Structure

Physi-Chem Properties

Molecular Weight:  177.1
Volume:  167.23
LogP:  -1.825
LogD:  -2.181
LogS:  0.009
# Rotatable Bonds:  3
TPSA:  84.16
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.379
Synthetic Accessibility Score:  3.724
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:  -5.23
MDCK Permeability:  0.00029244853067211807
Pgp-inhibitor:  0.001
Pgp-substrate:  0.593
Human Intestinal Absorption (HIA):  0.023
20% Bioavailability (F20%):  0.419
30% Bioavailability (F30%):  0.717

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.286
Plasma Protein Binding (PPB):  11.419506072998047%
Volume Distribution (VD):  0.455
Pgp-substrate:  87.48219299316406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.049
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.746
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.19
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.227
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.049

ADMET: Excretion

Clearance (CL):  2.443
Half-life (T1/2):  0.787

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.244
Drug-inuced Liver Injury (DILI):  0.079
AMES Toxicity:  0.057
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.004
Skin Sensitization:  0.302
Carcinogencity:  0.03
Eye Corrosion:  0.027
Eye Irritation:  0.877
Respiratory Toxicity:  0.163

Download Data

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

  Natural Product: NPC275727

Natural Product ID:  NPC275727
Common Name*:   1,4-Dideoxy-1,4-(Hydroxyethyliminiumyl)-D-Arabinitol
IUPAC Name:   (2R,3R,4R)-1-(2-hydroxyethyl)-2-(hydroxymethyl)pyrrolidine-3,4-diol
Synonyms:  
Standard InCHIKey:  SPYQWYTVWZBEHS-FSDSQADBSA-N
Standard InCHI:  InChI=1S/C7H15NO4/c9-2-1-8-3-6(11)7(12)5(8)4-10/h5-7,9-12H,1-4H2/t5-,6-,7-/m1/s1
SMILES:  OCCN1C[C@H]([C@@H]([C@H]1CO)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL247666
PubChem CID:   10419725
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines
        • [CHEMONTID:0003449] N-alkylpyrrolidines

*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
NPO25301 Angylocalyx pynaertii Species Fabaceae Eukaryota pods n.a. n.a. PMID[11858756]
NPO25301 Angylocalyx pynaertii Species Fabaceae Eukaryota seeds n.a. n.a. PMID[8229017]
NPO25301 Angylocalyx pynaertii 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 = 12000.0 nM PMID[565029]
NPT462 Individual Protein Sucrase-isomaltase Rattus norvegicus IC50 = 720000.0 nM PMID[565029]
NPT462 Individual Protein Sucrase-isomaltase Rattus norvegicus IC50 = 70000.0 nM PMID[565029]
NPT462 Individual Protein Sucrase-isomaltase Rattus norvegicus IC50 = 120000.0 nM PMID[565029]
NPT5854 Individual Protein Uncharacterized protein Sus scrofa Inhibition < 50.0 % PMID[565030]
NPT506 Individual Protein Beta-mannosidase Rattus norvegicus Inhibition < 50.0 % PMID[565030]
NPT509 Individual Protein Beta-galactosidase Bos taurus Inhibition < 50.0 % PMID[565030]
NPT496 Individual Protein Alpha-L-fucosidase 1 Bos taurus Inhibition < 50.0 % PMID[565030]
NPT462 Individual Protein Sucrase-isomaltase Rattus norvegicus IC50 = 250000.0 nM PMID[565030]
NPT462 Individual Protein Sucrase-isomaltase Rattus norvegicus IC50 = 84000.0 nM PMID[565030]
NPT1131 Individual Protein Alpha-galactosidase Coffea arabica IC50 = 700000.0 nM PMID[565030]
NPT526 Individual Protein Alpha-glucosidase MAL62 Saccharomyces cerevisiae IC50 = 78000.0 nM PMID[565030]
NPT2 Others Unspecified IC50 = 100000.0 nM PMID[565029]
NPT2 Others Unspecified IC50 = 290000.0 nM PMID[565029]
NPT2 Others Unspecified IC50 = 620000.0 nM PMID[565030]
NPT2 Others Unspecified Inhibition < 50.0 % PMID[565030]
NPT2 Others Unspecified IC50 = 290000.0 nM PMID[565030]
NPT671 Individual Protein Acidic alpha-glucosidase Rattus norvegicus Inhibition < 50.0 % PMID[565030]
NPT2 Others Unspecified IC50 = 12000.0 nM PMID[565030]

