Structure

Physi-Chem Properties

Molecular Weight:  279.22
Volume:  302.86
LogP:  4.061
LogD:  3.972
LogS:  -3.836
# Rotatable Bonds:  3
TPSA:  29.54
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.743
Synthetic Accessibility Score:  4.116
Fsp3:  0.941
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.6
MDCK Permeability:  4.422438723850064e-05
Pgp-inhibitor:  0.171
Pgp-substrate:  0.021
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.817
30% Bioavailability (F30%):  0.613

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.356
Plasma Protein Binding (PPB):  54.652305603027344%
Volume Distribution (VD):  1.56
Pgp-substrate:  45.51990509033203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.04
CYP1A2-substrate:  0.094
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.894
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.115
CYP2D6-inhibitor:  0.842
CYP2D6-substrate:  0.805
CYP3A4-inhibitor:  0.585
CYP3A4-substrate:  0.558

ADMET: Excretion

Clearance (CL):  9.896
Half-life (T1/2):  0.2

ADMET: Toxicity

hERG Blockers:  0.269
Human Hepatotoxicity (H-HT):  0.633
Drug-inuced Liver Injury (DILI):  0.804
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.038
Maximum Recommended Daily Dose:  0.325
Skin Sensitization:  0.951
Carcinogencity:  0.284
Eye Corrosion:  0.553
Eye Irritation:  0.8
Respiratory Toxicity:  0.94

Download Data

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

  Natural Product: NPC216090

Natural Product ID:  NPC216090
Common Name*:   Stemaphylline
IUPAC Name:   (3R,5S)-5-[(2R)-2-[(9R,9aS)-2,3,5,6,7,8,9,9a-octahydro-1H-pyrrolo[1,2-a]azepin-9-yl]propyl]-3-methyloxolan-2-one
Synonyms:   stemaphylline
Standard InCHIKey:  MQYIKLXMSSMGLX-LJIZCISZSA-N
Standard InCHI:  InChI=1S/C17H29NO2/c1-12(10-14-11-13(2)17(19)20-14)15-6-3-4-8-18-9-5-7-16(15)18/h12-16H,3-11H2,1-2H3/t12-,13-,14+,15-,16+/m1/s1
SMILES:  C[C@H](C[C@H]1C[C@@H](C)C(=O)O1)[C@H]1CCCCN2CCC[C@@H]12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL563774
PubChem CID:   44139893
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001990] Pyrroloazepines

*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
NPO221 Stemona aphylla Species Stemonaceae Eukaryota Roots; Stems n.a. n.a. PMID[19374387]
NPO221 Stemona aphylla Species Stemonaceae Eukaryota Stems n.a. n.a. PMID[20415428]
NPO221 Stemona aphylla Species Stemonaceae Eukaryota n.a. root n.a. PMID[21126060]
NPO221 Stemona aphylla Species Stemonaceae Eukaryota Roots Lampang Province, Thailand 2009-APR PMID[21126060]
NPO221 Stemona aphylla Species Stemonaceae Eukaryota n.a. n.a. n.a. PMID[21902195]
NPO866 Heliomeris longifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28187 Duguetia confinis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10593 Aspergillus pulvinus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13984 Helenium radiatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9624 Myoporum bontioides Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO221 Stemona aphylla Species Stemonaceae 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
NPT204 Individual Protein Acetylcholinesterase Homo sapiens Activity = 0.18 nmol PMID[476769]
NPT849 Organism Plutella xylostella Plutella xylostella LC50 = 1824.0 ug.mL-1 PMID[476769]
NPT19 Organism Escherichia coli Escherichia coli MIC = 62.5 ug.mL-1 PMID[476769]
NPT19 Organism Escherichia coli Escherichia coli MBC = 125.0 ug ml-1 PMID[476769]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 125.0 ug.mL-1 PMID[476769]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MBC = 250.0 ug ml-1 PMID[476769]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 62.5 ug.mL-1 PMID[476769]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MBC = 125.0 ug ml-1 PMID[476769]
NPT20 Organism Candida albicans Candida albicans MIC = 125.0 ug.mL-1 PMID[476769]
NPT20 Organism Candida albicans Candida albicans MFC = 125.0 ug ml-1 PMID[476769]

