Structure

Physi-Chem Properties

Molecular Weight:  191.12
Volume:  184.526
LogP:  -1.872
LogD:  -1.88
LogS:  -0.056
# Rotatable Bonds:  3
TPSA:  92.95
# H-Bond Aceptor:  5
# H-Bond Donor:  5
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.349
Synthetic Accessibility Score:  4.351
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:  -5.293
MDCK Permeability:  0.00021441384160425514
Pgp-inhibitor:  0.0
Pgp-substrate:  0.759
Human Intestinal Absorption (HIA):  0.721
20% Bioavailability (F20%):  0.227
30% Bioavailability (F30%):  0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.19
Plasma Protein Binding (PPB):  13.322013854980469%
Volume Distribution (VD):  0.55
Pgp-substrate:  86.84827423095703%

ADMET: Metabolism

CYP1A2-inhibitor:  0.02
CYP1A2-substrate:  0.052
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.815
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.194
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.156
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.064

ADMET: Excretion

Clearance (CL):  2.57
Half-life (T1/2):  0.706

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.904
Drug-inuced Liver Injury (DILI):  0.234
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.056
Skin Sensitization:  0.263
Carcinogencity:  0.01
Eye Corrosion:  0.009
Eye Irritation:  0.157
Respiratory Toxicity:  0.45

Download Data

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

  Natural Product: NPC473710

Natural Product ID:  NPC473710
Common Name*:   Alpha-1-C-(2-Hydroxypropyl)-1,4-Dideoxy-1,4-Imino-D-Arabinitol
IUPAC Name:   (2R,3R,4R,5R)-2-(hydroxymethyl)-5-(2-hydroxypropyl)pyrrolidine-3,4-diol
Synonyms:  
Standard InCHIKey:  SKCBFFYDHKQEQU-NMBMWNOXSA-N
Standard InCHI:  InChI=1S/C8H17NO4/c1-4(11)2-5-7(12)8(13)6(3-10)9-5/h4-13H,2-3H2,1H3/t4?,5-,6-,7-,8-/m1/s1
SMILES:  OC[C@H]1N[C@@H]([C@H]([C@@H]1O)O)CC(O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL449851
PubChem CID:   11183118
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
NPO22662 Scilla peruviana Species Hyacinthaceae Eukaryota n.a. n.a. n.a. PMID[15165148]
NPO22662 Scilla peruviana Species Hyacinthaceae 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
NPT509 Individual Protein Beta-galactosidase Bos taurus IC50 = 260000.0 nM PMID[530790]
NPT506 Individual Protein Beta-mannosidase Rattus norvegicus IC50 = 610000.0 nM PMID[530790]
NPT496 Individual Protein Alpha-L-fucosidase 1 Bos taurus Inhibition < 50.0 % PMID[530790]
NPT61 Individual Protein Beta-glucocerebrosidase Homo sapiens Inhibition < 50.0 % PMID[530790]
NPT1131 Individual Protein Alpha-galactosidase Coffea arabica Inhibition < 50.0 % PMID[530790]
NPT2 Others Unspecified IC50 = 210000.0 nM PMID[530790]
NPT2 Others Unspecified IC50 = 100000.0 nM PMID[530790]
NPT2 Others Unspecified IC50 = 700000.0 nM PMID[530790]
NPT2 Others Unspecified Inhibition < 50.0 % PMID[530790]
NPT671 Individual Protein Acidic alpha-glucosidase Rattus norvegicus Inhibition < 50.0 % PMID[530790]

