Structure

Physi-Chem Properties

Molecular Weight:  117.08
Volume:  115.057
LogP:  -1.685
LogD:  -1.476
LogS:  0.699
# Rotatable Bonds:  1
TPSA:  52.49
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.4
Synthetic Accessibility Score:  3.761
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:  -5.024
MDCK Permeability:  9.864028834272176e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.696
Human Intestinal Absorption (HIA):  0.236
20% Bioavailability (F20%):  0.094
30% Bioavailability (F30%):  0.85

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.183
Plasma Protein Binding (PPB):  11.855728149414062%
Volume Distribution (VD):  0.764
Pgp-substrate:  91.867919921875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.017
CYP1A2-substrate:  0.073
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.603
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.094
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.235
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.083

ADMET: Excretion

Clearance (CL):  7.014
Half-life (T1/2):  0.69

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.179
Drug-inuced Liver Injury (DILI):  0.029
AMES Toxicity:  0.048
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.033
Skin Sensitization:  0.715
Carcinogencity:  0.202
Eye Corrosion:  0.697
Eye Irritation:  0.743
Respiratory Toxicity:  0.663

Download Data

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

  Natural Product: NPC272396

Natural Product ID:  NPC272396
Common Name*:   1,4-Imino-1,2,4-Trideoxy-D-Arabinitol
IUPAC Name:   (2R,3S)-2-(hydroxymethyl)pyrrolidin-3-ol
Synonyms:  
Standard InCHIKey:  TYLFLHPQWQQWRD-UHNVWZDZSA-N
Standard InCHI:  InChI=1S/C5H11NO2/c7-3-4-5(8)1-2-6-4/h4-8H,1-3H2/t4-,5+/m1/s1
SMILES:  OC[C@H]1NCC[C@@H]1O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL408355
PubChem CID:   11073391
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
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]
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]
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]

☑ 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 = 48000.0 nM PMID[487479]
NPT462 Individual Protein Sucrase-isomaltase Rattus norvegicus IC50 = 160000.0 nM PMID[487479]
NPT462 Individual Protein Sucrase-isomaltase Rattus norvegicus IC50 = 730000.0 nM PMID[487479]
NPT462 Individual Protein Sucrase-isomaltase Rattus norvegicus IC50 = 300000.0 nM PMID[487479]
NPT2 Others Unspecified Inhibition < 50.0 % PMID[487479]

