Structure

Physi-Chem Properties

Molecular Weight:  189.1
Volume:  175.969
LogP:  -1.652
LogD:  -1.585
LogS:  -0.205
# Rotatable Bonds:  0
TPSA:  84.16
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.339
Synthetic Accessibility Score:  4.047
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:  -5.327
MDCK Permeability:  5.0808059313567355e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.99
Human Intestinal Absorption (HIA):  0.148
20% Bioavailability (F20%):  0.081
30% Bioavailability (F30%):  0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.272
Plasma Protein Binding (PPB):  12.871525764465332%
Volume Distribution (VD):  0.524
Pgp-substrate:  85.6445541381836%

ADMET: Metabolism

CYP1A2-inhibitor:  0.025
CYP1A2-substrate:  0.064
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.753
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.193
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.336
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.043

ADMET: Excretion

Clearance (CL):  2.054
Half-life (T1/2):  0.775

ADMET: Toxicity

hERG Blockers:  0.066
Human Hepatotoxicity (H-HT):  0.154
Drug-inuced Liver Injury (DILI):  0.048
AMES Toxicity:  0.065
Rat Oral Acute Toxicity:  0.083
Maximum Recommended Daily Dose:  0.017
Skin Sensitization:  0.296
Carcinogencity:  0.028
Eye Corrosion:  0.025
Eye Irritation:  0.322
Respiratory Toxicity:  0.823

Download Data

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

  Natural Product: NPC34291

Natural Product ID:  NPC34291
Common Name*:   6-Epi-Castanospermine
IUPAC Name:   (1S,6R,7R,8R,8aR)-1,2,3,5,6,7,8,8a-octahydroindolizine-1,6,7,8-tetrol
Synonyms:   6-Epi-Castanospermine
Standard InCHIKey:  JDVVGAQPNNXQDW-SLBCVNJHSA-N
Standard InCHI:  InChI=1S/C8H15NO4/c10-4-1-2-9-3-5(11)7(12)8(13)6(4)9/h4-8,10-13H,1-3H2/t4-,5+,6+,7+,8+/m0/s1
SMILES:  O[C@@H]1[C@H](O)CN2[C@@H]([C@H]1O)[C@@H](O)CC2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464490
PubChem CID:   184806
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000251] Indolizidines

*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
NPO23250 Plakortis angulospiculatus Species Plakinidae Eukaryota n.a. n.a. n.a. PMID[14703354]
NPO23250 Plakortis angulospiculatus Species Plakinidae Eukaryota n.a. n.a. n.a. PMID[1800643]
NPO23250 Plakortis angulospiculatus Species Plakinidae Eukaryota n.a. Brazil n.a. PMID[18177008]
NPO23250 Plakortis angulospiculatus Species Plakinidae Eukaryota n.a. caribbean n.a. PMID[20738102]
NPO12473 Castanospermum australe Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[2213032]
NPO12473 Castanospermum australe Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9544568]
NPO12473 Castanospermum australe Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27030 Commiphora sphaerocarpa Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10677 Prunus prostrata Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26218 Prosopis africana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10350 Erythrina speciosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23250 Plakortis angulospiculatus Species Plakinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17806 Richteria pyrethroides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25832 Helichrysum drakensbergense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26847 Lecidea quernea Species Lecideaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26151 Santolina pectinata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25797 Piper divaricatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27103 Satureja vulgaris 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
NPT1053 Individual Protein Alpha-mannosidase 2C1 Rattus norvegicus IC50 > 1000000.0 nM PMID[502161]
NPT2 Others Unspecified Inhibition = 50.0 % PMID[502162]