☑ 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 NPC275727 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
0.8545 High Similarity NPC10262
0.8545 High Similarity NPC311668
0.8545 High Similarity NPC65832
0.8333 Intermediate Similarity NPC12514
0.8333 Intermediate Similarity NPC294883
0.8276 Intermediate Similarity NPC8087
0.8276 Intermediate Similarity NPC62507
0.8197 Intermediate Similarity NPC141156
0.8197 Intermediate Similarity NPC184150
0.8167 Intermediate Similarity NPC233034
0.8065 Intermediate Similarity NPC74555
0.8065 Intermediate Similarity NPC266242
0.8065 Intermediate Similarity NPC474469
0.8065 Intermediate Similarity NPC34291
0.8065 Intermediate Similarity NPC126664
0.8065 Intermediate Similarity NPC254617
0.8065 Intermediate Similarity NPC306763
0.8 Intermediate Similarity NPC272396
0.7966 Intermediate Similarity NPC474014
0.7966 Intermediate Similarity NPC30126
0.7966 Intermediate Similarity NPC57846
0.7937 Intermediate Similarity NPC475127
0.7937 Intermediate Similarity NPC475715
0.7937 Intermediate Similarity NPC473419
0.7903 Intermediate Similarity NPC59221
0.7869 Intermediate Similarity NPC474928
0.7812 Intermediate Similarity NPC115800
0.7812 Intermediate Similarity NPC163538
0.7742 Intermediate Similarity NPC473952
0.7742 Intermediate Similarity NPC101746
0.7742 Intermediate Similarity NPC69798
0.7742 Intermediate Similarity NPC116377
0.7742 Intermediate Similarity NPC77191
0.7627 Intermediate Similarity NPC170172
0.7302 Intermediate Similarity NPC160661
0.7288 Intermediate Similarity NPC293551
0.7273 Intermediate Similarity NPC475694
0.7273 Intermediate Similarity NPC473710
0.7164 Intermediate Similarity NPC255535
0.7164 Intermediate Similarity NPC285014
0.7164 Intermediate Similarity NPC299603
0.7164 Intermediate Similarity NPC137554
0.7164 Intermediate Similarity NPC28959
0.7143 Intermediate Similarity NPC471419
0.7143 Intermediate Similarity NPC163134
0.7059 Intermediate Similarity NPC474468
0.7049 Intermediate Similarity NPC290106
0.7049 Intermediate Similarity NPC76726
0.7049 Intermediate Similarity NPC193593
0.7049 Intermediate Similarity NPC143809
0.6984 Remote Similarity NPC306462
0.6984 Remote Similarity NPC218150
0.6984 Remote Similarity NPC2432
0.6984 Remote Similarity NPC22774
0.6984 Remote Similarity NPC69669
0.6984 Remote Similarity NPC150680
0.697 Remote Similarity NPC171850
0.6923 Remote Similarity NPC315980
0.6885 Remote Similarity NPC204709
0.678 Remote Similarity NPC178263
0.678 Remote Similarity NPC277072
0.6769 Remote Similarity NPC471892
0.6769 Remote Similarity NPC223386
0.6769 Remote Similarity NPC142290
0.6769 Remote Similarity NPC198341
0.6769 Remote Similarity NPC75435
0.6769 Remote Similarity NPC471780
0.6714 Remote Similarity NPC315806
0.6667 Remote Similarity NPC286851
0.6667 Remote Similarity NPC303798
0.6567 Remote Similarity NPC78312
0.6567 Remote Similarity NPC221764
0.6567 Remote Similarity NPC135539
0.6567 Remote Similarity NPC196359
0.6528 Remote Similarity NPC470782
0.6508 Remote Similarity NPC471421
0.6508 Remote Similarity NPC233364
0.6479 Remote Similarity NPC126186
0.6471 Remote Similarity NPC471418
0.6438 Remote Similarity NPC329077
0.64 Remote Similarity NPC83248
0.64 Remote Similarity NPC100204
0.6393 Remote Similarity NPC471442
0.6393 Remote Similarity NPC471423
0.6377 Remote Similarity NPC268922
0.6197 Remote Similarity NPC476695
0.6197 Remote Similarity NPC476696
0.6197 Remote Similarity NPC476694
0.619 Remote Similarity NPC471443
0.619 Remote Similarity NPC471605
0.6173 Remote Similarity NPC52533
0.6154 Remote Similarity NPC165119
0.6029 Remote Similarity NPC472609
0.6 Remote Similarity NPC224624
0.5972 Remote Similarity NPC470781
0.597 Remote Similarity NPC145627
0.5938 Remote Similarity NPC8979
0.5926 Remote Similarity NPC469363
0.5897 Remote Similarity NPC470783
0.5854 Remote Similarity NPC306838
0.5844 Remote Similarity NPC150557
0.5806 Remote Similarity NPC8488
0.5806 Remote Similarity NPC333075
0.5806 Remote Similarity NPC274499
0.5763 Remote Similarity NPC81384
0.5735 Remote Similarity NPC243964
0.5735 Remote Similarity NPC17455
0.5714 Remote Similarity NPC275715
0.5714 Remote Similarity NPC325902
0.5696 Remote Similarity NPC471420
0.5676 Remote Similarity NPC29326
0.5641 Remote Similarity NPC98750
0.5634 Remote Similarity NPC322801
0.5634 Remote Similarity NPC291650
0.5634 Remote Similarity NPC129100
0.5618 Remote Similarity NPC313821
0.5616 Remote Similarity NPC223174
0.5616 Remote Similarity NPC327753
0.5616 Remote Similarity NPC327486
0.5606 Remote Similarity NPC11433
0.5606 Remote Similarity NPC245346
0.5606 Remote Similarity NPC302003

