Structure

Physi-Chem Properties

Molecular Weight:  219.11
Volume:  202.055
LogP:  -1.611
LogD:  -1.632
LogS:  -0.082
# Rotatable Bonds:  1
TPSA:  104.39
# H-Bond Aceptor:  6
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.319
Synthetic Accessibility Score:  4.752
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.362
MDCK Permeability:  0.00017466997087467462
Pgp-inhibitor:  0.001
Pgp-substrate:  0.642
Human Intestinal Absorption (HIA):  0.934
20% Bioavailability (F20%):  0.027
30% Bioavailability (F30%):  0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.283
Plasma Protein Binding (PPB):  15.624506950378418%
Volume Distribution (VD):  0.326
Pgp-substrate:  79.90669250488281%

ADMET: Metabolism

CYP1A2-inhibitor:  0.026
CYP1A2-substrate:  0.056
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.074
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.143
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.176
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.021

ADMET: Excretion

Clearance (CL):  2.759
Half-life (T1/2):  0.857

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.675
Drug-inuced Liver Injury (DILI):  0.885
AMES Toxicity:  0.06
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.007
Skin Sensitization:  0.376
Carcinogencity:  0.013
Eye Corrosion:  0.017
Eye Irritation:  0.351
Respiratory Toxicity:  0.455

Download Data

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

  Natural Product: NPC163538

Natural Product ID:  NPC163538
Common Name*:   Hyacinthacine C5
IUPAC Name:   (1R,2R,3R,5S,6S,7S,8R)-3-(hydroxymethyl)-5-methyl-2,3,5,6,7,8-hexahydro-1H-pyrrolizine-1,2,6,7-tetrol
Synonyms:   hyacinthacine C5
Standard InCHIKey:  TXKSAMJHOAHOGY-FDQLZJOISA-N
Standard InCHI:  InChI=1S/C9H17NO5/c1-3-6(12)8(14)5-9(15)7(13)4(2-11)10(3)5/h3-9,11-15H,2H2,1H3/t3-,4+,5+,6-,7+,8-,9+/m0/s1
SMILES:  C[C@H]1[C@@H]([C@H]([C@@H]2[C@H]([C@@H]([C@@H](CO)N12)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL227057
PubChem CID:   16737239
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000220] Pyrrolizidines

*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
NPO7198 Scilla socialis Species Hyacinthaceae Eukaryota n.a. n.a. n.a. PMID[17536859]
NPO7198 Scilla socialis 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
NPT6343 Individual Protein Beta-galactosidase Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903) IC50 = 48000.0 nM PMID[469156]
NPT509 Individual Protein Beta-galactosidase Bos taurus IC50 = 900000.0 nM PMID[469156]
NPT503 Individual Protein Alpha-L-fucosidase I Homo sapiens Inhibition < 50.0 % PMID[469156]
NPT507 Individual Protein Alpha-galactosidase Coffea arabica Inhibition < 50.0 % PMID[469156]
NPT2 Others Unspecified Inhibition < 50.0 % PMID[469156]
NPT2 Others Unspecified IC50 = 77000.0 nM PMID[469156]
NPT2 Others Unspecified IC50 = 57000.0 nM PMID[469156]

