Structure

Physi-Chem Properties

Molecular Weight:  219.11
Volume:  202.055
LogP:  -1.818
LogD:  -1.71
LogS:  0.021
# Rotatable Bonds:  2
TPSA:  104.39
# H-Bond Aceptor:  6
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.336
Synthetic Accessibility Score:  4.651
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:  -5.479
MDCK Permeability:  0.00030264045926742256
Pgp-inhibitor:  0.0
Pgp-substrate:  0.95
Human Intestinal Absorption (HIA):  0.915
20% Bioavailability (F20%):  0.121
30% Bioavailability (F30%):  0.966

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.267
Plasma Protein Binding (PPB):  13.18424129486084%
Volume Distribution (VD):  0.324
Pgp-substrate:  84.22216796875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.014
CYP1A2-substrate:  0.038
CYP2C19-inhibitor:  0.009
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.094
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.146
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.012

ADMET: Excretion

Clearance (CL):  2.509
Half-life (T1/2):  0.808

ADMET: Toxicity

hERG Blockers:  0.034
Human Hepatotoxicity (H-HT):  0.928
Drug-inuced Liver Injury (DILI):  0.682
AMES Toxicity:  0.153
Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.019
Skin Sensitization:  0.593
Carcinogencity:  0.053
Eye Corrosion:  0.013
Eye Irritation:  0.29
Respiratory Toxicity:  0.853

Download Data

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

  Natural Product: NPC184150

Natural Product ID:  NPC184150
Common Name*:   Hyacinthacine C2
IUPAC Name:   (1S,2R,3R,5S,7S,8R)-3,5-bis(hydroxymethyl)-2,3,5,6,7,8-hexahydro-1H-pyrrolizine-1,2,7-triol
Synonyms:   hyacinthacine C2
Standard InCHIKey:  FKQQQROPNALGDM-ARADLNFTSA-N
Standard InCHI:  InChI=1S/C9H17NO5/c11-2-4-1-6(13)7-9(15)8(14)5(3-12)10(4)7/h4-9,11-15H,1-3H2/t4-,5+,6-,7+,8+,9-/m0/s1
SMILES:  OC[C@@H]1C[C@@H]([C@H]2N1[C@H](CO)[C@H]([C@H]2O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL226576
PubChem CID:   16737240
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
NPT503 Individual Protein Alpha-L-fucosidase I Homo sapiens IC50 = 17000.0 nM PMID[514272]
NPT6343 Individual Protein Beta-galactosidase Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903) IC50 = 13000.0 nM PMID[514272]
NPT509 Individual Protein Beta-galactosidase Bos taurus IC50 = 370000.0 nM PMID[514272]
NPT507 Individual Protein Alpha-galactosidase Coffea arabica Inhibition < 50.0 % PMID[514272]
NPT2 Others Unspecified Inhibition < 50.0 % PMID[514272]
NPT2 Others Unspecified IC50 = 550000.0 nM PMID[514272]

