Structure

Physi-Chem Properties

Molecular Weight:  207.11
Volume:  193.316
LogP:  -2.254
LogD:  -2.303
LogS:  -0.125
# Rotatable Bonds:  2
TPSA:  104.39
# H-Bond Aceptor:  6
# H-Bond Donor:  5
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.325
Synthetic Accessibility Score:  4.064
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:  -5.363
MDCK Permeability:  0.00018797199300024658
Pgp-inhibitor:  0.002
Pgp-substrate:  0.365
Human Intestinal Absorption (HIA):  0.93
20% Bioavailability (F20%):  0.373
30% Bioavailability (F30%):  0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.258
Plasma Protein Binding (PPB):  14.817488670349121%
Volume Distribution (VD):  0.333
Pgp-substrate:  81.62283325195312%

ADMET: Metabolism

CYP1A2-inhibitor:  0.02
CYP1A2-substrate:  0.062
CYP2C19-inhibitor:  0.009
CYP2C19-substrate:  0.578
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.086
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.224
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.029

ADMET: Excretion

Clearance (CL):  2.096
Half-life (T1/2):  0.85

ADMET: Toxicity

hERG Blockers:  0.051
Human Hepatotoxicity (H-HT):  0.196
Drug-inuced Liver Injury (DILI):  0.2
AMES Toxicity:  0.059
Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.003
Skin Sensitization:  0.216
Carcinogencity:  0.014
Eye Corrosion:  0.01
Eye Irritation:  0.368
Respiratory Toxicity:  0.097

Download Data

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

  Natural Product: NPC163134

Natural Product ID:  NPC163134
Common Name*:   CVSZHOAOIZMVHV-YQXRAVKXSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CVSZHOAOIZMVHV-YQXRAVKXSA-N
Standard InCHI:  InChI=1S/C8H17NO5/c1-9-4(2-10)6(12)8(14)7(13)5(9)3-11/h4-8,10-14H,2-3H2,1H3/t4-,5-,6-,7+,8+/m1/s1
SMILES:  CN1[C@H](CO)[C@H]([C@@H]([C@H]([C@H]1CO)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2442258
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000195] Piperidines

*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
NPO25280 Suregada glomerulata Species Euphorbiaceae Eukaryota Roots n.a. n.a. PMID[18205316]
NPO25280 Suregada glomerulata Species Euphorbiaceae Eukaryota leaves n.a. n.a. PMID[23993676]
NPO25280 Suregada glomerulata Species Euphorbiaceae 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
NPT497 Individual Protein Maltase-glucoamylase Homo sapiens IC50 = 60.0 nM PMID[506786]
NPT671 Individual Protein Acidic alpha-glucosidase Rattus norvegicus IC50 = 170.0 nM PMID[506786]
NPT671 Individual Protein Acidic alpha-glucosidase Rattus norvegicus IC50 = 20.0 nM PMID[506786]
NPT671 Individual Protein Acidic alpha-glucosidase Rattus norvegicus IC50 = 1000.0 nM PMID[506786]
NPT671 Individual Protein Acidic alpha-glucosidase Rattus norvegicus IC50 = 2800.0 nM PMID[506786]
NPT671 Individual Protein Acidic alpha-glucosidase Rattus norvegicus IC50 = 50000.0 nM PMID[506786]
NPT32 Organism Mus musculus Mus musculus AUC = 2723000.0 ng.hr.mL-1 PMID[506787]
NPT32 Organism Mus musculus Mus musculus Activity = 141.2 mg/dl PMID[506787]
NPT32 Organism Mus musculus Mus musculus Activity = 144.8 mg/dl PMID[506787]
NPT32 Organism Mus musculus Mus musculus Activity = 141.0 mg/dl PMID[506787]
NPT32 Organism Mus musculus Mus musculus AUC = 2278000.0 ng.hr.mL-1 PMID[506787]
NPT32 Organism Mus musculus Mus musculus Activity = 115.6 mg/dl PMID[506787]
NPT32 Organism Mus musculus Mus musculus Activity = 114.0 mg/dl PMID[506787]
NPT32 Organism Mus musculus Mus musculus Activity = 121.4 mg/dl PMID[506787]
NPT2 Others Unspecified IC50 = 80.0 nM PMID[506787]

