Structure

Physi-Chem Properties

Molecular Weight:  182.09
Volume:  191.421
LogP:  2.012
LogD:  1.866
LogS:  -1.335
# Rotatable Bonds:  4
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:  3.328
Fsp3:  0.4
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:  -4.666
MDCK Permeability:  2.420560304017272e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.048
Human Intestinal Absorption (HIA):  0.028
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.532

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.811
Plasma Protein Binding (PPB):  91.82598114013672%
Volume Distribution (VD):  2.476
Pgp-substrate:  18.7438907623291%

ADMET: Metabolism

CYP1A2-inhibitor:  0.215
CYP1A2-substrate:  0.622
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.071
CYP2C9-inhibitor:  0.018
CYP2C9-substrate:  0.728
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.871
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.166

ADMET: Excretion

Clearance (CL):  12.178
Half-life (T1/2):  0.903

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.461
Drug-inuced Liver Injury (DILI):  0.198
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.091
Maximum Recommended Daily Dose:  0.19
Skin Sensitization:  0.854
Carcinogencity:  0.882
Eye Corrosion:  0.1
Eye Irritation:  0.359
Respiratory Toxicity:  0.03

Download Data

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

  Natural Product: NPC287705

Natural Product ID:  NPC287705
Common Name*:   (E/Z)-Bombardolide B
IUPAC Name:   (5Z)-3-(3-hydroxypropyl)-5-propylidenefuran-2-one
Synonyms:  
Standard InCHIKey:  YNRNIKRFIIHGPK-WTKPLQERSA-N
Standard InCHI:  InChI=1S/C10H14O3/c1-2-4-9-7-8(5-3-6-11)10(12)13-9/h4,7,11H,2-3,5-6H2,1H3/b9-4-
SMILES:  CC/C=C1/C=C(CCCO)C(=O)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL507030
PubChem CID:   10397433
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 = 11.0 mm PMID[564750]

