Structure

Physi-Chem Properties

Molecular Weight:  98.04
Volume:  98.787
LogP:  0.382
LogD:  0.645
LogS:  -1.066
# Rotatable Bonds:  0
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.325
Synthetic Accessibility Score:  3.413
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.289
MDCK Permeability:  5.432522812043317e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.109

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.456
Plasma Protein Binding (PPB):  24.784055709838867%
Volume Distribution (VD):  0.834
Pgp-substrate:  73.36454772949219%

ADMET: Metabolism

CYP1A2-inhibitor:  0.917
CYP1A2-substrate:  0.361
CYP2C19-inhibitor:  0.336
CYP2C19-substrate:  0.334
CYP2C9-inhibitor:  0.087
CYP2C9-substrate:  0.198
CYP2D6-inhibitor:  0.025
CYP2D6-substrate:  0.401
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.212

ADMET: Excretion

Clearance (CL):  9.198
Half-life (T1/2):  0.783

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.037
Drug-inuced Liver Injury (DILI):  0.236
AMES Toxicity:  0.25
Rat Oral Acute Toxicity:  0.053
Maximum Recommended Daily Dose:  0.026
Skin Sensitization:  0.866
Carcinogencity:  0.477
Eye Corrosion:  0.924
Eye Irritation:  0.991
Respiratory Toxicity:  0.202