☑ 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 NPC163134 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 NPC471419
0.931 High Similarity NPC471421
0.931 High Similarity NPC170172
0.931 High Similarity NPC233364
0.8906 High Similarity NPC268922
0.875 High Similarity NPC126664
0.875 High Similarity NPC471418
0.875 High Similarity NPC34291
0.873 High Similarity NPC286851
0.873 High Similarity NPC303798
0.8636 High Similarity NPC476694
0.8636 High Similarity NPC476695
0.8636 High Similarity NPC476696
0.8571 High Similarity NPC198341
0.8571 High Similarity NPC142290
0.8571 High Similarity NPC75435
0.8571 High Similarity NPC471892
0.8571 High Similarity NPC471780
0.8571 High Similarity NPC223386
0.8281 Intermediate Similarity NPC233034
0.8254 Intermediate Similarity NPC2432
0.8254 Intermediate Similarity NPC150680
0.8254 Intermediate Similarity NPC22774
0.8254 Intermediate Similarity NPC69669
0.8254 Intermediate Similarity NPC306462
0.8254 Intermediate Similarity NPC218150
0.8056 Intermediate Similarity NPC150557
0.7941 Intermediate Similarity NPC163538
0.7941 Intermediate Similarity NPC115800
0.791 Intermediate Similarity NPC171850
0.7879 Intermediate Similarity NPC315980
0.7838 Intermediate Similarity NPC471420
0.7826 Intermediate Similarity NPC137554
0.7826 Intermediate Similarity NPC28959
0.7826 Intermediate Similarity NPC285014
0.7826 Intermediate Similarity NPC299603
0.7826 Intermediate Similarity NPC255535
0.7794 Intermediate Similarity NPC475127
0.7794 Intermediate Similarity NPC473419
0.7794 Intermediate Similarity NPC475715
0.7778 Intermediate Similarity NPC193593
0.7778 Intermediate Similarity NPC290106
0.7778 Intermediate Similarity NPC143809
0.7778 Intermediate Similarity NPC76726
0.7681 Intermediate Similarity NPC475694
0.7681 Intermediate Similarity NPC473710
0.7647 Intermediate Similarity NPC254617
0.7647 Intermediate Similarity NPC474469
0.7647 Intermediate Similarity NPC74555
0.7647 Intermediate Similarity NPC306763
0.7647 Intermediate Similarity NPC266242
0.7619 Intermediate Similarity NPC204709
0.7541 Intermediate Similarity NPC178263
0.7541 Intermediate Similarity NPC277072
0.75 Intermediate Similarity NPC184150
0.75 Intermediate Similarity NPC59221
0.75 Intermediate Similarity NPC141156
0.7353 Intermediate Similarity NPC473952
0.7353 Intermediate Similarity NPC77191
0.7353 Intermediate Similarity NPC69798
0.7353 Intermediate Similarity NPC294883
0.7353 Intermediate Similarity NPC101746
0.7353 Intermediate Similarity NPC12514
0.7353 Intermediate Similarity NPC116377
0.7273 Intermediate Similarity NPC36927
0.7273 Intermediate Similarity NPC271772
0.7222 Intermediate Similarity NPC474468
0.7206 Intermediate Similarity NPC474928
0.7143 Intermediate Similarity NPC275727
0.7105 Intermediate Similarity NPC98750
0.7013 Intermediate Similarity NPC70574
0.6923 Remote Similarity NPC8979
0.6912 Remote Similarity NPC145627
0.6765 Remote Similarity NPC8087
0.6765 Remote Similarity NPC62507
0.6765 Remote Similarity NPC57846
0.6765 Remote Similarity NPC474014
0.6765 Remote Similarity NPC30126
0.675 Remote Similarity NPC165119