  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 NPC275727 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
0.8167 Intermediate Similarity NPD9440 Discontinued
0.8065 Intermediate Similarity NPD9444 Discontinued
0.8065 Intermediate Similarity NPD9443 Clinical (unspecified phase)
0.75 Intermediate Similarity NPD9455 Approved
0.7377 Intermediate Similarity NPD393 Approved
0.6984 Remote Similarity NPD9026 Phase 2
0.6984 Remote Similarity NPD9027 Phase 3
0.6984 Remote Similarity NPD9029 Phase 3
0.6984 Remote Similarity NPD9028 Phase 2
0.6935 Remote Similarity NPD9239 Approved
0.6935 Remote Similarity NPD9240 Approved
0.6825 Remote Similarity NPD9024 Phase 2
0.6825 Remote Similarity NPD9022 Phase 2
0.6714 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6579 Remote Similarity NPD882 Phase 2
0.6579 Remote Similarity NPD883 Phase 2
0.6567 Remote Similarity NPD8868 Approved
0.6308 Remote Similarity NPD3192 Approved
0.6308 Remote Similarity NPD3193 Approved
0.6301 Remote Similarity NPD9407 Approved
0.6 Remote Similarity NPD9401 Discovery
0.6 Remote Similarity NPD372 Clinical (unspecified phase)
0.5974 Remote Similarity NPD9429 Discontinued
0.589 Remote Similarity NPD9405 Approved
0.5882 Remote Similarity NPD9211 Clinical (unspecified phase)
0.5797 Remote Similarity NPD1457 Discontinued
0.5763 Remote Similarity NPD9462 Approved
0.5763 Remote Similarity NPD9463 Phase 3
0.5634 Remote Similarity NPD9031 Approved
0.5634 Remote Similarity NPD9032 Approved
0.5634 Remote Similarity NPD9033 Approved
0.5634 Remote Similarity NPD9030 Approved
0.5618 Remote Similarity NPD3189 Approved
0.5618 Remote Similarity NPD3190 Approved
0.5618 Remote Similarity NPD3191 Approved
0.5616 Remote Similarity NPD9445 Approved
0.5606 Remote Similarity NPD8865 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