Structure

Physi-Chem Properties

Molecular Weight:  194.06
Volume:  194.938
LogP:  2.658
LogD:  2.321
LogS:  -2.212
# Rotatable Bonds:  3
TPSA:  70.67
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.723
Synthetic Accessibility Score:  3.333
Fsp3:  0.1
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.913
MDCK Permeability:  1.687897020019591e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.07
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.707

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.222
Plasma Protein Binding (PPB):  95.09822082519531%
Volume Distribution (VD):  0.368
Pgp-substrate:  8.012228012084961%

ADMET: Metabolism

CYP1A2-inhibitor:  0.041
CYP1A2-substrate:  0.093
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.05
CYP2C9-inhibitor:  0.159
CYP2C9-substrate:  0.477
CYP2D6-inhibitor:  0.017
CYP2D6-substrate:  0.23
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.073

ADMET: Excretion

Clearance (CL):  2.925
Half-life (T1/2):  0.925

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.752
Drug-inuced Liver Injury (DILI):  0.879
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.716
Maximum Recommended Daily Dose:  0.152
Skin Sensitization:  0.939
Carcinogencity:  0.498
Eye Corrosion:  0.312
Eye Irritation:  0.551
Respiratory Toxicity:  0.24

Download Data

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

  Natural Product: NPC189700

Natural Product ID:  NPC189700
Common Name*:   (E/Z)-Bombardolide C
IUPAC Name:   (E)-3-[(5Z)-2-oxo-5-propylidenefuran-3-yl]prop-2-enoic acid
Synonyms:   (E/Z)-Bombardolide C
Standard InCHIKey:  LNEPPGKBSBTFDF-GOZDTHDVSA-N
Standard InCHI:  InChI=1S/C10H10O4/c1-2-3-8-6-7(10(13)14-8)4-5-9(11)12/h3-6H,2H2,1H3,(H,11,12)/b5-4+,8-3-
SMILES:  CC/C=C1/C=C(/C=C/C(=O)O)C(=O)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL458419
PubChem CID:   10330245
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001983] Dihydrofurans
        • [CHEMONTID:0001982] Furanones
          • [CHEMONTID:0002223] Butenolides

*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
NPO5602 Bombardioidea anartia Species Lasiosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[11421752]

☑ 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
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 26.0 mm PMID[536670]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 18.0 mm PMID[536670]