☑ 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 NPC34291 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 NPC126664
0.9516 High Similarity NPC233034
0.875 High Similarity NPC163134
0.875 High Similarity NPC471419
0.8529 High Similarity NPC163538
0.8529 High Similarity NPC115800
0.8507 High Similarity NPC474469
0.8485 Intermediate Similarity NPC12514
0.8485 Intermediate Similarity NPC294883
0.8413 Intermediate Similarity NPC170172
0.8406 Intermediate Similarity NPC28959
0.8406 Intermediate Similarity NPC285014
0.8406 Intermediate Similarity NPC137554
0.8406 Intermediate Similarity NPC299603
0.8406 Intermediate Similarity NPC255535
0.8382 Intermediate Similarity NPC473419
0.8382 Intermediate Similarity NPC475127
0.8382 Intermediate Similarity NPC475715
0.8358 Intermediate Similarity NPC141156
0.8358 Intermediate Similarity NPC184150
0.8235 Intermediate Similarity NPC74555
0.8235 Intermediate Similarity NPC266242
0.8235 Intermediate Similarity NPC306763
0.8235 Intermediate Similarity NPC254617
0.8235 Intermediate Similarity NPC471418
0.8125 Intermediate Similarity NPC233364
0.8125 Intermediate Similarity NPC471421
0.8116 Intermediate Similarity NPC268922
0.8088 Intermediate Similarity NPC59221
0.8065 Intermediate Similarity NPC275727
0.806 Intermediate Similarity NPC198341
0.806 Intermediate Similarity NPC471780
0.806 Intermediate Similarity NPC223386
0.806 Intermediate Similarity NPC142290
0.806 Intermediate Similarity NPC471892
0.806 Intermediate Similarity NPC75435
0.8 Intermediate Similarity NPC473710
0.8 Intermediate Similarity NPC475694
0.7971 Intermediate Similarity NPC171850
0.7941 Intermediate Similarity NPC473952
0.7941 Intermediate Similarity NPC77191
0.7941 Intermediate Similarity NPC303798
0.7941 Intermediate Similarity NPC101746
0.7941 Intermediate Similarity NPC116377
0.7941 Intermediate Similarity NPC69798
0.7941 Intermediate Similarity NPC286851
0.7887 Intermediate Similarity NPC476695
0.7887 Intermediate Similarity NPC476696
0.7887 Intermediate Similarity NPC476694
0.7778 Intermediate Similarity NPC474468
0.7761 Intermediate Similarity NPC218150
0.7761 Intermediate Similarity NPC150680
0.7761 Intermediate Similarity NPC2432
0.7761 Intermediate Similarity NPC22774
0.7761 Intermediate Similarity NPC69669
0.7761 Intermediate Similarity NPC306462
0.7681 Intermediate Similarity NPC315980
0.7619 Intermediate Similarity NPC277072
0.7619 Intermediate Similarity NPC178263
0.7536 Intermediate Similarity NPC474928
0.7353 Intermediate Similarity NPC62507
0.7353 Intermediate Similarity NPC8087
0.7313 Intermediate Similarity NPC143809
0.7313 Intermediate Similarity NPC290106
0.7313 Intermediate Similarity NPC76726
0.7313 Intermediate Similarity NPC193593
0.7179 Intermediate Similarity NPC150557
0.7101 Intermediate Similarity NPC57846
0.7101 Intermediate Similarity NPC474014
0.7101 Intermediate Similarity NPC30126
0.7037 Intermediate Similarity NPC165119
0.7015 Intermediate Similarity NPC311668
0.7015 Intermediate Similarity NPC65832
0.7015 Intermediate Similarity NPC10262
0.7 Intermediate Similarity NPC471420
0.6912 Remote Similarity NPC204709
0.6875 Remote Similarity NPC83248
0.6875 Remote Similarity NPC100204
0.6786 Remote Similarity NPC469363
0.6778 Remote Similarity NPC313821
0.6765 Remote Similarity NPC293551
0.6716 Remote Similarity NPC471423
0.6716 Remote Similarity NPC471442
0.6707 Remote Similarity NPC271772
0.6707 Remote Similarity NPC36927
0.6706 Remote Similarity NPC306838
0.6567 Remote Similarity NPC272396
0.6543 Remote Similarity NPC98750
0.6538 Remote Similarity NPC315806
0.6522 Remote Similarity NPC471443
0.6522 Remote Similarity NPC471605
0.6463 Remote Similarity NPC70574
0.6389 Remote Similarity NPC112398
0.6364 Remote Similarity NPC223174
0.6364 Remote Similarity NPC327753
0.6364 Remote Similarity NPC327486
0.6338 Remote Similarity NPC319991
0.6301 Remote Similarity NPC145627
0.6296 Remote Similarity NPC329077
0.6286 Remote Similarity NPC8979
0.625 Remote Similarity NPC52533
0.6184 Remote Similarity NPC322801
0.6184 Remote Similarity NPC291650
0.6184 Remote Similarity NPC129100
0.6133 Remote Similarity NPC472609
0.6133 Remote Similarity NPC160661
0.6118 Remote Similarity NPC81006
0.6092 Remote Similarity NPC277918
0.6082 Remote Similarity NPC314387
0.6081 Remote Similarity NPC17455
0.6076 Remote Similarity NPC306973
0.6071 Remote Similarity NPC90839
0.6024 Remote Similarity NPC314772
0.6024 Remote Similarity NPC314968
0.6 Remote Similarity NPC219340
0.5976 Remote Similarity NPC470782
0.593 Remote Similarity NPC45906
0.593 Remote Similarity NPC149908
0.593 Remote Similarity NPC288415
0.593 Remote Similarity NPC31313
0.5926 Remote Similarity NPC126186
0.5897 Remote Similarity NPC195165
0.5862 Remote Similarity NPC93630
0.5857 Remote Similarity NPC270041
0.5802 Remote Similarity NPC29326
0.5783 Remote Similarity NPC477002
0.5783 Remote Similarity NPC244539
0.5773 Remote Similarity NPC315170
0.5765 Remote Similarity NPC316807
0.5714 Remote Similarity NPC123814
0.5714 Remote Similarity NPC313762
0.5696 Remote Similarity NPC316445
0.5696 Remote Similarity NPC107224
0.5679 Remote Similarity NPC477200
0.5652 Remote Similarity NPC292345
0.5652 Remote Similarity NPC470284
0.5647 Remote Similarity NPC233108
0.5647 Remote Similarity NPC325902
0.5625 Remote Similarity NPC23721
0.56 Remote Similarity NPC328786
0.56 Remote Similarity NPC201338
0.56 Remote Similarity NPC474627

