Structure

Physi-Chem Properties

Molecular Weight:  193.1
Volume:  176.02
LogP:  -2.367
LogD:  -2.207
LogS:  -0.042
# Rotatable Bonds:  3
TPSA:  113.18
# H-Bond Aceptor:  6
# H-Bond Donor:  6
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.276
Synthetic Accessibility Score:  4.505
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:  -5.32
MDCK Permeability:  0.00040453646215610206
Pgp-inhibitor:  0.0
Pgp-substrate:  0.762
Human Intestinal Absorption (HIA):  0.851
20% Bioavailability (F20%):  0.97
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.188
Plasma Protein Binding (PPB):  13.976703643798828%
Volume Distribution (VD):  0.37
Pgp-substrate:  86.89020538330078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.034
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.31
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.086
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.123
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.013

ADMET: Excretion

Clearance (CL):  1.767
Half-life (T1/2):  0.788

ADMET: Toxicity

hERG Blockers:  0.034
Human Hepatotoxicity (H-HT):  0.617
Drug-inuced Liver Injury (DILI):  0.306
AMES Toxicity:  0.039
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.005
Skin Sensitization:  0.292
Carcinogencity:  0.009
Eye Corrosion:  0.004
Eye Irritation:  0.055
Respiratory Toxicity:  0.081

Download Data

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

  Natural Product: NPC101746

Natural Product ID:  NPC101746
Common Name*:   2,5-Dideoxy-2,5-Imino-D-Glycero-D-Manno-Heptitol
IUPAC Name:   (2R,3R,4R,5R)-2-[(1S)-1,2-dihydroxyethyl]-5-(hydroxymethyl)pyrrolidine-3,4-diol
Synonyms:  
Standard InCHIKey:  ZJRUOSSQTZGFJV-NYMZXIIRSA-N
Standard InCHI:  InChI=1S/C7H15NO5/c9-1-3-6(12)7(13)5(8-3)4(11)2-10/h3-13H,1-2H2/t3-,4-,5-,6-,7-/m1/s1
SMILES:  OC[C@H]([C@H]1N[C@@H]([C@H]([C@@H]1O)O)CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL406972
PubChem CID:   10198040
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines

*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
NPT514 Individual Protein Glycogen debranching enzyme Homo sapiens IC50 = 100000.0 nM PMID[545285]
NPT2 Others Unspecified IC50 = 150000.0 nM PMID[545285]
NPT32 Organism Mus musculus Mus musculus AUC = 3905000.0 ng.hr.mL-1 PMID[545286]
NPT32 Organism Mus musculus Mus musculus Activity = 150.3 mg/dl PMID[545286]
NPT32 Organism Mus musculus Mus musculus Activity = 216.2 mg/dl PMID[545286]
NPT32 Organism Mus musculus Mus musculus Activity = 262.8 mg/dl PMID[545286]
NPT32 Organism Mus musculus Mus musculus AUC = 2936000.0 ng.hr.mL-1 PMID[545286]
NPT32 Organism Mus musculus Mus musculus Activity = 136.7 mg/dl PMID[545286]
NPT32 Organism Mus musculus Mus musculus Activity = 147.3 mg/dl PMID[545286]
NPT32 Organism Mus musculus Mus musculus Activity = 179.0 mg/dl PMID[545286]
NPT2 Others Unspecified IC50 = 920.0 nM PMID[545286]