☑ 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 NPC189700 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
0.9298 High Similarity NPC98519
0.9298 High Similarity NPC130953
0.8571 High Similarity NPC218486
0.8361 Intermediate Similarity NPC473737
0.8276 Intermediate Similarity NPC150717
0.8214 Intermediate Similarity NPC191643
0.8167 Intermediate Similarity NPC133600
0.7966 Intermediate Similarity NPC51846
0.7966 Intermediate Similarity NPC221763
0.7857 Intermediate Similarity NPC221467
0.7812 Intermediate Similarity NPC471566
0.7812 Intermediate Similarity NPC471565
0.7797 Intermediate Similarity NPC478117
0.7797 Intermediate Similarity NPC173157
0.7778 Intermediate Similarity NPC2328
0.7778 Intermediate Similarity NPC475073
0.7742 Intermediate Similarity NPC309408
0.7719 Intermediate Similarity NPC43053
0.7679 Intermediate Similarity NPC126184
0.7679 Intermediate Similarity NPC234084
0.7656 Intermediate Similarity NPC475618
0.7571 Intermediate Similarity NPC478192
0.7571 Intermediate Similarity NPC478195
0.7571 Intermediate Similarity NPC478193
0.7571 Intermediate Similarity NPC478196
0.7571 Intermediate Similarity NPC478194
0.7571 Intermediate Similarity NPC478191
0.7544 Intermediate Similarity NPC15789
0.7538 Intermediate Similarity NPC471556
0.75 Intermediate Similarity NPC59558
0.75 Intermediate Similarity NPC128520
0.75 Intermediate Similarity NPC179087
0.75 Intermediate Similarity NPC44343
0.75 Intermediate Similarity NPC210303
0.75 Intermediate Similarity NPC132243
0.75 Intermediate Similarity NPC90490
0.7463 Intermediate Similarity NPC287705
0.7419 Intermediate Similarity NPC474084
0.7419 Intermediate Similarity NPC254095
0.7385 Intermediate Similarity NPC471611
0.7368 Intermediate Similarity NPC82446
0.7333 Intermediate Similarity NPC478120
0.7302 Intermediate Similarity NPC82465
0.7273 Intermediate Similarity NPC476589
0.7273 Intermediate Similarity NPC273600
0.7258 Intermediate Similarity NPC135863
0.7258 Intermediate Similarity NPC474825
0.7258 Intermediate Similarity NPC249850
0.7258 Intermediate Similarity NPC293437
0.7258 Intermediate Similarity NPC129150
0.7258 Intermediate Similarity NPC294938
0.7231 Intermediate Similarity NPC68110
0.7206 Intermediate Similarity NPC474823
0.7183 Intermediate Similarity NPC470686
0.7164 Intermediate Similarity NPC37382
0.7164 Intermediate Similarity NPC315115
0.7143 Intermediate Similarity NPC223679
0.7143 Intermediate Similarity NPC21946
0.7101 Intermediate Similarity NPC470693
0.7101 Intermediate Similarity NPC475004
0.7097 Intermediate Similarity NPC86948
0.7097 Intermediate Similarity NPC230296
0.7059 Intermediate Similarity NPC225272
0.7059 Intermediate Similarity NPC132286
0.7049 Intermediate Similarity NPC159535
0.7049 Intermediate Similarity NPC151761
0.7018 Intermediate Similarity NPC87137
0.7015 Intermediate Similarity NPC282760
0.7015 Intermediate Similarity NPC182794
0.7015 Intermediate Similarity NPC220766
0.7015 Intermediate Similarity NPC470123
0.7015 Intermediate Similarity NPC133904
0.7 Intermediate Similarity NPC315597
0.6986 Remote Similarity NPC470705
0.6957 Remote Similarity NPC238223
0.6957 Remote Similarity NPC313444
0.6957 Remote Similarity NPC477117
0.6949 Remote Similarity NPC236338
0.6912 Remote Similarity NPC146811
0.6912 Remote Similarity NPC191233
0.6912 Remote Similarity NPC475675
0.6912 Remote Similarity NPC475555
0.6912 Remote Similarity NPC470033
0.6901 Remote Similarity NPC316185
0.6852 Remote Similarity NPC8270
0.6849 Remote Similarity NPC161038
0.6825 Remote Similarity NPC245002
0.6818 Remote Similarity NPC151648
0.6818 Remote Similarity NPC15193
0.6774 Remote Similarity NPC474127
0.6769 Remote Similarity NPC302564
0.6769 Remote Similarity NPC286189
0.6769 Remote Similarity NPC97570
0.6765 Remote Similarity NPC131174
0.6765 Remote Similarity NPC7940
0.6761 Remote Similarity NPC315285
0.6761 Remote Similarity NPC316029
0.6727 Remote Similarity NPC221250
0.6716 Remote Similarity NPC474723
0.6716 Remote Similarity NPC474729
0.6714 Remote Similarity NPC63873
0.6712 Remote Similarity NPC315843
0.6667 Remote Similarity NPC429928
0.6667 Remote Similarity NPC248125