0.6714 Remote Similarity NPC472609
0.6712 Remote Similarity NPC223174
0.6712 Remote Similarity NPC327753
0.6712 Remote Similarity NPC327486
0.6707 Remote Similarity NPC469363
0.6667 Remote Similarity NPC293551
0.6622 Remote Similarity NPC306973
0.6615 Remote Similarity NPC471423
0.6615 Remote Similarity NPC471442
0.6582 Remote Similarity NPC83248
0.6582 Remote Similarity NPC100204
0.6471 Remote Similarity NPC319991
0.6462 Remote Similarity NPC270041
0.6438 Remote Similarity NPC195165
0.6429 Remote Similarity NPC306838
0.6418 Remote Similarity NPC10262
0.6418 Remote Similarity NPC311668
0.6418 Remote Similarity NPC471443
0.6418 Remote Similarity NPC65832
0.6418 Remote Similarity NPC471605
0.6351 Remote Similarity NPC23721
0.6333 Remote Similarity NPC313821
0.6329 Remote Similarity NPC314968
0.6329 Remote Similarity NPC314772
0.6308 Remote Similarity NPC123814
0.6301 Remote Similarity NPC129100
0.6301 Remote Similarity NPC291650
0.6301 Remote Similarity NPC322801
0.6296 Remote Similarity NPC219340
0.6286 Remote Similarity NPC112398
0.6282 Remote Similarity NPC477002
0.625 Remote Similarity NPC316807
0.6234 Remote Similarity NPC315806
0.6197 Remote Similarity NPC17455
0.619 Remote Similarity NPC96966
0.619 Remote Similarity NPC121062
0.619 Remote Similarity NPC29222
0.6184 Remote Similarity NPC477200
0.6154 Remote Similarity NPC470992
0.6154 Remote Similarity NPC470993
0.6143 Remote Similarity NPC328786
0.6143 Remote Similarity NPC201338
0.6143 Remote Similarity NPC474627
0.6061 Remote Similarity NPC474322
0.6024 Remote Similarity NPC81006
0.6 Remote Similarity NPC476523
0.6 Remote Similarity NPC107224
0.5977 Remote Similarity NPC52533
0.5976 Remote Similarity NPC90839
0.597 Remote Similarity NPC272396
0.5952 Remote Similarity NPC93630
0.5915 Remote Similarity NPC319131
0.5909 Remote Similarity NPC470284
0.5909 Remote Similarity NPC292345
0.5875 Remote Similarity NPC217095
0.5875 Remote Similarity NPC244539
0.5875 Remote Similarity NPC264417
0.5851 Remote Similarity NPC315170
0.5833 Remote Similarity NPC288415
0.5833 Remote Similarity NPC149908
0.5833 Remote Similarity NPC31313
0.5833 Remote Similarity NPC45906
0.5823 Remote Similarity NPC26932
0.5802 Remote Similarity NPC313762
0.5802 Remote Similarity NPC329077
0.5795 Remote Similarity NPC470282
0.5789 Remote Similarity NPC471628
0.5789 Remote Similarity NPC315036
0.5789 Remote Similarity NPC56298
0.5783 Remote Similarity NPC318258
0.5781 Remote Similarity NPC81384
0.5733 Remote Similarity NPC238646
0.5732 Remote Similarity NPC233108
0.5714 Remote Similarity NPC208537
0.5714 Remote Similarity NPC270005
0.5696 Remote Similarity NPC185084
0.5696 Remote Similarity NPC55274
0.567 Remote Similarity NPC314387
0.5663 Remote Similarity NPC475363
0.5663 Remote Similarity NPC473971
0.5663 Remote Similarity NPC473972
0.5652 Remote Similarity NPC471917
0.5647 Remote Similarity NPC315969
0.5632 Remote Similarity NPC125253
0.5632 Remote Similarity NPC277918
0.5632 Remote Similarity NPC192025
0.5632 Remote Similarity NPC253975
0.5625 Remote Similarity NPC208657
0.56 Remote Similarity NPC160661