☑ 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 NPC163538 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 NPC115800
0.9688 High Similarity NPC306763
0.9688 High Similarity NPC266242
0.9688 High Similarity NPC254617
0.9688 High Similarity NPC74555
0.9538 High Similarity NPC473419
0.9538 High Similarity NPC475715
0.9538 High Similarity NPC475127
0.9531 High Similarity NPC184150
0.9531 High Similarity NPC59221
0.9531 High Similarity NPC141156
0.9385 High Similarity NPC474469
0.9375 High Similarity NPC294883
0.9375 High Similarity NPC12514
0.8551 High Similarity NPC473710
0.8551 High Similarity NPC475694
0.8529 High Similarity NPC34291
0.8529 High Similarity NPC126664
0.8088 Intermediate Similarity NPC233034
0.8056 Intermediate Similarity NPC474468
0.8 Intermediate Similarity NPC171850
0.7971 Intermediate Similarity NPC116377
0.7971 Intermediate Similarity NPC473952
0.7971 Intermediate Similarity NPC101746
0.7971 Intermediate Similarity NPC69798
0.7971 Intermediate Similarity NPC77191
0.7941 Intermediate Similarity NPC471419
0.7941 Intermediate Similarity NPC163134
0.7826 Intermediate Similarity NPC474928
0.7812 Intermediate Similarity NPC471423
0.7812 Intermediate Similarity NPC275727
0.7812 Intermediate Similarity NPC471442
0.7576 Intermediate Similarity NPC471605
0.7576 Intermediate Similarity NPC471443
0.7432 Intermediate Similarity NPC137554
0.7432 Intermediate Similarity NPC255535
0.7432 Intermediate Similarity NPC285014
0.7432 Intermediate Similarity NPC28959
0.7432 Intermediate Similarity NPC299603
0.7397 Intermediate Similarity NPC268922
0.7391 Intermediate Similarity NPC30126
0.7391 Intermediate Similarity NPC8087
0.7391 Intermediate Similarity NPC62507
0.7391 Intermediate Similarity NPC474014
0.7391 Intermediate Similarity NPC57846
0.7353 Intermediate Similarity NPC471421
0.7353 Intermediate Similarity NPC233364
0.7353 Intermediate Similarity NPC170172
0.726 Intermediate Similarity NPC471418
0.72 Intermediate Similarity NPC476695
0.72 Intermediate Similarity NPC476696
0.72 Intermediate Similarity NPC476694
0.6986 Remote Similarity NPC286851
0.6986 Remote Similarity NPC303798
0.6867 Remote Similarity NPC165119
0.6866 Remote Similarity NPC277072
0.6866 Remote Similarity NPC178263
0.686 Remote Similarity NPC52533
0.6849 Remote Similarity NPC198341
0.6849 Remote Similarity NPC223386
0.6849 Remote Similarity NPC142290
0.6849 Remote Similarity NPC75435
0.6849 Remote Similarity NPC471892
0.6849 Remote Similarity NPC471780
0.6812 Remote Similarity NPC10262
0.6812 Remote Similarity NPC293551
0.6812 Remote Similarity NPC65832
0.6812 Remote Similarity NPC311668
0.6757 Remote Similarity NPC315980
0.663 Remote Similarity NPC313821
0.6585 Remote Similarity NPC150557
0.6575 Remote Similarity NPC306462
0.6575 Remote Similarity NPC218150
0.6575 Remote Similarity NPC2432
0.6575 Remote Similarity NPC145627
0.6575 Remote Similarity NPC69669
0.6575 Remote Similarity NPC22774
0.6575 Remote Similarity NPC150680
0.6571 Remote Similarity NPC8979
0.6552 Remote Similarity NPC306838
0.6506 Remote Similarity NPC83248
0.6506 Remote Similarity NPC100204
0.6429 Remote Similarity NPC471420
0.6377 Remote Similarity NPC272396
0.6351 Remote Similarity NPC17455
0.6265 Remote Similarity NPC233108
0.6184 Remote Similarity NPC160661
0.6173 Remote Similarity NPC315806
0.6164 Remote Similarity NPC193593
0.6164 Remote Similarity NPC290106
0.6164 Remote Similarity NPC143809
0.6164 Remote Similarity NPC76726
0.6154 Remote Similarity NPC195165
0.6143 Remote Similarity NPC270041
0.61 Remote Similarity NPC471844
0.6067 Remote Similarity NPC469363
0.6027 Remote Similarity NPC204709
0.6 Remote Similarity NPC327753
0.6 Remote Similarity NPC327486
0.6 Remote Similarity NPC123814
0.6 Remote Similarity NPC223174
0.5977 Remote Similarity NPC36927
0.5977 Remote Similarity NPC271772
0.596 Remote Similarity NPC314387
0.5955 Remote Similarity NPC277918
0.5946 Remote Similarity NPC319991
0.5926 Remote Similarity NPC477200
0.5882 Remote Similarity NPC96966
0.5882 Remote Similarity NPC121062
0.5882 Remote Similarity NPC29222
0.5867 Remote Similarity NPC201338
0.5867 Remote Similarity NPC474627
0.5867 Remote Similarity NPC328786
0.5814 Remote Similarity NPC98750
0.5789 Remote Similarity NPC112398
0.5783 Remote Similarity NPC126186
0.5775 Remote Similarity NPC474322
0.5765 Remote Similarity NPC329077
0.575 Remote Similarity NPC316445
0.5747 Remote Similarity NPC70574
0.5699 Remote Similarity NPC322966
0.5698 Remote Similarity NPC314968
0.5698 Remote Similarity NPC314772
0.5658 Remote Similarity NPC319131
0.5647 Remote Similarity NPC470782
0.5647 Remote Similarity NPC264417
0.5647 Remote Similarity NPC217095
0.5632 Remote Similarity NPC316807
0.5625 Remote Similarity NPC322801
0.5625 Remote Similarity NPC291650
0.5625 Remote Similarity NPC129100
0.5616 Remote Similarity NPC471917
0.5612 Remote Similarity NPC471843

