Structure

Physi-Chem Properties

Molecular Weight:  180.08
Volume:  188.785
LogP:  2.101
LogD:  2.193
LogS:  -1.931
# Rotatable Bonds:  3
TPSA:  53.6
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.748
Synthetic Accessibility Score:  3.647
Fsp3:  0.2
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:  -4.692
MDCK Permeability:  1.6686577509972267e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.042
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.88

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.426
Plasma Protein Binding (PPB):  90.83985900878906%
Volume Distribution (VD):  0.613
Pgp-substrate:  19.340044021606445%

ADMET: Metabolism

CYP1A2-inhibitor:  0.328
CYP1A2-substrate:  0.271
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.109
CYP2C9-inhibitor:  0.018
CYP2C9-substrate:  0.929
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.88
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.174

ADMET: Excretion

Clearance (CL):  10.538
Half-life (T1/2):  0.9

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.774
Drug-inuced Liver Injury (DILI):  0.678
AMES Toxicity:  0.05
Rat Oral Acute Toxicity:  0.123
Maximum Recommended Daily Dose:  0.43
Skin Sensitization:  0.899
Carcinogencity:  0.923
Eye Corrosion:  0.17
Eye Irritation:  0.663
Respiratory Toxicity:  0.127

Download Data

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

  Natural Product: NPC130953

Natural Product ID:  NPC130953
Common Name*:   (E/Z)-Bombardolide A
IUPAC Name:   (5Z)-3-[(E)-3-hydroxyprop-1-enyl]-5-propylidenefuran-2-one
Synonyms:   (E/Z)-Bombardolide A
Standard InCHIKey:  YGPGUEZTBZXORL-PVOUKABXSA-N
Standard InCHI:  InChI=1S/C10H12O3/c1-2-4-9-7-8(5-3-6-11)10(12)13-9/h3-5,7,11H,2,6H2,1H3/b5-3+,9-4-
SMILES:  CC/C=C1/C=C(/C=C/CO)C(=O)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL471484
PubChem CID:   10261701
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 = 19.0 mm PMID[487887]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 14.0 mm PMID[487887]
NPT20 Organism Candida albicans Candida albicans IZ = 35.0 mm PMID[487887]