☑ 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 NPC216090 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
0.8202 Intermediate Similarity NPC471843
0.7766 Intermediate Similarity NPC233274
0.7766 Intermediate Similarity NPC287638
0.7766 Intermediate Similarity NPC194750
0.7526 Intermediate Similarity NPC471844
0.7473 Intermediate Similarity NPC469998
0.7356 Intermediate Similarity NPC277918
0.7222 Intermediate Similarity NPC322966
0.7033 Intermediate Similarity NPC203170
0.697 Remote Similarity NPC265094
0.6941 Remote Similarity NPC233108
0.6887 Remote Similarity NPC39041
0.6887 Remote Similarity NPC471846
0.6887 Remote Similarity NPC471845
0.6887 Remote Similarity NPC202722
0.6887 Remote Similarity NPC241294
0.6759 Remote Similarity NPC174463
0.6702 Remote Similarity NPC476019
0.6636 Remote Similarity NPC230849
0.6636 Remote Similarity NPC11379
0.6602 Remote Similarity NPC271562
0.6559 Remote Similarity NPC52533
0.6509 Remote Similarity NPC58281
0.6494 Remote Similarity NPC319991
0.6471 Remote Similarity NPC97336
0.6301 Remote Similarity NPC305182
0.6273 Remote Similarity NPC470538
0.6239 Remote Similarity NPC173173
0.622 Remote Similarity NPC157518
0.6216 Remote Similarity NPC314084
0.6134 Remote Similarity NPC215507
0.6133 Remote Similarity NPC471607
0.6117 Remote Similarity NPC474348
0.6092 Remote Similarity NPC208657
0.604 Remote Similarity NPC134504
0.604 Remote Similarity NPC47076
0.6024 Remote Similarity NPC322319
0.6024 Remote Similarity NPC326651
0.6024 Remote Similarity NPC325117
0.6019 Remote Similarity NPC469388
0.6019 Remote Similarity NPC472737
0.6019 Remote Similarity NPC469389
0.6 Remote Similarity NPC477145
0.6 Remote Similarity NPC473741
0.598 Remote Similarity NPC472736
0.5977 Remote Similarity NPC470243
0.5963 Remote Similarity NPC63511
0.5941 Remote Similarity NPC150041
0.5932 Remote Similarity NPC474371
0.593 Remote Similarity NPC5714
0.5926 Remote Similarity NPC15413
0.5922 Remote Similarity NPC220234
0.5904 Remote Similarity NPC314103
0.5897 Remote Similarity NPC473477
0.5889 Remote Similarity NPC330017
0.5888 Remote Similarity NPC233256
0.5888 Remote Similarity NPC195841
0.587 Remote Similarity NPC474702
0.5859 Remote Similarity NPC312637
0.5856 Remote Similarity NPC469466
0.5856 Remote Similarity NPC76660
0.5856 Remote Similarity NPC276995
0.5851 Remote Similarity NPC47135
0.5847 Remote Similarity NPC469999
0.5825 Remote Similarity NPC476344
0.5823 Remote Similarity NPC471605
0.5823 Remote Similarity NPC471443
0.578 Remote Similarity NPC470535
0.5776 Remote Similarity NPC88190
0.5769 Remote Similarity NPC471442
0.5769 Remote Similarity NPC471423
0.5765 Remote Similarity NPC315525
0.5765 Remote Similarity NPC59221
0.5765 Remote Similarity NPC135043
0.5753 Remote Similarity NPC282440
0.5753 Remote Similarity NPC145045
0.5753 Remote Similarity NPC52700
0.5753 Remote Similarity NPC105329
0.5753 Remote Similarity NPC63182
0.5747 Remote Similarity NPC144511
0.5747 Remote Similarity NPC296522
0.5741 Remote Similarity NPC236644
0.5739 Remote Similarity NPC476952
0.5738 Remote Similarity NPC307165
0.573 Remote Similarity NPC475232
0.573 Remote Similarity NPC51249
0.573 Remote Similarity NPC475260
0.573 Remote Similarity NPC474100
0.573 Remote Similarity NPC473699
0.573 Remote Similarity NPC43219
0.573 Remote Similarity NPC473775
0.5728 Remote Similarity NPC476449
0.5727 Remote Similarity NPC470536
0.5714 Remote Similarity NPC324506
0.5714 Remote Similarity NPC477518
0.5714 Remote Similarity NPC239768
0.5714 Remote Similarity NPC128698
0.5714 Remote Similarity NPC43648
0.5714 Remote Similarity NPC160661
0.57 Remote Similarity NPC159568
0.5698 Remote Similarity NPC266242
0.5698 Remote Similarity NPC306763
0.5698 Remote Similarity NPC74555
0.5698 Remote Similarity NPC254617
0.5682 Remote Similarity NPC472955
0.5676 Remote Similarity NPC470530
0.5676 Remote Similarity NPC470531
0.5676 Remote Similarity NPC470532
0.5676 Remote Similarity NPC470529
0.5676 Remote Similarity NPC470528
0.5676 Remote Similarity NPC470527
0.5676 Remote Similarity NPC470533
0.5667 Remote Similarity NPC86064
0.5667 Remote Similarity NPC469641
0.5667 Remote Similarity NPC215030
0.5667 Remote Similarity NPC469643
0.5663 Remote Similarity NPC306750
0.5648 Remote Similarity NPC323720
0.5648 Remote Similarity NPC119329
0.5647 Remote Similarity NPC295256
0.5647 Remote Similarity NPC469926
0.5645 Remote Similarity NPC133089
0.5644 Remote Similarity NPC62263
0.5644 Remote Similarity NPC173763
0.5644 Remote Similarity NPC471098
0.5632 Remote Similarity NPC473419
0.5632 Remote Similarity NPC119838
0.5632 Remote Similarity NPC82315
0.5632 Remote Similarity NPC475127
0.5632 Remote Similarity NPC475715
0.5625 Remote Similarity NPC320936
0.5625 Remote Similarity NPC470534
0.562 Remote Similarity NPC280903
0.5618 Remote Similarity NPC477643
0.5618 Remote Similarity NPC477641
0.5618 Remote Similarity NPC320865
0.5616 Remote Similarity NPC273545
0.5607 Remote Similarity NPC301148
0.5607 Remote Similarity NPC124554
0.5607 Remote Similarity NPC5864
0.5604 Remote Similarity NPC228411
0.5604 Remote Similarity NPC179922
0.56 Remote Similarity NPC475801
0.56 Remote Similarity NPC474593

