Structure

Physi-Chem Properties

Molecular Weight:  203.12
Volume:  193.265
LogP:  -1.395
LogD:  -0.61
LogS:  -0.005
# Rotatable Bonds:  1
TPSA:  84.16
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.392
Synthetic Accessibility Score:  4.638
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:  -5.275
MDCK Permeability:  6.588660471607e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.961
Human Intestinal Absorption (HIA):  0.9
20% Bioavailability (F20%):  0.073
30% Bioavailability (F30%):  0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.213
Plasma Protein Binding (PPB):  16.93056869506836%
Volume Distribution (VD):  0.371
Pgp-substrate:  81.20479583740234%

ADMET: Metabolism

CYP1A2-inhibitor:  0.023
CYP1A2-substrate:  0.066
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.14
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.192
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.235
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.051

ADMET: Excretion

Clearance (CL):  3.938
Half-life (T1/2):  0.804

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.512
Drug-inuced Liver Injury (DILI):  0.641
AMES Toxicity:  0.059
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.045
Skin Sensitization:  0.44
Carcinogencity:  0.027
Eye Corrosion:  0.033
Eye Irritation:  0.207
Respiratory Toxicity:  0.863

Download Data

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

  Natural Product: NPC254617

Natural Product ID:  NPC254617
Common Name*:   Hyacinthacine B5
IUPAC Name:   (1S,2R,3R,5R,7S,8R)-3-(hydroxymethyl)-5-methyl-2,3,5,6,7,8-hexahydro-1H-pyrrolizine-1,2,7-triol
Synonyms:   Hyacinthacine B5
Standard InCHIKey:  PIBHCJDPQRCONN-MWRHRVLASA-N
Standard InCHI:  InChI=1S/C9H17NO4/c1-4-2-6(12)7-9(14)8(13)5(3-11)10(4)7/h4-9,11-14H,2-3H2,1H3/t4-,5-,6+,7-,8-,9+/m1/s1
SMILES:  OC[C@@H]1[C@@H](O)[C@H]([C@@H]2N1[C@H](C)C[C@@H]2O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL497927
PubChem CID:   11009014
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
NPO33353 scilla sibirica Species Hyacinthaceae Eukaryota n.a. n.a. n.a. PMID[12502331]

☑ 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
NPT2 Others Unspecified IC50 = 110000.0 nM PMID[480994]

☑ 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 NPC254617 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 NPC74555
1.0 High Similarity NPC306763
1.0 High Similarity NPC266242
0.9841 High Similarity NPC473419
0.9841 High Similarity NPC475715
0.9841 High Similarity NPC475127
0.9839 High Similarity NPC59221
0.9839 High Similarity NPC141156
0.9839 High Similarity NPC184150
0.9688 High Similarity NPC115800
0.9688 High Similarity NPC163538
0.9683 High Similarity NPC474469
0.9677 High Similarity NPC12514
0.9677 High Similarity NPC294883
0.8333 Intermediate Similarity NPC233034
0.8261 Intermediate Similarity NPC475694
0.8261 Intermediate Similarity NPC473710
0.8235 Intermediate Similarity NPC34291
0.8235 Intermediate Similarity NPC126664
0.8065 Intermediate Similarity NPC471442
0.8065 Intermediate Similarity NPC275727
0.8065 Intermediate Similarity NPC471423
0.806 Intermediate Similarity NPC474928
0.7812 Intermediate Similarity NPC471605
0.7812 Intermediate Similarity NPC471443
0.7778 Intermediate Similarity NPC474468
0.7714 Intermediate Similarity NPC171850
0.7681 Intermediate Similarity NPC116377
0.7681 Intermediate Similarity NPC101746
0.7681 Intermediate Similarity NPC77191
0.7681 Intermediate Similarity NPC69798
0.7681 Intermediate Similarity NPC473952
0.7647 Intermediate Similarity NPC471419
0.7647 Intermediate Similarity NPC163134
0.7612 Intermediate Similarity NPC57846
0.7612 Intermediate Similarity NPC474014
0.7612 Intermediate Similarity NPC30126
0.7612 Intermediate Similarity NPC8087
0.7612 Intermediate Similarity NPC62507
0.7162 Intermediate Similarity NPC255535
0.7162 Intermediate Similarity NPC285014
0.7162 Intermediate Similarity NPC299603
0.7162 Intermediate Similarity NPC137554
0.7162 Intermediate Similarity NPC28959
0.7123 Intermediate Similarity NPC268922
0.7077 Intermediate Similarity NPC277072
0.7077 Intermediate Similarity NPC178263
0.7059 Intermediate Similarity NPC471421
0.7059 Intermediate Similarity NPC233364
0.7059 Intermediate Similarity NPC170172
0.7024 Intermediate Similarity NPC52533
0.7015 Intermediate Similarity NPC293551
0.7015 Intermediate Similarity NPC311668
0.7015 Intermediate Similarity NPC65832
0.7015 Intermediate Similarity NPC10262
0.6986 Remote Similarity NPC471418
0.6933 Remote Similarity NPC476696
0.6933 Remote Similarity NPC476695
0.6933 Remote Similarity NPC476694
0.6765 Remote Similarity NPC8979
0.6761 Remote Similarity NPC145627
0.6712 Remote Similarity NPC303798
0.6712 Remote Similarity NPC286851
0.6627 Remote Similarity NPC165119
0.6575 Remote Similarity NPC471892
0.6575 Remote Similarity NPC471780
0.6575 Remote Similarity NPC223386
0.6575 Remote Similarity NPC142290
0.6575 Remote Similarity NPC75435
0.6575 Remote Similarity NPC198341
0.6567 Remote Similarity NPC272396
0.6528 Remote Similarity NPC17455
0.6486 Remote Similarity NPC315980
0.642 Remote Similarity NPC233108
0.6413 Remote Similarity NPC313821
0.6351 Remote Similarity NPC160661
0.6341 Remote Similarity NPC150557
0.6338 Remote Similarity NPC290106
0.6338 Remote Similarity NPC143809
0.6338 Remote Similarity NPC76726
0.6338 Remote Similarity NPC193593
0.6324 Remote Similarity NPC270041
0.6322 Remote Similarity NPC306838
0.6316 Remote Similarity NPC195165
0.6301 Remote Similarity NPC69669
0.6301 Remote Similarity NPC218150
0.6301 Remote Similarity NPC150680
0.6301 Remote Similarity NPC2432
0.6301 Remote Similarity NPC306462
0.6301 Remote Similarity NPC22774
0.6265 Remote Similarity NPC83248
0.6265 Remote Similarity NPC100204
0.6197 Remote Similarity NPC204709
0.619 Remote Similarity NPC471420
0.6176 Remote Similarity NPC123814
0.6125 Remote Similarity NPC315806
0.6111 Remote Similarity NPC319991
0.6092 Remote Similarity NPC277918
0.6082 Remote Similarity NPC314387
0.6076 Remote Similarity NPC477200
0.6061 Remote Similarity NPC96966
0.6061 Remote Similarity NPC29222
0.6061 Remote Similarity NPC121062
0.6027 Remote Similarity NPC328786
0.6027 Remote Similarity NPC474627
0.6027 Remote Similarity NPC201338
0.5946 Remote Similarity NPC112398
0.5942 Remote Similarity NPC474322
0.5926 Remote Similarity NPC126186
0.59 Remote Similarity NPC471844
0.5843 Remote Similarity NPC469363
0.5824 Remote Similarity NPC322966
0.5811 Remote Similarity NPC319131
0.5783 Remote Similarity NPC264417
0.5783 Remote Similarity NPC217095
0.5783 Remote Similarity NPC470782
0.5775 Remote Similarity NPC471917
0.575 Remote Similarity NPC327753
0.575 Remote Similarity NPC327486
0.575 Remote Similarity NPC223174
0.5747 Remote Similarity NPC36927
0.5747 Remote Similarity NPC271772
0.5714 Remote Similarity NPC329077
0.5714 Remote Similarity NPC472609
0.5698 Remote Similarity NPC216090
0.5679 Remote Similarity NPC306973
0.5652 Remote Similarity NPC275715
0.5645 Remote Similarity NPC166030
0.5641 Remote Similarity NPC238646
0.5632 Remote Similarity NPC470783
0.561 Remote Similarity NPC29326