☑ 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 NPC130953 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
0.9649 High Similarity NPC98519
0.9298 High Similarity NPC189700
0.9 High Similarity NPC473737
0.8387 Intermediate Similarity NPC2328
0.8276 Intermediate Similarity NPC218486
0.803 Intermediate Similarity NPC287705
0.8 Intermediate Similarity NPC51846
0.8 Intermediate Similarity NPC150717
0.7931 Intermediate Similarity NPC191643
0.7903 Intermediate Similarity NPC133600
0.7895 Intermediate Similarity NPC15789
0.7857 Intermediate Similarity NPC478194
0.7857 Intermediate Similarity NPC478191
0.7857 Intermediate Similarity NPC478195
0.7857 Intermediate Similarity NPC478193
0.7857 Intermediate Similarity NPC478196
0.7857 Intermediate Similarity NPC478192
0.7812 Intermediate Similarity NPC44343
0.7812 Intermediate Similarity NPC210303
0.7812 Intermediate Similarity NPC179087
0.7794 Intermediate Similarity NPC59558
0.7778 Intermediate Similarity NPC309408
0.7761 Intermediate Similarity NPC474823
0.7727 Intermediate Similarity NPC37382
0.7705 Intermediate Similarity NPC230296
0.7705 Intermediate Similarity NPC221763
0.7692 Intermediate Similarity NPC471611
0.7647 Intermediate Similarity NPC475004
0.7586 Intermediate Similarity NPC221467
0.7581 Intermediate Similarity NPC135863
0.7581 Intermediate Similarity NPC129150
0.7576 Intermediate Similarity NPC471566
0.7576 Intermediate Similarity NPC471565
0.7576 Intermediate Similarity NPC273600
0.7541 Intermediate Similarity NPC173157
0.7541 Intermediate Similarity NPC478117
0.7538 Intermediate Similarity NPC475073
0.7465 Intermediate Similarity NPC470686
0.746 Intermediate Similarity NPC254095
0.746 Intermediate Similarity NPC223679
0.7424 Intermediate Similarity NPC475618
0.7414 Intermediate Similarity NPC126184
0.7414 Intermediate Similarity NPC234084
0.7353 Intermediate Similarity NPC132286
0.7353 Intermediate Similarity NPC225272
0.7344 Intermediate Similarity NPC82465
0.7344 Intermediate Similarity NPC302564
0.7313 Intermediate Similarity NPC471556
0.7313 Intermediate Similarity NPC476589
0.7313 Intermediate Similarity NPC133904
0.7313 Intermediate Similarity NPC182794
0.7313 Intermediate Similarity NPC282760
0.7313 Intermediate Similarity NPC470123
0.7302 Intermediate Similarity NPC293437
0.7302 Intermediate Similarity NPC294938
0.7302 Intermediate Similarity NPC249850
0.7288 Intermediate Similarity NPC236338
0.7273 Intermediate Similarity NPC132243
0.7273 Intermediate Similarity NPC68110
0.726 Intermediate Similarity NPC470705
0.7246 Intermediate Similarity NPC238223
0.7241 Intermediate Similarity NPC128520
0.7241 Intermediate Similarity NPC90490
0.7206 Intermediate Similarity NPC475555
0.7206 Intermediate Similarity NPC146811
0.7206 Intermediate Similarity NPC475675
0.7188 Intermediate Similarity NPC474084
0.7188 Intermediate Similarity NPC21946
0.7183 Intermediate Similarity NPC316185
0.7167 Intermediate Similarity NPC43053
0.7123 Intermediate Similarity NPC161038
0.7121 Intermediate Similarity NPC151648
0.7119 Intermediate Similarity NPC82446
0.7097 Intermediate Similarity NPC159535
0.7097 Intermediate Similarity NPC151761
0.7097 Intermediate Similarity NPC478120
0.7077 Intermediate Similarity NPC286189
0.7077 Intermediate Similarity NPC97570
0.7059 Intermediate Similarity NPC7940
0.7059 Intermediate Similarity NPC220766
0.7059 Intermediate Similarity NPC131174
0.7031 Intermediate Similarity NPC474825
0.7 Intermediate Similarity NPC477117
0.7 Intermediate Similarity NPC275316
0.7 Intermediate Similarity NPC63873
0.6986 Remote Similarity NPC315843
0.6957 Remote Similarity NPC276299
0.6957 Remote Similarity NPC315115
0.6957 Remote Similarity NPC470033
0.6957 Remote Similarity NPC191233
0.6944 Remote Similarity NPC293114
0.6944 Remote Similarity NPC178575
0.6935 Remote Similarity NPC327103
0.6933 Remote Similarity NPC275530
0.6912 Remote Similarity NPC470808
0.6901 Remote Similarity NPC470693
0.6875 Remote Similarity NPC472808
0.6875 Remote Similarity NPC245002
0.6875 Remote Similarity NPC86948
0.6875 Remote Similarity NPC324224
0.6866 Remote Similarity NPC26810
0.6866 Remote Similarity NPC15193
0.6857 Remote Similarity NPC122627
0.6849 Remote Similarity NPC316851
0.6849 Remote Similarity NPC284006
0.6842 Remote Similarity NPC473471
0.6812 Remote Similarity NPC19769
0.6812 Remote Similarity NPC96414
0.6806 Remote Similarity NPC202011
0.6806 Remote Similarity NPC476037
0.68 Remote Similarity NPC127118
0.68 Remote Similarity NPC301207
0.68 Remote Similarity NPC209113
0.6765 Remote Similarity NPC474723
0.6765 Remote Similarity NPC474729
0.6761 Remote Similarity NPC313444
0.6757 Remote Similarity NPC107654
0.6757 Remote Similarity NPC114727
0.6757 Remote Similarity NPC476590
0.6714 Remote Similarity NPC201356
0.6714 Remote Similarity NPC248125
0.6711 Remote Similarity NPC315394
0.6711 Remote Similarity NPC51809
0.6711 Remote Similarity NPC49302
0.6711 Remote Similarity NPC474818
0.6711 Remote Similarity NPC125365
0.6711 Remote Similarity NPC176329
0.6667 Remote Similarity NPC151481
0.6667 Remote Similarity NPC315552
0.6667 Remote Similarity NPC57923
0.6667 Remote Similarity NPC90463
0.6667 Remote Similarity NPC475982
0.6667 Remote Similarity NPC474424
0.6667 Remote Similarity NPC41409
0.6667 Remote Similarity NPC260396
0.6623 Remote Similarity NPC279214
0.6623 Remote Similarity NPC221095
0.6622 Remote Similarity NPC329890
0.662 Remote Similarity NPC203335
0.6618 Remote Similarity NPC55376
0.661 Remote Similarity NPC47946
0.661 Remote Similarity NPC26600
0.661 Remote Similarity NPC270706
0.6607 Remote Similarity NPC8270
0.6579 Remote Similarity NPC238554
0.6579 Remote Similarity NPC203277
0.6579 Remote Similarity NPC225022
0.6575 Remote Similarity NPC316029
0.6575 Remote Similarity NPC315597
0.6575 Remote Similarity NPC476012
0.6575 Remote Similarity NPC315285
0.6567 Remote Similarity NPC222852
0.6562 Remote Similarity NPC474127
0.6562 Remote Similarity NPC151923
0.6562 Remote Similarity NPC9611
0.6557 Remote Similarity NPC135698
0.6543 Remote Similarity NPC475706
0.6533 Remote Similarity NPC177030
0.6528 Remote Similarity NPC218477
0.6522 Remote Similarity NPC474658
0.6515 Remote Similarity NPC212730
0.6515 Remote Similarity NPC265551
0.6515 Remote Similarity NPC472445
0.6515 Remote Similarity NPC71755
0.6515 Remote Similarity NPC44542
0.65 Remote Similarity NPC474028
0.65 Remote Similarity NPC128280
0.65 Remote Similarity NPC16321
0.65 Remote Similarity NPC87137
0.65 Remote Similarity NPC197467
0.65 Remote Similarity NPC474439
0.6494 Remote Similarity NPC228902
0.6494 Remote Similarity NPC473825
0.6494 Remote Similarity NPC68156
0.6494 Remote Similarity NPC24827
0.6491 Remote Similarity NPC221250
0.6471 Remote Similarity NPC429928
0.6471 Remote Similarity NPC476585
0.6471 Remote Similarity NPC79756
0.6462 Remote Similarity NPC25038
0.6447 Remote Similarity NPC469414
0.6447 Remote Similarity NPC329826
0.6441 Remote Similarity NPC6963
0.6441 Remote Similarity NPC304079
0.6438 Remote Similarity NPC236208
0.6438 Remote Similarity NPC232812
0.6429 Remote Similarity NPC260343
0.6429 Remote Similarity NPC475739
0.6429 Remote Similarity NPC200147
0.6429 Remote Similarity NPC147824
0.642 Remote Similarity NPC475714
0.641 Remote Similarity NPC279532
0.64 Remote Similarity NPC326126
0.64 Remote Similarity NPC12815
0.64 Remote Similarity NPC215745
0.64 Remote Similarity NPC329914
0.64 Remote Similarity NPC287878
0.64 Remote Similarity NPC238948
0.6389 Remote Similarity NPC21998
0.6386 Remote Similarity NPC211892