0.6667 Remote Similarity NPC304079
0.6667 Remote Similarity NPC178575
0.6667 Remote Similarity NPC200147
0.6667 Remote Similarity NPC275530
0.6667 Remote Similarity NPC6963
0.6667 Remote Similarity NPC25038
0.6667 Remote Similarity NPC276299
0.6667 Remote Similarity NPC293114
0.6667 Remote Similarity NPC275316
0.662 Remote Similarity NPC151481
0.6618 Remote Similarity NPC470808
0.6613 Remote Similarity NPC327103
0.6607 Remote Similarity NPC41409
0.6575 Remote Similarity NPC316851
0.6575 Remote Similarity NPC215745
0.6575 Remote Similarity NPC287878
0.6575 Remote Similarity NPC238948
0.6575 Remote Similarity NPC284006
0.6575 Remote Similarity NPC12815
0.6571 Remote Similarity NPC203335
0.6571 Remote Similarity NPC21998
0.6571 Remote Similarity NPC122627
0.6567 Remote Similarity NPC26810
0.6552 Remote Similarity NPC270706
0.6528 Remote Similarity NPC476037
0.6528 Remote Similarity NPC202011
0.6522 Remote Similarity NPC470688
0.6522 Remote Similarity NPC19769
0.6522 Remote Similarity NPC96414
0.65 Remote Similarity NPC122212
0.65 Remote Similarity NPC137419
0.6486 Remote Similarity NPC107654
0.6486 Remote Similarity NPC476590
0.6486 Remote Similarity NPC114727
0.6481 Remote Similarity NPC63598
0.6479 Remote Similarity NPC79220
0.6462 Remote Similarity NPC283502
0.6456 Remote Similarity NPC474028
0.6456 Remote Similarity NPC474439
0.6447 Remote Similarity NPC315394
0.6447 Remote Similarity NPC316324
0.6447 Remote Similarity NPC68156
0.6447 Remote Similarity NPC473825
0.6441 Remote Similarity NPC308331
0.6441 Remote Similarity NPC128280
0.6429 Remote Similarity NPC201356
0.642 Remote Similarity NPC474424
0.6418 Remote Similarity NPC79756
0.64 Remote Similarity NPC315552
0.64 Remote Similarity NPC260396
0.6393 Remote Similarity NPC27264
0.6389 Remote Similarity NPC473277
0.6389 Remote Similarity NPC232812
0.6389 Remote Similarity NPC475982
0.6386 Remote Similarity NPC260343
0.6377 Remote Similarity NPC173409
0.6377 Remote Similarity NPC53136
0.6375 Remote Similarity NPC475714
0.6364 Remote Similarity NPC471619
0.6364 Remote Similarity NPC298413
0.6364 Remote Similarity NPC473471
0.6351 Remote Similarity NPC329890
0.6324 Remote Similarity NPC217537
0.6324 Remote Similarity NPC55376
0.6324 Remote Similarity NPC263732
0.6316 Remote Similarity NPC57923
0.6316 Remote Similarity NPC51391
0.6316 Remote Similarity NPC127118
0.6316 Remote Similarity NPC4492
0.6316 Remote Similarity NPC209113
0.6316 Remote Similarity NPC301207
0.6316 Remote Similarity NPC102879
0.6316 Remote Similarity NPC203277
0.6316 Remote Similarity NPC263266
0.6308 Remote Similarity NPC324224
0.6308 Remote Similarity NPC472808
0.6301 Remote Similarity NPC64234
0.6301 Remote Similarity NPC67183
0.6301 Remote Similarity NPC476012
0.6301 Remote Similarity NPC37929
0.6296 Remote Similarity NPC475706
0.6296 Remote Similarity NPC107877
0.629 Remote Similarity NPC148056
0.6271 Remote Similarity NPC47946
0.6271 Remote Similarity NPC26600
0.6269 Remote Similarity NPC86789
0.625 Remote Similarity NPC218477
0.625 Remote Similarity NPC16321
0.625 Remote Similarity NPC9611
0.625 Remote Similarity NPC280374
0.625 Remote Similarity NPC129710
0.625 Remote Similarity NPC151923
0.625 Remote Similarity NPC281043
0.625 Remote Similarity NPC135537
0.6234 Remote Similarity NPC176329
0.6234 Remote Similarity NPC51809

  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 NPC189700 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
0.7069 Intermediate Similarity NPD4220 Pre-registration
0.6491 Remote Similarity NPD9411 Phase 1
0.6234 Remote Similarity NPD4756 Discovery
0.6032 Remote Similarity NPD6927 Phase 3
0.6 Remote Similarity NPD539 Approved
0.6 Remote Similarity NPD9115 Approved
0.5882 Remote Similarity NPD9119 Approved
0.5882 Remote Similarity NPD69 Approved
0.5857 Remote Similarity NPD4191 Approved
0.5857 Remote Similarity NPD4192 Approved
0.5857 Remote Similarity NPD4194 Approved
0.5857 Remote Similarity NPD4193 Approved
0.5741 Remote Similarity NPD8573 Approved
0.5735 Remote Similarity NPD9118 Approved
0.5663 Remote Similarity NPD5209 Approved
0.5634 Remote Similarity NPD9418 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