☑ 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 NPC101746 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 NPC77191
1.0 High Similarity NPC473952
1.0 High Similarity NPC69798
1.0 High Similarity NPC116377
0.9508 High Similarity NPC474928
0.9375 High Similarity NPC475694
0.9375 High Similarity NPC473710
0.9333 High Similarity NPC8087
0.9333 High Similarity NPC62507
0.9231 High Similarity NPC255535
0.9231 High Similarity NPC299603
0.9231 High Similarity NPC285014
0.9231 High Similarity NPC28959
0.9231 High Similarity NPC137554
0.9091 High Similarity NPC474468
0.9016 High Similarity NPC474014
0.9016 High Similarity NPC57846
0.9016 High Similarity NPC30126
0.8667 High Similarity NPC311668
0.8667 High Similarity NPC65832
0.8667 High Similarity NPC10262
0.8594 High Similarity NPC223386
0.8594 High Similarity NPC471780
0.8594 High Similarity NPC198341
0.8594 High Similarity NPC142290
0.8594 High Similarity NPC75435
0.8594 High Similarity NPC471892
0.8462 Intermediate Similarity NPC315980
0.8462 Intermediate Similarity NPC303798
0.8462 Intermediate Similarity NPC286851
0.8281 Intermediate Similarity NPC306462
0.8281 Intermediate Similarity NPC218150
0.8281 Intermediate Similarity NPC22774
0.8281 Intermediate Similarity NPC2432
0.8281 Intermediate Similarity NPC69669
0.8281 Intermediate Similarity NPC150680
0.8209 Intermediate Similarity NPC471418
0.8167 Intermediate Similarity NPC272396
0.8088 Intermediate Similarity NPC268922
0.7971 Intermediate Similarity NPC115800
0.7971 Intermediate Similarity NPC163538
0.7941 Intermediate Similarity NPC126664
0.7941 Intermediate Similarity NPC34291
0.791 Intermediate Similarity NPC12514
0.791 Intermediate Similarity NPC294883
0.7895 Intermediate Similarity NPC165119
0.7857 Intermediate Similarity NPC476696
0.7857 Intermediate Similarity NPC476694
0.7857 Intermediate Similarity NPC476695
0.7812 Intermediate Similarity NPC193593
0.7812 Intermediate Similarity NPC290106
0.7812 Intermediate Similarity NPC76726
0.7812 Intermediate Similarity NPC143809
0.7794 Intermediate Similarity NPC141156
0.7794 Intermediate Similarity NPC184150
0.7742 Intermediate Similarity NPC275727
0.7681 Intermediate Similarity NPC266242
0.7681 Intermediate Similarity NPC254617
0.7681 Intermediate Similarity NPC474469
0.7681 Intermediate Similarity NPC74555
0.7681 Intermediate Similarity NPC306763
0.7571 Intermediate Similarity NPC475715
0.7571 Intermediate Similarity NPC473419
0.7571 Intermediate Similarity NPC475127
0.7536 Intermediate Similarity NPC59221
0.75 Intermediate Similarity NPC83248
0.75 Intermediate Similarity NPC306838
0.75 Intermediate Similarity NPC100204
0.75 Intermediate Similarity NPC233034
0.7385 Intermediate Similarity NPC204709
0.7353 Intermediate Similarity NPC163134
0.7353 Intermediate Similarity NPC471419
0.7273 Intermediate Similarity NPC170172
0.7183 Intermediate Similarity NPC171850
0.697 Remote Similarity NPC8979
0.6875 Remote Similarity NPC36927
0.6875 Remote Similarity NPC271772
0.6806 Remote Similarity NPC129100
0.6806 Remote Similarity NPC322801
0.6806 Remote Similarity NPC221764
0.6806 Remote Similarity NPC196359
0.6806 Remote Similarity NPC78312
0.6806 Remote Similarity NPC291650
0.6806 Remote Similarity NPC135539
0.6765 Remote Similarity NPC233364
0.6765 Remote Similarity NPC471421
0.6747 Remote Similarity NPC469363
0.6714 Remote Similarity NPC17455
0.6709 Remote Similarity NPC98750
0.6625 Remote Similarity NPC70574
0.6538 Remote Similarity NPC244539
0.6515 Remote Similarity NPC277072
0.6515 Remote Similarity NPC178263
0.6456 Remote Similarity NPC313762
0.6364 Remote Similarity NPC123814
0.6341 Remote Similarity NPC219340
0.6267 Remote Similarity NPC107224
0.625 Remote Similarity NPC121062
0.625 Remote Similarity NPC29222
0.625 Remote Similarity NPC96966
0.6176 Remote Similarity NPC471442
0.6176 Remote Similarity NPC471423
0.6119 Remote Similarity NPC474322
0.6098 Remote Similarity NPC150557
0.6064 Remote Similarity NPC315170
0.6027 Remote Similarity NPC145627
0.6026 Remote Similarity NPC306973
0.6 Remote Similarity NPC293551
0.6 Remote Similarity NPC471605
0.6 Remote Similarity NPC471443
0.5972 Remote Similarity NPC319131
0.5952 Remote Similarity NPC471420
0.5949 Remote Similarity NPC185084
0.5915 Remote Similarity NPC245346
0.5915 Remote Similarity NPC11433
0.5915 Remote Similarity NPC302003
0.5897 Remote Similarity NPC327486
0.5897 Remote Similarity NPC223174
0.5897 Remote Similarity NPC327753
0.5867 Remote Similarity NPC160661
0.5851 Remote Similarity NPC313821
0.5844 Remote Similarity NPC316445
0.5833 Remote Similarity NPC315036
0.5833 Remote Similarity NPC314762
0.5833 Remote Similarity NPC56298
0.5833 Remote Similarity NPC318258
0.5833 Remote Similarity NPC471628
0.5778 Remote Similarity NPC275715
0.5769 Remote Similarity NPC223893
0.575 Remote Similarity NPC55274
0.5732 Remote Similarity NPC3094
0.5732 Remote Similarity NPC477002
0.573 Remote Similarity NPC313552
0.5698 Remote Similarity NPC315969
0.5679 Remote Similarity NPC315806
0.5676 Remote Similarity NPC314510
0.5667 Remote Similarity NPC214376
0.5667 Remote Similarity NPC470282
0.5667 Remote Similarity NPC52533
0.5644 Remote Similarity NPC313272
0.5644 Remote Similarity NPC319537
0.5641 Remote Similarity NPC195165
0.5632 Remote Similarity NPC263058
0.56 Remote Similarity NPC47333