☑ 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 NPC287705 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
0.8333 Intermediate Similarity NPC478193
0.8333 Intermediate Similarity NPC478196
0.8333 Intermediate Similarity NPC478195
0.8333 Intermediate Similarity NPC478191
0.8333 Intermediate Similarity NPC478194
0.8333 Intermediate Similarity NPC478192
0.806 Intermediate Similarity NPC473737
0.806 Intermediate Similarity NPC68110
0.803 Intermediate Similarity NPC130953
0.7794 Intermediate Similarity NPC2328
0.7761 Intermediate Similarity NPC98519
0.7746 Intermediate Similarity NPC474823
0.7647 Intermediate Similarity NPC151648
0.7639 Intermediate Similarity NPC475004
0.7612 Intermediate Similarity NPC133600
0.7538 Intermediate Similarity NPC49028
0.75 Intermediate Similarity NPC79220
0.7465 Intermediate Similarity NPC37382
0.7463 Intermediate Similarity NPC189700
0.7368 Intermediate Similarity NPC161038
0.7361 Intermediate Similarity NPC132286
0.7324 Intermediate Similarity NPC471565
0.7324 Intermediate Similarity NPC471566
0.7324 Intermediate Similarity NPC470123
0.7324 Intermediate Similarity NPC471556
0.7324 Intermediate Similarity NPC131174
0.7324 Intermediate Similarity NPC282760
0.7313 Intermediate Similarity NPC135863
0.7297 Intermediate Similarity NPC202011
0.7286 Intermediate Similarity NPC132243
0.7273 Intermediate Similarity NPC225022
0.7273 Intermediate Similarity NPC238554
0.7273 Intermediate Similarity NPC173157
0.726 Intermediate Similarity NPC238223
0.7246 Intermediate Similarity NPC309408
0.7237 Intermediate Similarity NPC114727
0.7237 Intermediate Similarity NPC470686
0.7237 Intermediate Similarity NPC476590
0.7237 Intermediate Similarity NPC177030
0.7222 Intermediate Similarity NPC248125
0.7183 Intermediate Similarity NPC475618
0.7179 Intermediate Similarity NPC24827
0.7179 Intermediate Similarity NPC275530
0.7179 Intermediate Similarity NPC228902
0.7179 Intermediate Similarity NPC68156
0.7143 Intermediate Similarity NPC469414
0.7143 Intermediate Similarity NPC329852
0.7143 Intermediate Similarity NPC329826
0.7123 Intermediate Similarity NPC203335
0.7121 Intermediate Similarity NPC218486
0.7121 Intermediate Similarity NPC154626
0.7108 Intermediate Similarity NPC100921
0.7108 Intermediate Similarity NPC477018
0.7108 Intermediate Similarity NPC474424
0.7083 Intermediate Similarity NPC133904
0.7083 Intermediate Similarity NPC182794
0.7083 Intermediate Similarity NPC220766
0.7077 Intermediate Similarity NPC191643
0.7067 Intermediate Similarity NPC59558
0.7067 Intermediate Similarity NPC476012
0.7067 Intermediate Similarity NPC315285
0.7059 Intermediate Similarity NPC293437
0.7059 Intermediate Similarity NPC249850
0.7042 Intermediate Similarity NPC179087
0.7042 Intermediate Similarity NPC475073
0.7042 Intermediate Similarity NPC44343
0.7042 Intermediate Similarity NPC210303
0.7042 Intermediate Similarity NPC474658
0.7031 Intermediate Similarity NPC236338
0.7027 Intermediate Similarity NPC218477
0.7024 Intermediate Similarity NPC477010
0.7024 Intermediate Similarity NPC309211
0.7 Intermediate Similarity NPC286816
0.7 Intermediate Similarity NPC199134
0.7 Intermediate Similarity NPC79756
0.6988 Remote Similarity NPC156804
0.6986 Remote Similarity NPC315115
0.6986 Remote Similarity NPC191233
0.6986 Remote Similarity NPC276299
0.6986 Remote Similarity NPC146811
0.6974 Remote Similarity NPC133098
0.6974 Remote Similarity NPC316185
0.6962 Remote Similarity NPC315394
0.6957 Remote Similarity NPC223679
0.6957 Remote Similarity NPC254095
0.6951 Remote Similarity NPC180363
0.6951 Remote Similarity NPC131002
0.6951 Remote Similarity NPC473529
0.6951 Remote Similarity NPC473712
0.6951 Remote Similarity NPC473780
0.6951 Remote Similarity NPC65930
0.6951 Remote Similarity NPC94875
0.6951 Remote Similarity NPC475159
0.6951 Remote Similarity NPC11332
0.6951 Remote Similarity NPC73310
0.6951 Remote Similarity NPC329829
0.6951 Remote Similarity NPC145914
0.6944 Remote Similarity NPC53136
0.6944 Remote Similarity NPC173409
0.6941 Remote Similarity NPC470401
0.6941 Remote Similarity NPC473649
0.6941 Remote Similarity NPC154097
0.6941 Remote Similarity NPC159750
0.6933 Remote Similarity NPC475982
0.6933 Remote Similarity NPC470693
0.6933 Remote Similarity NPC236208
0.6923 Remote Similarity NPC260396
0.6912 Remote Similarity NPC472808
0.6912 Remote Similarity NPC150717
0.6912 Remote Similarity NPC86948
0.6912 Remote Similarity NPC324224
0.6905 Remote Similarity NPC470400
0.6905 Remote Similarity NPC235809
0.6905 Remote Similarity NPC471567
0.6905 Remote Similarity NPC329838
0.6905 Remote Similarity NPC473671
0.6905 Remote Similarity NPC319036
0.6905 Remote Similarity NPC39167
