity NPC86412
0.6905 Remote Similarity NPC66052
0.6863 Remote Similarity NPC329095
0.6744 Remote Similarity NPC313405
0.6735 Remote Similarity NPC88638
0.6731 Remote Similarity NPC103672
0.6731 Remote Similarity NPC320043
0.6724 Remote Similarity NPC317651
0.6724 Remote Similarity NPC268243
0.6724 Remote Similarity NPC277570
0.6724 Remote Similarity NPC325773
0.6724 Remote Similarity NPC258690
0.6667 Remote Similarity NPC301586
0.6667 Remote Similarity NPC33415
0.6667 Remote Similarity NPC107091
0.6667 Remote Similarity NPC207656
0.661 Remote Similarity NPC294813
0.661 Remote Similarity NPC31496
0.661 Remote Similarity NPC13143
0.661 Remote Similarity NPC6848
0.6522 Remote Similarity NPC88278
0.6522 Remote Similarity NPC111882
0.6522 Remote Similarity NPC227707
0.6522 Remote Similarity NPC99573
0.6522 Remote Similarity NPC102981
0.65 Remote Similarity NPC471760
0.65 Remote Similarity NPC471761
0.65 Remote Similarity NPC76881
0.65 Remote Similarity NPC12040
0.65 Remote Similarity NPC190418
0.65 Remote Similarity NPC147292
0.641 Remote Similarity NPC320326
0.6393 Remote Similarity NPC477752
0.6393 Remote Similarity NPC477756
0.6393 Remote Similarity NPC477764
0.6393 Remote Similarity NPC477751
0.6393 Remote Similarity NPC322801
0.6393 Remote Similarity NPC129100
0.6393 Remote Similarity NPC291650
0.629 Remote Similarity NPC477761
0.629 Remote Similarity NPC206601
0.629 Remote Similarity NPC32148
0.629 Remote Similarity NPC477759
0.629 Remote Similarity NPC477754
0.629 Remote Similarity NPC477760
0.629 Remote Similarity NPC477758
0.6275 Remote Similarity NPC112363
0.619 Remote Similarity NPC250619
0.619 Remote Similarity NPC50228
0.619 Remote Similarity NPC67099
0.619 Remote Similarity NPC97736
0.6154 Remote Similarity NPC46254
0.614 Remote Similarity NPC220922
0.6094 Remote Similarity NPC241265
0.6094 Remote Similarity NPC223174
0.6094 Remote Similarity NPC211428
0.6094 Remote Similarity NPC327753
0.6094 Remote Similarity NPC285003
0.6094 Remote Similarity NPC327486
0.6087 Remote Similarity NPC473991
0.6 Remote Similarity NPC471879
0.6 Remote Similarity NPC53760
0.6 Remote Similarity NPC474078
0.6 Remote Similarity NPC52268
0.6 Remote Similarity NPC272307
0.5918 Remote Similarity NPC313565
0.5918 Remote Similarity NPC228782
0.5918 Remote Similarity NPC259982
0.5909 Remote Similarity NPC185419
0.5909 Remote Similarity NPC184550
0.5821 Remote Similarity NPC225748
0.5821 Remote Similarity NPC132938
0.5821 Remote Similarity NPC39266
0.5821 Remote Similarity NPC308096
0.5821 Remote Similarity NPC163812
0.5821 Remote Similarity NPC206823
0.5821 Remote Similarity NPC55652
0.5821 Remote Similarity NPC9763
0.5821 Remote Similarity NPC248427
0.5821 Remote Similarity NPC169085
0.5821 Remote Similarity NPC291228
0.5781 Remote Similarity NPC179823
0.5769 Remote Similarity NPC314613
0.575 Remote Similarity NPC128335
0.5735 Remote Similarity NPC166250
0.5735 Remote Similarity NPC472173
0.5735 Remote Similarity NPC308489
0.5735 Remote Similarity NPC472174
0.5686 Remote Similarity NPC242655
0.5686 Remote Similarity NPC38891