  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 NPC216090 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
0.7564 Intermediate Similarity NPD2697 Approved
0.7564 Intermediate Similarity NPD2696 Approved
0.7564 Intermediate Similarity NPD2694 Approved
0.7564 Intermediate Similarity NPD2695 Approved
0.6531 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6506 Remote Similarity NPD3726 Approved
0.6506 Remote Similarity NPD3725 Approved
0.63 Remote Similarity NPD3715 Approved
0.63 Remote Similarity NPD3714 Approved
0.63 Remote Similarity NPD3713 Approved
0.6292 Remote Similarity NPD617 Approved
0.602 Remote Similarity NPD2682 Approved
0.6 Remote Similarity NPD8143 Approved
0.6 Remote Similarity NPD8144 Approved
0.5851 Remote Similarity NPD883 Phase 2
0.5851 Remote Similarity NPD882 Phase 2
0.5851 Remote Similarity NPD7345 Approved
0.5816 Remote Similarity NPD4264 Clinical (unspecified phase)
0.5778 Remote Similarity NPD2257 Approved
0.5752 Remote Similarity NPD7916 Approved
0.5752 Remote Similarity NPD7915 Approved
0.5714 Remote Similarity NPD4272 Discontinued
0.569 Remote Similarity NPD7518 Approved
0.569 Remote Similarity NPD7517 Approved
0.569 Remote Similarity NPD7519 Approved
0.5688 Remote Similarity NPD8307 Discontinued
0.5688 Remote Similarity NPD8140 Approved
0.567 Remote Similarity NPD3723 Clinical (unspecified phase)
0.5663 Remote Similarity NPD9676 Phase 3
0.5647 Remote Similarity NPD9496 Clinical (unspecified phase)
0.5632 Remote Similarity NPD229 Approved
0.5618 Remote Similarity NPD2256 Clinical (unspecified phase)
0.561 Remote Similarity NPD3198 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