  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 NPC34291 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 NPD9443 Clinical (unspecified phase)
0.9516 High Similarity NPD9440 Discontinued
0.8788 High Similarity NPD9444 Discontinued
0.8571 High Similarity NPD9455 Approved
0.8438 Intermediate Similarity NPD393 Approved
0.8158 Intermediate Similarity NPD883 Phase 2
0.8158 Intermediate Similarity NPD882 Phase 2
0.7761 Intermediate Similarity NPD9029 Phase 3
0.7761 Intermediate Similarity NPD9027 Phase 3
0.7761 Intermediate Similarity NPD9026 Phase 2
0.7761 Intermediate Similarity NPD9028 Phase 2
0.6957 Remote Similarity NPD9240 Approved
0.6957 Remote Similarity NPD9239 Approved
0.6867 Remote Similarity NPD9401 Discovery
0.6778 Remote Similarity NPD3189 Approved
0.6778 Remote Similarity NPD3191 Approved
0.6778 Remote Similarity NPD3190 Approved
0.6709 Remote Similarity NPD372 Clinical (unspecified phase)
0.662 Remote Similarity NPD9024 Phase 2
0.662 Remote Similarity NPD9022 Phase 2
0.6538 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6395 Remote Similarity NPD394 Phase 3
0.6364 Remote Similarity NPD9445 Approved
0.6203 Remote Similarity NPD6704 Discontinued
0.6184 Remote Similarity NPD9031 Approved
0.6184 Remote Similarity NPD9030 Approved
0.6184 Remote Similarity NPD9032 Approved
0.6184 Remote Similarity NPD9033 Approved
0.6173 Remote Similarity NPD9407 Approved
0.6118 Remote Similarity NPD2691 Clinical (unspecified phase)
0.6082 Remote Similarity NPD3185 Approved
0.6082 Remote Similarity NPD3183 Approved
0.6082 Remote Similarity NPD3184 Approved
0.6082 Remote Similarity NPD3182 Approved
0.6024 Remote Similarity NPD9434 Approved
0.6024 Remote Similarity NPD9435 Approved
0.5921 Remote Similarity NPD1457 Discontinued
0.5882 Remote Similarity NPD9429 Discontinued
0.5833 Remote Similarity NPD6439 Phase 3
0.5802 Remote Similarity NPD9405 Approved
0.5778 Remote Similarity NPD241 Discontinued
0.5732 Remote Similarity NPD9034 Approved
0.5732 Remote Similarity NPD67 Phase 2
0.5714 Remote Similarity NPD3215 Phase 1
0.5699 Remote Similarity NPD6943 Clinical (unspecified phase)
0.5694 Remote Similarity NPD6706 Discontinued
0.5686 Remote Similarity NPD8140 Approved
0.5673 Remote Similarity NPD3188 Approved
0.5652 Remote Similarity NPD618 Clinical (unspecified phase)
0.5644 Remote Similarity NPD2700 Approved
0.561 Remote Similarity NPD3187 Discontinued

  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