0.5686 Remote Similarity NPC62014
0.5641 Remote Similarity NPC199270
0.5641 Remote Similarity NPC157340
0.5614 Remote Similarity NPC289979

  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 NPC298699 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 NPD8788 Approved
0.9286 High Similarity NPD8999 Phase 3
0.9286 High Similarity NPD9000 Phase 3
0.9286 High Similarity NPD8998 Phase 2
0.9286 High Similarity NPD8993 Phase 1
0.9286 High Similarity NPD8997 Approved
0.8864 High Similarity NPD8965 Approved
0.8864 High Similarity NPD8966 Approved
0.8298 Intermediate Similarity NPD905 Approved
0.8298 Intermediate Similarity NPD904 Phase 3
0.7959 Intermediate Similarity NPD9036 Phase 3
0.7959 Intermediate Similarity NPD890 Clinical (unspecified phase)
0.7959 Intermediate Similarity NPD893 Approved
0.7959 Intermediate Similarity NPD892 Phase 3
0.7959 Intermediate Similarity NPD891 Phase 3
0.7959 Intermediate Similarity NPD888 Phase 3
0.7959 Intermediate Similarity NPD887 Approved
0.7959 Intermediate Similarity NPD895 Approved
0.7959 Intermediate Similarity NPD9035 Clinical (unspecified phase)
0.7959 Intermediate Similarity NPD894 Approved
0.7959 Intermediate Similarity NPD889 Approved
0.7955 Intermediate Similarity NPD9006 Approved
0.7755 Intermediate Similarity NPD2269 Approved
0.7436 Intermediate Similarity NPD8814 Phase 3
0.7358 Intermediate Similarity NPD369 Approved
0.7234 Intermediate Similarity NPD8994 Approved
0.6964 Remote Similarity NPD6123 Approved
0.6957 Remote Similarity NPD8957 Approved
0.6905 Remote Similarity NPD9052 Approved
0.6905 Remote Similarity NPD9053 Approved
0.6905 Remote Similarity NPD9051 Approved
0.6852 Remote Similarity NPD2267 Suspended
0.6739 Remote Similarity NPD8967 Approved
0.6731 Remote Similarity NPD9049 Discontinued
0.6731 Remote Similarity NPD9050 Approved
0.6724 Remote Similarity NPD847 Phase 1
0.6724 Remote Similarity NPD8961 Approved
0.6667 Remote Similarity NPD9219 Approved
0.6667 Remote Similarity NPD8549 Clinical (unspecified phase)
0.6667 Remote Similarity NPD9218 Clinical (unspecified phase)
0.6596 Remote Similarity NPD8958 Phase 2
0.6522 Remote Similarity NPD8995 Clinical (unspecified phase)
0.6522 Remote Similarity NPD8996 Phase 3
0.6393 Remote Similarity NPD9032 Approved
0.6393 Remote Similarity NPD9033 Approved
0.6393 Remote Similarity NPD9031 Approved
0.6393 Remote Similarity NPD9030 Approved
0.629 Remote Similarity NPD897 Approved
0.629 Remote Similarity NPD898 Approved
0.629 Remote Similarity NPD896 Approved
0.6275 Remote Similarity NPD9139 Approved
0.6182 Remote Similarity NPD7346 Approved
0.614 Remote Similarity NPD8959 Approved
0.6094 Remote Similarity NPD9445 Approved
0.6087 Remote Similarity NPD8977 Phase 3
0.6087 Remote Similarity NPD8976 Approved
0.6066 Remote Similarity NPD1457 Discontinued
0.5821 Remote Similarity NPD3181 Approved
0.5821 Remote Similarity NPD389 Phase 3
0.5821 Remote Similarity NPD9034 Approved
0.5821 Remote Similarity NPD67 Phase 2
0.5641 Remote Similarity NPD8226 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