  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 NPC163134 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
0.9655 High Similarity NPD393 Approved
0.9483 High Similarity NPD9455 Approved
0.875 High Similarity NPD9443 Clinical (unspecified phase)
0.8281 Intermediate Similarity NPD9440 Discontinued
0.8254 Intermediate Similarity NPD9029 Phase 3
0.8254 Intermediate Similarity NPD9027 Phase 3
0.8254 Intermediate Similarity NPD9026 Phase 2
0.8254 Intermediate Similarity NPD9028 Phase 2
0.7647 Intermediate Similarity NPD9444 Discontinued
0.7632 Intermediate Similarity NPD883 Phase 2
0.7632 Intermediate Similarity NPD882 Phase 2
0.7385 Intermediate Similarity NPD9240 Approved
0.7385 Intermediate Similarity NPD9239 Approved
0.6986 Remote Similarity NPD6704 Discontinued
0.6842 Remote Similarity NPD372 Clinical (unspecified phase)
0.6712 Remote Similarity NPD9445 Approved
0.6585 Remote Similarity NPD9401 Discovery
0.6522 Remote Similarity NPD9024 Phase 2
0.6522 Remote Similarity NPD9022 Phase 2
0.6506 Remote Similarity NPD394 Phase 3
0.6418 Remote Similarity NPD6439 Phase 3
0.6333 Remote Similarity NPD3189 Approved
0.6333 Remote Similarity NPD3190 Approved
0.6333 Remote Similarity NPD3191 Approved
0.6329 Remote Similarity NPD9434 Approved
0.6329 Remote Similarity NPD9435 Approved
0.6308 Remote Similarity NPD3215 Phase 1
0.6301 Remote Similarity NPD9033 Approved
0.6301 Remote Similarity NPD9031 Approved
0.6301 Remote Similarity NPD9032 Approved
0.6301 Remote Similarity NPD9030 Approved
0.6269 Remote Similarity NPD6706 Discontinued
0.625 Remote Similarity NPD1457 Discontinued
0.6234 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6104 Remote Similarity NPD3187 Discontinued
0.6061 Remote Similarity NPD9668 Phase 2
0.6056 Remote Similarity NPD3193 Approved
0.6056 Remote Similarity NPD3192 Approved
0.6 Remote Similarity NPD3214 Discontinued
0.5909 Remote Similarity NPD618 Clinical (unspecified phase)
0.589 Remote Similarity NPD9211 Clinical (unspecified phase)
0.5876 Remote Similarity NPD2700 Approved
0.5833 Remote Similarity NPD2691 Clinical (unspecified phase)
0.5823 Remote Similarity NPD355 Phase 2
0.5823 Remote Similarity NPD9034 Approved
0.5823 Remote Similarity NPD67 Phase 2
0.5814 Remote Similarity NPD361 Discontinued
0.5789 Remote Similarity NPD4836 Approved
0.5789 Remote Similarity NPD4835 Approved
0.5789 Remote Similarity NPD4838 Approved
0.5789 Remote Similarity NPD4837 Approved
0.5781 Remote Similarity NPD9463 Phase 3
0.5781 Remote Similarity NPD9462 Approved
0.5769 Remote Similarity NPD9446 Approved
0.5758 Remote Similarity NPD8140 Approved
0.5747 Remote Similarity NPD619 Phase 3
0.5682 Remote Similarity NPD241 Discontinued
0.5679 Remote Similarity NPD9407 Approved
0.567 Remote Similarity NPD3182 Approved
0.567 Remote Similarity NPD3185 Approved
0.567 Remote Similarity NPD3183 Approved
0.567 Remote Similarity NPD3184 Approved
0.5641 Remote Similarity NPD2697 Approved
0.5641 Remote Similarity NPD2695 Approved
0.5641 Remote Similarity NPD2694 Approved
0.5641 Remote Similarity NPD2696 Approved
0.56 Remote Similarity NPD8307 Discontinued
0.56 Remote Similarity NPD1831 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