0.6905 Remote Similarity NPC475268
0.6905 Remote Similarity NPC9678
0.6905 Remote Similarity NPC202055
0.6905 Remote Similarity NPC322529
0.6905 Remote Similarity NPC473156
0.6905 Remote Similarity NPC120398
0.6905 Remote Similarity NPC77871
0.6905 Remote Similarity NPC25764
0.6905 Remote Similarity NPC39279
0.6905 Remote Similarity NPC292809
0.6905 Remote Similarity NPC329615
0.6901 Remote Similarity NPC26810
0.6901 Remote Similarity NPC15193
0.6901 Remote Similarity NPC217537
0.6897 Remote Similarity NPC274075
0.6883 Remote Similarity NPC329914
0.6883 Remote Similarity NPC284006
0.6875 Remote Similarity NPC135698
0.6867 Remote Similarity NPC188717
0.6867 Remote Similarity NPC211455
0.6867 Remote Similarity NPC144415
0.6867 Remote Similarity NPC253801
0.686 Remote Similarity NPC89001
0.686 Remote Similarity NPC475739
0.6857 Remote Similarity NPC286189
0.6857 Remote Similarity NPC97570
0.6849 Remote Similarity NPC476589
0.6842 Remote Similarity NPC67183
0.6842 Remote Similarity NPC315597
0.6842 Remote Similarity NPC476037
0.6835 Remote Similarity NPC301207
0.6835 Remote Similarity NPC470705
0.6835 Remote Similarity NPC68819
0.6824 Remote Similarity NPC132940
0.6824 Remote Similarity NPC171174
0.6824 Remote Similarity NPC107717
0.6824 Remote Similarity NPC112685
0.6824 Remote Similarity NPC219652
0.6824 Remote Similarity NPC475581
0.6824 Remote Similarity NPC473840
0.6824 Remote Similarity NPC282815
0.6824 Remote Similarity NPC293136
0.6824 Remote Similarity NPC164393
0.6824 Remote Similarity NPC142117
0.6824 Remote Similarity NPC62118
0.6824 Remote Similarity NPC231096
0.6824 Remote Similarity NPC232555
0.6824 Remote Similarity NPC47937
0.6824 Remote Similarity NPC241360
0.6824 Remote Similarity NPC25703
0.6824 Remote Similarity NPC122502
0.6824 Remote Similarity NPC240695
0.6824 Remote Similarity NPC114694
0.6818 Remote Similarity NPC114345
0.6818 Remote Similarity NPC327760
0.6818 Remote Similarity NPC303230
0.6818 Remote Similarity NPC6099
0.6812 Remote Similarity NPC129150
0.6806 Remote Similarity NPC155849
0.68 Remote Similarity NPC63873
0.68 Remote Similarity NPC470256
0.68 Remote Similarity NPC313444
0.6795 Remote Similarity NPC92558
0.6795 Remote Similarity NPC315843
0.6795 Remote Similarity NPC107654
0.679 Remote Similarity NPC99651
0.6786 Remote Similarity NPC163093
0.6786 Remote Similarity NPC475706
0.6786 Remote Similarity NPC474251
0.6782 Remote Similarity NPC295312
0.6782 Remote Similarity NPC477016
0.6782 Remote Similarity NPC477017
0.6782 Remote Similarity NPC477011
0.6765 Remote Similarity NPC478117
0.6757 Remote Similarity NPC470033
0.6753 Remote Similarity NPC112983
0.6753 Remote Similarity NPC186531
0.6753 Remote Similarity NPC84038
0.6753 Remote Similarity NPC293114
0.6753 Remote Similarity NPC162571
0.675 Remote Similarity NPC474818
0.675 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 NPC287705 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
0.6667 Remote Similarity NPD6927 Phase 3
0.6543 Remote Similarity NPD4756 Discovery
0.6528 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6447 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6163 Remote Similarity NPD5209 Approved
0.6154 Remote Similarity NPD7838 Discovery
0.6119 Remote Similarity NPD4220 Pre-registration
0.6027 Remote Similarity NPD9119 Approved
0.6027 Remote Similarity NPD69 Approved
0.5978 Remote Similarity NPD46 Approved
0.5978 Remote Similarity NPD6698 Approved
0.5974 Remote Similarity NPD2685 Clinical (unspecified phase)
0.597 Remote Similarity NPD5343 Approved
0.5909 Remote Similarity NPD7154 Phase 3
0.5909 Remote Similarity NPD4222 Approved
0.5909 Remote Similarity NPD6110 Phase 1
0.5904 Remote Similarity NPD1452 Discontinued
0.589 Remote Similarity NPD9118 Approved
0.5889 Remote Similarity NPD4249 Approved
0.5876 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5846 Remote Similarity NPD9411 Phase 1
0.5843 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5824 Remote Similarity NPD4251 Approved
0.5824 Remote Similarity NPD4250 Approved
0.5811 Remote Similarity NPD6109 Phase 1
0.5795 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5778 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5745 Remote Similarity NPD7983 Approved
0.5729 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7638 Approved
0.5714 Remote Similarity NPD8039 Approved
0.5672 Remote Similarity NPD4265 Approved
0.5657 Remote Similarity NPD7639 Approved
0.5657 Remote Similarity NPD7640 Approved
0.5652 Remote Similarity NPD3173 Approved
0.5638 Remote Similarity NPD5785 Approved
0.5604 Remote Similarity NPD6082 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