☑ 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 NPC473710 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 NPC475694
0.9403 High Similarity NPC474468
0.9375 High Similarity NPC69798
0.9375 High Similarity NPC116377
0.9375 High Similarity NPC473952
0.9375 High Similarity NPC101746
0.9375 High Similarity NPC77191
0.9219 High Similarity NPC474928
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
0.8696 High Similarity NPC28959
0.8696 High Similarity NPC299603
0.8696 High Similarity NPC255535
0.8696 High Similarity NPC285014
0.8696 High Similarity NPC137554
0.8676 High Similarity NPC268922
0.8551 High Similarity NPC163538
0.8551 High Similarity NPC115800
0.8529 High Similarity NPC471418
0.8429 Intermediate Similarity NPC476695
0.8429 Intermediate Similarity NPC476694
0.8429 Intermediate Similarity NPC476696
0.8261 Intermediate Similarity NPC266242
0.8261 Intermediate Similarity NPC254617
0.8261 Intermediate Similarity NPC306763
0.8261 Intermediate Similarity NPC74555
0.8235 Intermediate Similarity NPC286851
0.8235 Intermediate Similarity NPC303798
0.8143 Intermediate Similarity NPC473419
0.8143 Intermediate Similarity NPC475715
0.8143 Intermediate Similarity NPC475127
0.8125 Intermediate Similarity NPC10262
0.8125 Intermediate Similarity NPC65832
0.8125 Intermediate Similarity NPC311668
0.8116 Intermediate Similarity NPC59221
0.8116 Intermediate Similarity NPC141156
0.8116 Intermediate Similarity NPC184150
0.8088 Intermediate Similarity NPC471780
0.8088 Intermediate Similarity NPC142290
0.8088 Intermediate Similarity NPC75435
0.8088 Intermediate Similarity NPC471892
0.8088 Intermediate Similarity NPC223386
0.8088 Intermediate Similarity NPC198341
0.8 Intermediate Similarity NPC474469
0.8 Intermediate Similarity NPC126664
0.8 Intermediate Similarity NPC34291
0.7971 Intermediate Similarity NPC12514
0.7971 Intermediate Similarity NPC294883
0.7971 Intermediate Similarity NPC315980
0.7949 Intermediate Similarity NPC165119
0.7794 Intermediate Similarity NPC22774
0.7794 Intermediate Similarity NPC306462
0.7794 Intermediate Similarity NPC150680
0.7794 Intermediate Similarity NPC218150
0.7794 Intermediate Similarity NPC2432
0.7794 Intermediate Similarity NPC69669
0.7681 Intermediate Similarity NPC471419
0.7681 Intermediate Similarity NPC163134
0.7656 Intermediate Similarity NPC272396
0.7576 Intermediate Similarity NPC8979
0.7571 Intermediate Similarity NPC233034
0.7564 Intermediate Similarity NPC83248
0.7564 Intermediate Similarity NPC100204
0.7561 Intermediate Similarity NPC306838
0.7353 Intermediate Similarity NPC290106
0.7353 Intermediate Similarity NPC76726
0.7353 Intermediate Similarity NPC193593
0.7353 Intermediate Similarity NPC143809
0.7286 Intermediate Similarity NPC17455
0.7273 Intermediate Similarity NPC275727
0.726 Intermediate Similarity NPC171850
0.7206 Intermediate Similarity NPC204709
0.7101 Intermediate Similarity NPC471421
0.7101 Intermediate Similarity NPC233364
0.7101 Intermediate Similarity NPC170172
0.697 Remote Similarity NPC123814
0.6951 Remote Similarity NPC271772
0.6951 Remote Similarity NPC36927
0.6875 Remote Similarity NPC96966
0.6875 Remote Similarity NPC121062
0.6875 Remote Similarity NPC29222
0.6824 Remote Similarity NPC469363
0.679 Remote Similarity NPC98750
0.6765 Remote Similarity NPC471442
0.6765 Remote Similarity NPC471423
0.6716 Remote Similarity NPC474322
0.6707 Remote Similarity NPC70574
0.6618 Remote Similarity NPC277072
0.6618 Remote Similarity NPC178263
0.6575 Remote Similarity NPC145627
0.6571 Remote Similarity NPC471605
0.6571 Remote Similarity NPC471443
0.6538 Remote Similarity NPC306973
0.6528 Remote Similarity NPC319131
0.6447 Remote Similarity NPC135539
0.6447 Remote Similarity NPC291650
0.6447 Remote Similarity NPC196359
0.6447 Remote Similarity NPC322801
0.6447 Remote Similarity NPC78312
0.6447 Remote Similarity NPC221764
0.6447 Remote Similarity NPC129100
0.6386 Remote Similarity NPC150557
0.6338 Remote Similarity NPC293551
0.6277 Remote Similarity NPC313821
0.625 Remote Similarity NPC315036
0.6235 Remote Similarity NPC471420
0.622 Remote Similarity NPC477002
0.622 Remote Similarity NPC244539
0.622 Remote Similarity NPC3094
0.6154 Remote Similarity NPC195165
0.6146 Remote Similarity NPC315170
0.6145 Remote Similarity NPC313762
0.6143 Remote Similarity NPC270041
0.6111 Remote Similarity NPC470282
0.6082 Remote Similarity NPC56298
0.6082 Remote Similarity NPC471628
0.6049 Remote Similarity NPC55274
0.6047 Remote Similarity NPC219340
0.6027 Remote Similarity NPC302569
0.6027 Remote Similarity NPC168308
0.6024 Remote Similarity NPC140327
0.6024 Remote Similarity NPC51055
0.6024 Remote Similarity NPC212008
0.6024 Remote Similarity NPC62293
0.6 Remote Similarity NPC327753
0.6 Remote Similarity NPC327486
0.6 Remote Similarity NPC314510
0.6 Remote Similarity NPC223174