  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 NPC254617 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
0.9375 High Similarity NPD9444 Discontinued
0.8333 Intermediate Similarity NPD9440 Discontinued
0.8235 Intermediate Similarity NPD9443 Clinical (unspecified phase)
0.7353 Intermediate Similarity NPD393 Approved
0.725 Intermediate Similarity NPD883 Phase 2
0.725 Intermediate Similarity NPD882 Phase 2
0.7206 Intermediate Similarity NPD9455 Approved
0.6714 Remote Similarity NPD9239 Approved
0.6714 Remote Similarity NPD9240 Approved
0.6413 Remote Similarity NPD3189 Approved
0.6413 Remote Similarity NPD3191 Approved
0.6413 Remote Similarity NPD3190 Approved
0.6351 Remote Similarity NPD1457 Discontinued
0.6301 Remote Similarity NPD9026 Phase 2
0.6301 Remote Similarity NPD9028 Phase 2
0.6301 Remote Similarity NPD9027 Phase 3
0.6301 Remote Similarity NPD9029 Phase 3
0.6176 Remote Similarity NPD3215 Phase 1
0.6125 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6082 Remote Similarity NPD3182 Approved
0.6082 Remote Similarity NPD3183 Approved
0.6082 Remote Similarity NPD3185 Approved
0.6082 Remote Similarity NPD3184 Approved
0.6023 Remote Similarity NPD394 Phase 3
0.593 Remote Similarity NPD2691 Clinical (unspecified phase)
0.5904 Remote Similarity NPD372 Clinical (unspecified phase)
0.5889 Remote Similarity NPD3177 Phase 3
0.5882 Remote Similarity NPD3214 Discontinued
0.5843 Remote Similarity NPD3723 Clinical (unspecified phase)
0.5802 Remote Similarity NPD3187 Discontinued
0.575 Remote Similarity NPD2220 Clinical (unspecified phase)
0.575 Remote Similarity NPD9445 Approved
0.5733 Remote Similarity NPD3193 Approved
0.5733 Remote Similarity NPD9024 Phase 2
0.5733 Remote Similarity NPD9022 Phase 2
0.5733 Remote Similarity NPD3192 Approved
0.573 Remote Similarity NPD9401 Discovery
0.5679 Remote Similarity NPD9446 Approved
0.5673 Remote Similarity NPD3188 Approved
0.5616 Remote Similarity NPD6439 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