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

  Natural Product: NPC40805

Natural Product ID:  NPC40805
Common Name*:   Tulipaline A
IUPAC Name:   3-methylideneoxolan-2-one
Synonyms:  
Standard InCHIKey:  GSLDEZOOOSBFGP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H6O2/c1-4-2-3-7-5(4)6/h1-3H2
SMILES:  C=C1CCOC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL275748
PubChem CID:   68352
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO11984 Tulipa gesneriana Species Liliaceae Eukaryota n.a. n.a. n.a. PMID[25126881]
NPO17118 Toronia toru Species Proteaceae Eukaryota n.a. New Zealand n.a. PMID[9214736]
NPO11984 Tulipa gesneriana Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11984 Tulipa gesneriana Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11984 Tulipa gesneriana Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11984 Tulipa gesneriana Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17118 Toronia toru Species Proteaceae 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
NPT308 Cell Line CAKI-1 Homo sapiens LC50 = 55400.0 nM PMID[496942]
NPT308 Cell Line CAKI-1 Homo sapiens LC50 = 49200.0 nM PMID[496942]
NPT308 Cell Line CAKI-1 Homo sapiens Fold selectivity = 1.13 n.a. PMID[496942]
NPT308 Cell Line CAKI-1 Homo sapiens Fold selectivity = 1.41 n.a. PMID[496942]
NPT168 Cell Line P388 Mus musculus IC50 = 0.8 ug.mL-1 PMID[496943]
NPT116 Cell Line HL-60 Homo sapiens IC50 = 35000.0 nM PMID[496945]
NPT91 Cell Line KB Homo sapiens ED50 = 15.0 ug ml-1 PMID[496947]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 0.09 mg ml-1 PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 0.17 mg ml-1 PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 0.01 mg ml-1 PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 0.04 mg ml-1 PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 0.1 mg ml-1 PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 0.32 mg ml-1 PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 0.7 mg ml-1 PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 0.39 mg ml-1 PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 47.9 % PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 33.5 % PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 22.2 % PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 38.8 % PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 57.2 % PMID[496938]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 71.6 % PMID[496938]
NPT938 Organism Cavia porcellus Cavia porcellus Average skin reaction = 2.0 n.a. PMID[496939]
NPT938 Organism Cavia porcellus Cavia porcellus Sensitized animals = 6.0 n.a. PMID[496939]
NPT938 Organism Cavia porcellus Cavia porcellus Average skin reaction = 1.1 n.a. PMID[496939]
NPT938 Organism Cavia porcellus Cavia porcellus Average skin reaction = 0.0 n.a. PMID[496939]
NPT938 Organism Cavia porcellus Cavia porcellus Sensitized animals = 0.0 n.a. PMID[496939]
NPT938 Organism Cavia porcellus Cavia porcellus Average skin reaction = 0.1 n.a. PMID[496940]
NPT938 Organism Cavia porcellus Cavia porcellus No. of sensitive = 1.0 n.a. PMID[496940]
NPT938 Organism Cavia porcellus Cavia porcellus Average skin reaction = 1.9 n.a. PMID[496940]
NPT938 Organism Cavia porcellus Cavia porcellus No. of sensitive = 10.0 n.a. PMID[496940]
NPT29 Organism Rattus norvegicus Rattus norvegicus Cytoprotective effect = 0.25 n.a. PMID[496941]
NPT2 Others Unspecified LC50 = 39300.0 nM PMID[496942]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 10.0 mm PMID[496943]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 0.0 mm PMID[496943]
NPT19 Organism Escherichia coli Escherichia coli IZ = 5.0 mm PMID[496943]
NPT19 Organism Escherichia coli Escherichia coli IZ = 0.0 mm PMID[496943]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 4.0 mm PMID[496943]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 0.0 mm PMID[496943]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes IZ = 8.0 mm PMID[496943]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes IZ = 0.0 mm PMID[496943]
NPT27 Others Unspecified Activity = 100.0 % PMID[496943]
NPT35 Others n.a. T1/2 = 25.0 hr PMID[496944]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 5.0 % PMID[496944]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 28800.0 nM PMID[496945]
NPT2720 Organism Nilaparvata lugens Nilaparvata lugens mortality = 30.0 % PMID[496946]
NPT2720 Organism Nilaparvata lugens Nilaparvata lugens mortality = 0.0 % PMID[496946]
NPT1175 Organism Spodoptera litura Spodoptera litura mortality = 20.0 % PMID[496946]
NPT1175 Organism Spodoptera litura Spodoptera litura mortality = 0.0 % PMID[496946]
NPT849 Organism Plutella xylostella Plutella xylostella mortality = 50.0 % PMID[496946]
NPT849 Organism Plutella xylostella Plutella xylostella mortality = 0.0 % PMID[496946]
NPT352 Organism Frankliniella occidentalis Frankliniella occidentalis mortality = 100.0 % PMID[496946]
NPT352 Organism Frankliniella occidentalis Frankliniella occidentalis mortality = 52.0 % PMID[496946]
NPT352 Organism Frankliniella occidentalis Frankliniella occidentalis mortality = 12.0 % PMID[496946]
NPT352 Organism Frankliniella occidentalis Frankliniella occidentalis mortality = 8.0 % PMID[496946]
NPT352 Organism Frankliniella occidentalis Frankliniella occidentalis mortality = 4.0 % PMID[496946]
NPT26291 ORGANISM Frankliniella intonsa Frankliniella intonsa mortality = 100.0 % PMID[496946]
NPT26291 ORGANISM Frankliniella intonsa Frankliniella intonsa mortality = 94.0 % PMID[496946]
NPT26291 ORGANISM Frankliniella intonsa Frankliniella intonsa mortality = 70.0 % PMID[496946]
NPT26291 ORGANISM Frankliniella intonsa Frankliniella intonsa mortality = 76.0 % PMID[496946]
NPT26291 ORGANISM Frankliniella intonsa Frankliniella intonsa mortality = 66.0 % PMID[496946]
NPT26291 ORGANISM Frankliniella intonsa Frankliniella intonsa mortality = 58.0 % PMID[496946]
NPT26291 ORGANISM Frankliniella intonsa Frankliniella intonsa mortality = 48.0 % PMID[496946]
NPT26291 ORGANISM Frankliniella intonsa Frankliniella intonsa mortality = 34.0 % PMID[496946]
NPT26291 ORGANISM Frankliniella intonsa Frankliniella intonsa mortality = 0.0 % PMID[496946]
NPT26292 ORGANISM Thrips palmi Thrips palmi mortality = 100.0 % PMID[496946]
NPT26292 ORGANISM Thrips palmi Thrips palmi mortality = 80.0 % PMID[496946]
NPT26292 ORGANISM Thrips palmi Thrips palmi mortality = 94.0 % PMID[496946]
NPT26292 ORGANISM Thrips palmi Thrips palmi mortality = 56.0 % PMID[496946]
NPT26292 ORGANISM Thrips palmi Thrips palmi mortality = 90.0 % PMID[496946]
NPT26292 ORGANISM Thrips palmi Thrips palmi mortality = 70.0 % PMID[496946]
NPT26292 ORGANISM Thrips palmi Thrips palmi mortality = 14.0 % PMID[496946]
NPT26292 ORGANISM Thrips palmi Thrips palmi mortality = 20.0 % PMID[496946]
NPT26292 ORGANISM Thrips palmi Thrips palmi mortality = 2.0 % PMID[496946]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. ED50 = 16.0 ug ml-1 PMID[496948]
NPT35 Others n.a. K = 1.3 10'-4/M/s PMID[496949]