0.5949 Remote Similarity NPC107224
0.5946 Remote Similarity NPC216415
0.5946 Remote Similarity NPC476537
0.5934 Remote Similarity NPC52533
0.593 Remote Similarity NPC318258
0.5926 Remote Similarity NPC477200
0.5921 Remote Similarity NPC47333
0.587 Remote Similarity NPC275715
0.5862 Remote Similarity NPC79367
0.5824 Remote Similarity NPC313552
0.5814 Remote Similarity NPC475363
0.5814 Remote Similarity NPC473971
0.5814 Remote Similarity NPC473972
0.5795 Remote Similarity NPC315969
0.5783 Remote Similarity NPC315806
0.5778 Remote Similarity NPC192025
0.5778 Remote Similarity NPC125253
0.5778 Remote Similarity NPC253975
0.5773 Remote Similarity NPC160066
0.5769 Remote Similarity NPC160661
0.5769 Remote Similarity NPC41429
0.5761 Remote Similarity NPC214376
0.5733 Remote Similarity NPC319991
0.573 Remote Similarity NPC263058
0.5728 Remote Similarity NPC319537
0.5728 Remote Similarity NPC313272
0.5714 Remote Similarity NPC83839
0.5698 Remote Similarity NPC314968
0.5698 Remote Similarity NPC37681
0.5698 Remote Similarity NPC314772
0.5682 Remote Similarity NPC207657
0.5679 Remote Similarity NPC223893
0.5663 Remote Similarity NPC185084
0.5658 Remote Similarity NPC474627
0.5658 Remote Similarity NPC201338
0.5658 Remote Similarity NPC328786
0.5652 Remote Similarity NPC193872
0.5647 Remote Similarity NPC264417
0.5647 Remote Similarity NPC217095
0.5644 Remote Similarity NPC314387
0.5638 Remote Similarity NPC195969
0.5638 Remote Similarity NPC176381
0.5632 Remote Similarity NPC316807
0.5625 Remote Similarity NPC113224
0.5616 Remote Similarity NPC471917
0.5604 Remote Similarity NPC277918
0.56 Remote Similarity NPC245346
0.56 Remote Similarity NPC11433
0.56 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 NPC473710 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
0.8261 Intermediate Similarity NPD9444 Discontinued
0.803 Intermediate Similarity NPD9240 Approved
0.803 Intermediate Similarity NPD9239 Approved
0.8 Intermediate Similarity NPD9443 Clinical (unspecified phase)
0.7794 Intermediate Similarity NPD9026 Phase 2
0.7794 Intermediate Similarity NPD9029 Phase 3
0.7794 Intermediate Similarity NPD9027 Phase 3
0.7794 Intermediate Similarity NPD9028 Phase 2
0.7571 Intermediate Similarity NPD9440 Discontinued
0.7391 Intermediate Similarity NPD393 Approved
0.7246 Intermediate Similarity NPD9455 Approved
0.7073 Intermediate Similarity NPD883 Phase 2
0.7073 Intermediate Similarity NPD882 Phase 2
0.7024 Intermediate Similarity NPD394 Phase 3
0.697 Remote Similarity NPD3215 Phase 1
0.6706 Remote Similarity NPD9401 Discovery
0.6667 Remote Similarity NPD3214 Discontinued
0.6447 Remote Similarity NPD9030 Approved
0.6447 Remote Similarity NPD9033 Approved
0.6447 Remote Similarity NPD8868 Approved
0.6447 Remote Similarity NPD9031 Approved
0.6447 Remote Similarity NPD9032 Approved
0.6438 Remote Similarity NPD9022 Phase 2
0.6438 Remote Similarity NPD9024 Phase 2
0.6277 Remote Similarity NPD3190 Approved
0.6277 Remote Similarity NPD3191 Approved
0.6277 Remote Similarity NPD3189 Approved
0.6082 Remote Similarity NPD4837 Approved
0.6082 Remote Similarity NPD4838 Approved
0.6082 Remote Similarity NPD4835 Approved
0.6082 Remote Similarity NPD4836 Approved
0.6 Remote Similarity NPD9445 Approved
0.5976 Remote Similarity NPD9034 Approved
0.5976 Remote Similarity NPD67 Phase 2
0.5974 Remote Similarity NPD1457 Discontinued
0.597 Remote Similarity NPD399 Approved
0.597 Remote Similarity NPD398 Approved
0.597 Remote Similarity NPD400 Approved
0.5876 Remote Similarity NPD4282 Approved
0.5842 Remote Similarity NPD2700 Approved
0.5783 Remote Similarity NPD9653 Clinical (unspecified phase)
0.5765 Remote Similarity NPD372 Clinical (unspecified phase)
0.5761 Remote Similarity NPD2698 Approved
0.5747 Remote Similarity NPD9429 Discontinued
0.5743 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5714 Remote Similarity NPD619 Phase 3
0.5698 Remote Similarity NPD9434 Approved
0.5698 Remote Similarity NPD9435 Approved
0.5663 Remote Similarity NPD3187 Discontinued
0.566 Remote Similarity NPD2690 Discontinued
0.5647 Remote Similarity NPD9407 Approved
0.5644 Remote Similarity NPD3184 Approved
0.5644 Remote Similarity NPD3183 Approved
0.5644 Remote Similarity NPD3185 Approved
0.5644 Remote Similarity NPD3182 Approved
0.5638 Remote Similarity NPD5798 Approved
0.5638 Remote Similarity NPD5797 Approved
0.5638 Remote Similarity NPD5794 Approved
0.5638 Remote Similarity NPD5796 Clinical (unspecified phase)
0.5638 Remote Similarity NPD5795 Approved
0.5632 Remote Similarity NPD617 Approved
0.5618 Remote Similarity NPD2691 Clinical (unspecified phase)
0.561 Remote Similarity NPD2704 Phase 3
0.561 Remote Similarity NPD2702 Phase 1
0.5604 Remote Similarity NPD9640 Clinical (unspecified phase)
0.56 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