☑ 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 NPC184150 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 NPC141156
0.9839 High Similarity NPC74555
0.9839 High Similarity NPC266242
0.9839 High Similarity NPC306763
0.9839 High Similarity NPC254617
0.9839 High Similarity NPC474469
0.9836 High Similarity NPC294883
0.9836 High Similarity NPC12514
0.9683 High Similarity NPC475715
0.9683 High Similarity NPC475127
0.9683 High Similarity NPC473419
0.9677 High Similarity NPC59221
0.9531 High Similarity NPC163538
0.9531 High Similarity NPC115800
0.8462 Intermediate Similarity NPC233034
0.8358 Intermediate Similarity NPC34291
0.8358 Intermediate Similarity NPC126664
0.8197 Intermediate Similarity NPC275727
0.8116 Intermediate Similarity NPC475694
0.8116 Intermediate Similarity NPC473710
0.791 Intermediate Similarity NPC474928
0.7903 Intermediate Similarity NPC471442
0.7903 Intermediate Similarity NPC471423
0.7887 Intermediate Similarity NPC474468
0.7794 Intermediate Similarity NPC473952
0.7794 Intermediate Similarity NPC116377
0.7794 Intermediate Similarity NPC101746
0.7794 Intermediate Similarity NPC77191
0.7794 Intermediate Similarity NPC69798
0.7727 Intermediate Similarity NPC62507
0.7727 Intermediate Similarity NPC8087
0.7656 Intermediate Similarity NPC471443
0.7656 Intermediate Similarity NPC471605
0.7571 Intermediate Similarity NPC171850
0.75 Intermediate Similarity NPC471419
0.75 Intermediate Similarity NPC163134
0.7463 Intermediate Similarity NPC30126
0.7463 Intermediate Similarity NPC474014
0.7463 Intermediate Similarity NPC57846
0.726 Intermediate Similarity NPC28959
0.726 Intermediate Similarity NPC285014
0.726 Intermediate Similarity NPC299603
0.726 Intermediate Similarity NPC255535
0.726 Intermediate Similarity NPC137554
0.7121 Intermediate Similarity NPC65832
0.7121 Intermediate Similarity NPC10262
0.7121 Intermediate Similarity NPC311668
0.7083 Intermediate Similarity NPC471418
0.6986 Remote Similarity NPC268922
0.6923 Remote Similarity NPC277072
0.6923 Remote Similarity NPC178263
0.6912 Remote Similarity NPC170172
0.6912 Remote Similarity NPC233364
0.6912 Remote Similarity NPC471421
0.6905 Remote Similarity NPC52533
0.6866 Remote Similarity NPC293551
0.68 Remote Similarity NPC476694
0.68 Remote Similarity NPC476695
0.68 Remote Similarity NPC476696
0.6707 Remote Similarity NPC165119
0.6667 Remote Similarity NPC272396
0.6667 Remote Similarity NPC223386
0.6667 Remote Similarity NPC471780
0.6667 Remote Similarity NPC142290
0.6667 Remote Similarity NPC471892
0.6667 Remote Similarity NPC198341
0.6667 Remote Similarity NPC75435
0.662 Remote Similarity NPC145627
0.6618 Remote Similarity NPC8979
0.6575 Remote Similarity NPC315980
0.6575 Remote Similarity NPC286851
0.6575 Remote Similarity NPC303798
0.6429 Remote Similarity NPC290106
0.6429 Remote Similarity NPC193593
0.6429 Remote Similarity NPC76726
0.6429 Remote Similarity NPC143809
0.6395 Remote Similarity NPC306838
0.6389 Remote Similarity NPC17455
0.6389 Remote Similarity NPC69669
0.6389 Remote Similarity NPC150680
0.6389 Remote Similarity NPC218150
0.6389 Remote Similarity NPC2432
0.6389 Remote Similarity NPC306462
0.6389 Remote Similarity NPC22774
0.6341 Remote Similarity NPC83248
0.6341 Remote Similarity NPC100204
0.6304 Remote Similarity NPC313821
0.6296 Remote Similarity NPC233108
0.622 Remote Similarity NPC150557
0.6216 Remote Similarity NPC160661
0.6203 Remote Similarity NPC315806
0.6184 Remote Similarity NPC195165
0.6176 Remote Similarity NPC270041
0.6071 Remote Similarity NPC471420
0.6056 Remote Similarity NPC204709
0.6029 Remote Similarity NPC123814
0.6027 Remote Similarity NPC112398
0.5979 Remote Similarity NPC314387
0.5977 Remote Similarity NPC277918
0.5972 Remote Similarity NPC319991
0.5949 Remote Similarity NPC477200
0.5909 Remote Similarity NPC469363
0.5909 Remote Similarity NPC29222
0.5909 Remote Similarity NPC121062
0.5909 Remote Similarity NPC96966
0.589 Remote Similarity NPC328786
0.589 Remote Similarity NPC474627
0.589 Remote Similarity NPC201338
0.5854 Remote Similarity NPC470782
0.5814 Remote Similarity NPC271772
0.5814 Remote Similarity NPC36927
0.5802 Remote Similarity NPC126186
0.58 Remote Similarity NPC471844
0.5797 Remote Similarity NPC474322
0.5783 Remote Similarity NPC329077
0.5714 Remote Similarity NPC322966
0.5714 Remote Similarity NPC275715
0.5679 Remote Similarity NPC29326
0.5676 Remote Similarity NPC319131
0.5663 Remote Similarity NPC217095
0.5663 Remote Similarity NPC264417
0.5647 Remote Similarity NPC98750
0.5641 Remote Similarity NPC196359
0.5641 Remote Similarity NPC221764
0.5641 Remote Similarity NPC135539
0.5641 Remote Similarity NPC78312
0.5634 Remote Similarity NPC471917
0.5632 Remote Similarity NPC81006
0.5625 Remote Similarity NPC223174
0.5625 Remote Similarity NPC327486
0.5625 Remote Similarity NPC327753

  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 NPC184150 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
0.9524 High Similarity NPD9444 Discontinued
0.8462 Intermediate Similarity NPD9440 Discontinued
0.8358 Intermediate Similarity NPD9443 Clinical (unspecified phase)
0.7313 Intermediate Similarity NPD9455 Approved
0.7206 Intermediate Similarity NPD393 Approved
0.7125 Intermediate Similarity NPD882 Phase 2
0.7125 Intermediate Similarity NPD883 Phase 2
0.6571 Remote Similarity NPD9240 Approved
0.6571 Remote Similarity NPD9239 Approved
0.6389 Remote Similarity NPD9026 Phase 2
0.6389 Remote Similarity NPD9028 Phase 2
0.6389 Remote Similarity NPD9029 Phase 3
0.6389 Remote Similarity NPD9027 Phase 3
0.6304 Remote Similarity NPD3191 Approved
0.6304 Remote Similarity NPD3189 Approved
0.6304 Remote Similarity NPD3190 Approved
0.6216 Remote Similarity NPD1457 Discontinued
0.6203 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6092 Remote Similarity NPD394 Phase 3
0.6029 Remote Similarity NPD3215 Phase 1
0.5979 Remote Similarity NPD3185 Approved
0.5979 Remote Similarity NPD3184 Approved
0.5979 Remote Similarity NPD3183 Approved
0.5979 Remote Similarity NPD3182 Approved
0.5976 Remote Similarity NPD372 Clinical (unspecified phase)
0.5823 Remote Similarity NPD2220 Clinical (unspecified phase)
0.5814 Remote Similarity NPD2691 Clinical (unspecified phase)
0.5811 Remote Similarity NPD9024 Phase 2
0.5811 Remote Similarity NPD3192 Approved
0.5811 Remote Similarity NPD3193 Approved
0.5811 Remote Similarity NPD9022 Phase 2
0.5795 Remote Similarity NPD9401 Discovery
0.5778 Remote Similarity NPD3177 Phase 3
0.5735 Remote Similarity NPD3214 Discontinued
0.573 Remote Similarity NPD3723 Clinical (unspecified phase)
0.5679 Remote Similarity NPD3187 Discontinued
0.5663 Remote Similarity NPD9407 Approved
0.5641 Remote Similarity NPD8868 Approved
0.5625 Remote Similarity NPD9445 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