  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 NPC101746 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
0.8281 Intermediate Similarity NPD9026 Phase 2
0.8281 Intermediate Similarity NPD9028 Phase 2
0.8281 Intermediate Similarity NPD9029 Phase 3
0.8281 Intermediate Similarity NPD9027 Phase 3
0.8209 Intermediate Similarity NPD9444 Discontinued
0.7969 Intermediate Similarity NPD9239 Approved
0.7969 Intermediate Similarity NPD9240 Approved
0.7941 Intermediate Similarity NPD9443 Clinical (unspecified phase)
0.75 Intermediate Similarity NPD9440 Discontinued
0.7164 Intermediate Similarity NPD9455 Approved
0.7059 Intermediate Similarity NPD393 Approved
0.6951 Remote Similarity NPD394 Phase 3
0.6829 Remote Similarity NPD9401 Discovery
0.6812 Remote Similarity NPD9022 Phase 2
0.6812 Remote Similarity NPD9024 Phase 2
0.6806 Remote Similarity NPD9032 Approved
0.6806 Remote Similarity NPD9033 Approved
0.6806 Remote Similarity NPD8868 Approved
0.6806 Remote Similarity NPD9030 Approved
0.6806 Remote Similarity NPD9031 Approved
0.6585 Remote Similarity NPD882 Phase 2
0.6585 Remote Similarity NPD883 Phase 2
0.6364 Remote Similarity NPD3215 Phase 1
0.6282 Remote Similarity NPD9034 Approved
0.6282 Remote Similarity NPD67 Phase 2
0.6061 Remote Similarity NPD3214 Discontinued
0.5915 Remote Similarity NPD8865 Approved
0.5897 Remote Similarity NPD9445 Approved
0.5851 Remote Similarity NPD3189 Approved
0.5851 Remote Similarity NPD3190 Approved
0.5851 Remote Similarity NPD3191 Approved
0.5833 Remote Similarity NPD4837 Approved
0.5833 Remote Similarity NPD9429 Discontinued
0.5833 Remote Similarity NPD4838 Approved
0.5833 Remote Similarity NPD4836 Approved
0.5833 Remote Similarity NPD4835 Approved
0.5732 Remote Similarity NPD9407 Approved
0.5679 Remote Similarity NPD9653 Clinical (unspecified phase)
0.5667 Remote Similarity NPD2698 Approved
0.5663 Remote Similarity NPD372 Clinical (unspecified phase)
0.5658 Remote Similarity NPD1457 Discontinued
0.5625 Remote Similarity NPD4282 Approved
0.5606 Remote Similarity NPD399 Approved
0.5606 Remote Similarity NPD398 Approved
0.5606 Remote Similarity NPD400 Approved
0.56 Remote Similarity NPD2700 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