☑ 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 NPC40805 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
0.9268 High Similarity NPC190649
0.6957 Remote Similarity NPC159773
0.6897 Remote Similarity NPC474658
0.6875 Remote Similarity NPC312547
0.6863 Remote Similarity NPC15789
0.6809 Remote Similarity NPC169098
0.6667 Remote Similarity NPC135698
0.6591 Remote Similarity NPC65353
0.6538 Remote Similarity NPC236338
0.6531 Remote Similarity NPC51329
0.6522 Remote Similarity NPC147824
0.65 Remote Similarity NPC234005
0.6471 Remote Similarity NPC68577
0.6452 Remote Similarity NPC194871
0.6441 Remote Similarity NPC151648
0.6349 Remote Similarity NPC470256
0.6346 Remote Similarity NPC223675
0.6271 Remote Similarity NPC309408
0.625 Remote Similarity NPC476591
0.625 Remote Similarity NPC88877
0.6222 Remote Similarity NPC9290
0.6136 Remote Similarity NPC63354
0.6102 Remote Similarity NPC286189
0.6078 Remote Similarity NPC26600
0.6078 Remote Similarity NPC47946
0.6066 Remote Similarity NPC473737
0.6066 Remote Similarity NPC68110
0.6061 Remote Similarity NPC163003
0.6038 Remote Similarity NPC122212
0.6038 Remote Similarity NPC137419
0.6032 Remote Similarity NPC248125
0.6 Remote Similarity NPC130953
0.6 Remote Similarity NPC98519
0.6 Remote Similarity NPC79756
0.597 Remote Similarity NPC269206
0.597 Remote Similarity NPC58956
0.597 Remote Similarity NPC295633
0.5965 Remote Similarity NPC173157
0.5962 Remote Similarity NPC197467
0.5938 Remote Similarity NPC203335
0.5938 Remote Similarity NPC21998
0.5926 Remote Similarity NPC275316
0.5882 Remote Similarity NPC140287
0.5882 Remote Similarity NPC476590
0.5882 Remote Similarity NPC476355
0.5882 Remote Similarity NPC48641
0.5882 Remote Similarity NPC143979
0.5882 Remote Similarity NPC320537
0.5882 Remote Similarity NPC114727
0.5873 Remote Similarity NPC131174
0.5862 Remote Similarity NPC51846
0.5854 Remote Similarity NPC283626
0.5806 Remote Similarity NPC210303
0.5806 Remote Similarity NPC44343
0.5806 Remote Similarity NPC179087
0.5806 Remote Similarity NPC2328
0.58 Remote Similarity NPC57923
0.58 Remote Similarity NPC187922
0.5797 Remote Similarity NPC193351
0.5797 Remote Similarity NPC155587
0.5797 Remote Similarity NPC138408
0.5797 Remote Similarity NPC161038
0.5797 Remote Similarity NPC226669
0.5778 Remote Similarity NPC217161
0.5769 Remote Similarity NPC172042
0.5769 Remote Similarity NPC270706
0.5763 Remote Similarity NPC135863
0.5763 Remote Similarity NPC293437
0.5763 Remote Similarity NPC249850
0.5714 Remote Similarity NPC151919
0.5714 Remote Similarity NPC123357
0.5714 Remote Similarity NPC123360
0.5714 Remote Similarity NPC68819
0.5714 Remote Similarity NPC127118
0.5714 Remote Similarity NPC281043
0.5714 Remote Similarity NPC209113
0.5714 Remote Similarity NPC301207
0.5714 Remote Similarity NPC203382
0.5714 Remote Similarity NPC235906
0.5714 Remote Similarity NPC191643
0.569 Remote Similarity NPC478117
0.5672 Remote Similarity NPC202011
0.5667 Remote Similarity NPC189700
0.5667 Remote Similarity NPC21946
0.5667 Remote Similarity NPC254095
0.566 Remote Similarity NPC87137
0.566 Remote Similarity NPC128280
0.5652 Remote Similarity NPC122676
0.5645 Remote Similarity NPC220894
0.5636 Remote Similarity NPC27264
0.5634 Remote Similarity NPC320630
0.5634 Remote Similarity NPC470240
0.5634 Remote Similarity NPC171204
0.5634 Remote Similarity NPC51809
0.5634 Remote Similarity NPC141789
0.5634 Remote Similarity NPC187568
0.5634 Remote Similarity NPC116177
0.5634 Remote Similarity NPC49302
0.5634 Remote Similarity NPC476028
0.5634 Remote Similarity NPC176329
0.5634 Remote Similarity NPC275530
0.5634 Remote Similarity NPC208223
0.5634 Remote Similarity NPC41780
0.5634 Remote Similarity NPC474818
0.5634 Remote Similarity NPC125365
0.5634 Remote Similarity NPC7563
0.5634 Remote Similarity NPC97516
0.5634 Remote Similarity NPC65603
0.5634 Remote Similarity NPC476794
0.5625 Remote Similarity NPC226511
0.5625 Remote Similarity NPC133904
0.5625 Remote Similarity NPC182794
0.5606 Remote Similarity NPC287705
0.5606 Remote Similarity NPC218477

  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 NPC40805 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
0.6415 Remote Similarity NPD6927 Phase 3
0.64 Remote Similarity NPD9378 Approved
0.6042 Remote Similarity NPD8839 Phase 3
0.5926 Remote Similarity NPD9437 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