  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 NPC130953 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
0.6833 Remote Similarity NPD4220 Pre-registration
0.6349 Remote Similarity NPD6927 Phase 3
0.6176 Remote Similarity NPD9119 Approved
0.6176 Remote Similarity NPD69 Approved
0.6076 Remote Similarity NPD4756 Discovery
0.6029 Remote Similarity NPD9118 Approved
0.6 Remote Similarity NPD9411 Phase 1
0.6 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5821 Remote Similarity NPD539 Approved
0.5806 Remote Similarity NPD9090 Phase 3
0.5789 Remote Similarity NPD9115 Approved
0.5765 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5753 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5733 Remote Similarity NPD4247 Clinical (unspecified phase)
0.573 Remote Similarity NPD7838 Discovery
0.5714 Remote Similarity NPD5209 Approved
0.5694 Remote Similarity NPD4194 Approved
0.5694 Remote Similarity NPD4193 Approved
0.5694 Remote Similarity NPD9418 Clinical (unspecified phase)
0.5694 Remote Similarity NPD4191 Approved
0.5694 Remote Similarity NPD4192 Approved
0.5676 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5647 Remote Similarity NPD7154 Phase 3
0.5645 Remote Similarity NPD6097 Approved
0.5645 Remote Similarity NPD6096 Approved
0.5618 Remote Similarity NPD689 Discontinued

  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