  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 NPC163538 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
0.9688 High Similarity NPD9444 Discontinued
0.8529 High Similarity NPD9443 Clinical (unspecified phase)
0.8088 Intermediate Similarity NPD9440 Discontinued
0.7647 Intermediate Similarity NPD393 Approved
0.75 Intermediate Similarity NPD9455 Approved
0.75 Intermediate Similarity NPD882 Phase 2
0.75 Intermediate Similarity NPD883 Phase 2
0.7 Intermediate Similarity NPD9240 Approved
0.7 Intermediate Similarity NPD9239 Approved
0.663 Remote Similarity NPD3190 Approved
0.663 Remote Similarity NPD3191 Approved
0.663 Remote Similarity NPD3189 Approved
0.6622 Remote Similarity NPD1457 Discontinued
0.6575 Remote Similarity NPD9027 Phase 3
0.6575 Remote Similarity NPD9029 Phase 3
0.6575 Remote Similarity NPD9026 Phase 2
0.6575 Remote Similarity NPD9028 Phase 2
0.625 Remote Similarity NPD394 Phase 3
0.6173 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6145 Remote Similarity NPD372 Clinical (unspecified phase)
0.6 Remote Similarity NPD9445 Approved
0.6 Remote Similarity NPD3215 Phase 1
0.5977 Remote Similarity NPD2691 Clinical (unspecified phase)
0.596 Remote Similarity NPD3183 Approved
0.596 Remote Similarity NPD3184 Approved
0.596 Remote Similarity NPD3185 Approved
0.596 Remote Similarity NPD3182 Approved
0.5955 Remote Similarity NPD9401 Discovery
0.5761 Remote Similarity NPD3177 Phase 3
0.5714 Remote Similarity NPD619 Phase 3
0.5714 Remote Similarity NPD3723 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3214 Discontinued
0.5698 Remote Similarity NPD9434 Approved
0.5698 Remote Similarity NPD9435 Approved
0.5663 Remote Similarity NPD6704 Discontinued
0.5663 Remote Similarity NPD3187 Discontinued
0.5647 Remote Similarity NPD9407 Approved
0.5625 Remote Similarity NPD9030 Approved
0.5625 Remote Similarity NPD9031 Approved
0.5625 Remote Similarity NPD9032 Approved
0.5625 Remote Similarity NPD9033 Approved
0.561 Remote Similarity NPD2220 Clinical (unspecified phase)

  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