☑ 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 NPC272396 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
0.9423 High Similarity NPC311668
0.9423 High Similarity NPC65832
0.9423 High Similarity NPC10262
0.875 High Similarity NPC57846
0.875 High Similarity NPC62507
0.875 High Similarity NPC474014
0.875 High Similarity NPC8087
0.875 High Similarity NPC30126
0.8305 Intermediate Similarity NPC474928
0.8167 Intermediate Similarity NPC116377
0.8167 Intermediate Similarity NPC69798
0.8167 Intermediate Similarity NPC101746
0.8167 Intermediate Similarity NPC77191
0.8167 Intermediate Similarity NPC473952
0.8 Intermediate Similarity NPC275727
0.7895 Intermediate Similarity NPC204709
0.7759 Intermediate Similarity NPC76726
0.7759 Intermediate Similarity NPC193593
0.7759 Intermediate Similarity NPC290106
0.7759 Intermediate Similarity NPC143809
0.7742 Intermediate Similarity NPC135539
0.7742 Intermediate Similarity NPC196359
0.7742 Intermediate Similarity NPC78312
0.7742 Intermediate Similarity NPC221764
0.7656 Intermediate Similarity NPC473710
0.7656 Intermediate Similarity NPC475694
0.7538 Intermediate Similarity NPC137554
0.7538 Intermediate Similarity NPC285014
0.7538 Intermediate Similarity NPC28959
0.7538 Intermediate Similarity NPC255535
0.7538 Intermediate Similarity NPC299603
0.7424 Intermediate Similarity NPC474468
0.7377 Intermediate Similarity NPC306462
0.7377 Intermediate Similarity NPC150680
0.7377 Intermediate Similarity NPC2432
0.7377 Intermediate Similarity NPC22774
0.7377 Intermediate Similarity NPC218150
0.7377 Intermediate Similarity NPC69669
0.7302 Intermediate Similarity NPC315980
0.7143 Intermediate Similarity NPC198341
0.7143 Intermediate Similarity NPC75435
0.7143 Intermediate Similarity NPC471780
0.7143 Intermediate Similarity NPC471892
0.7143 Intermediate Similarity NPC223386
0.7143 Intermediate Similarity NPC142290
0.7031 Intermediate Similarity NPC303798
0.7031 Intermediate Similarity NPC286851
0.7 Intermediate Similarity NPC11433
0.7 Intermediate Similarity NPC245346
0.7 Intermediate Similarity NPC302003
0.6875 Remote Similarity NPC233034
0.6818 Remote Similarity NPC471418
0.6769 Remote Similarity NPC12514
0.6769 Remote Similarity NPC294883
0.6716 Remote Similarity NPC268922
0.6712 Remote Similarity NPC83248
0.6712 Remote Similarity NPC100204
0.6667 Remote Similarity NPC141156
0.6667 Remote Similarity NPC314510
0.6667 Remote Similarity NPC59221
0.6667 Remote Similarity NPC184150
0.6615 Remote Similarity NPC160661
0.661 Remote Similarity NPC277072
0.661 Remote Similarity NPC178263
0.6567 Remote Similarity NPC306763
0.6567 Remote Similarity NPC474469
0.6567 Remote Similarity NPC74555
0.6567 Remote Similarity NPC266242
0.6567 Remote Similarity NPC34291
0.6567 Remote Similarity NPC126664
0.6567 Remote Similarity NPC254617
0.6567 Remote Similarity NPC107224
0.6522 Remote Similarity NPC476696
0.6522 Remote Similarity NPC476694
0.6522 Remote Similarity NPC476695
0.6471 Remote Similarity NPC473419
0.6471 Remote Similarity NPC475715
0.6471 Remote Similarity NPC475127
0.6447 Remote Similarity NPC165119
0.6441 Remote Similarity NPC123814
0.6377 Remote Similarity NPC115800
0.6377 Remote Similarity NPC163538
0.6349 Remote Similarity NPC170172
0.6327 Remote Similarity NPC328729
0.6316 Remote Similarity NPC29222
0.6316 Remote Similarity NPC121062
0.6316 Remote Similarity NPC96966
0.6308 Remote Similarity NPC17455
0.629 Remote Similarity NPC8979
0.629 Remote Similarity NPC293551
0.623 Remote Similarity NPC471442
0.623 Remote Similarity NPC471423
0.6167 Remote Similarity NPC474322
0.6125 Remote Similarity NPC306838
0.6094 Remote Similarity NPC471421
0.6094 Remote Similarity NPC233364
0.6087 Remote Similarity NPC171850
0.6056 Remote Similarity NPC306973
0.6032 Remote Similarity NPC471443
0.6032 Remote Similarity NPC471605
0.6 Remote Similarity NPC469363
0.6 Remote Similarity NPC15864
0.5972 Remote Similarity NPC185084
0.597 Remote Similarity NPC471419
0.597 Remote Similarity NPC163134
0.5921 Remote Similarity NPC98750
0.589 Remote Similarity NPC126186
0.5882 Remote Similarity NPC41429
0.5846 Remote Similarity NPC276928
0.5846 Remote Similarity NPC268927
0.5846 Remote Similarity NPC64250
0.5844 Remote Similarity NPC70574
0.5797 Remote Similarity NPC287693
0.5783 Remote Similarity NPC275715
0.5775 Remote Similarity NPC223893
0.5775 Remote Similarity NPC322274
0.5758 Remote Similarity NPC319131
0.5733 Remote Similarity NPC477002
0.5733 Remote Similarity NPC470782
0.5714 Remote Similarity NPC322801
0.5714 Remote Similarity NPC129100
0.5714 Remote Similarity NPC291650
0.5696 Remote Similarity NPC36927
0.5696 Remote Similarity NPC271772
0.5692 Remote Similarity NPC190385
0.5676 Remote Similarity NPC320221
0.5676 Remote Similarity NPC26932
0.5667 Remote Similarity NPC93888
0.5667 Remote Similarity NPC270805
0.5652 Remote Similarity NPC472609
0.5616 Remote Similarity NPC470781
0.56 Remote Similarity NPC84444
0.56 Remote Similarity NPC145217

  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 NPC272396 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
0.7742 Intermediate Similarity NPD8868 Approved
0.7377 Intermediate Similarity NPD9027 Phase 3
0.7377 Intermediate Similarity NPD9029 Phase 3
0.7377 Intermediate Similarity NPD9028 Phase 2
0.7377 Intermediate Similarity NPD9026 Phase 2
0.7213 Intermediate Similarity NPD9024 Phase 2
0.7213 Intermediate Similarity NPD9022 Phase 2
0.7049 Intermediate Similarity NPD9239 Approved
0.7049 Intermediate Similarity NPD9240 Approved
0.7 Intermediate Similarity NPD8865 Approved
0.6875 Remote Similarity NPD9440 Discontinued
0.6727 Remote Similarity NPD400 Approved
0.6727 Remote Similarity NPD398 Approved
0.6727 Remote Similarity NPD399 Approved
0.6567 Remote Similarity NPD9444 Discontinued
0.6567 Remote Similarity NPD9443 Clinical (unspecified phase)
0.6441 Remote Similarity NPD3215 Phase 1
0.6327 Remote Similarity NPD8556 Phase 3
0.625 Remote Similarity NPD9455 Approved
0.6154 Remote Similarity NPD393 Approved
0.6102 Remote Similarity NPD3214 Discontinued
0.6076 Remote Similarity NPD9401 Discovery
0.5854 Remote Similarity NPD3177 Phase 3
0.5846 Remote Similarity NPD8951 Approved
0.5818 Remote Similarity NPD9227 Discontinued
0.5714 Remote Similarity NPD9030 Approved
0.5714 Remote Similarity NPD9031 Approved
0.5714 Remote Similarity NPD9032 Approved
0.5714 Remote Similarity NPD9033 Approved
0.5692 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5667 Remote Similarity NPD8624 Approved
0.5641 Remote Similarity NPD9429 Discontinued
0.561 Remote Similarity NPD394 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