NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	182.09
Volume:	191.421
LogP:	2.205
LogD:	2.236
LogS:	-2.267
# 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:	3.234
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:	-4.635
MDCK Permeability:	1.6708137991372496e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.011
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.109
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.286
Plasma Protein Binding (PPB):	90.48375701904297%
Volume Distribution (VD):	0.693
Pgp-substrate:	16.652286529541016%

ADMET: Metabolism

CYP1A2-inhibitor:	0.657
CYP1A2-substrate:	0.491
CYP2C19-inhibitor:	0.046
CYP2C19-substrate:	0.276
CYP2C9-inhibitor:	0.062
CYP2C9-substrate:	0.941
CYP2D6-inhibitor:	0.01
CYP2D6-substrate:	0.765
CYP3A4-inhibitor:	0.015
CYP3A4-substrate:	0.203

ADMET: Excretion

Clearance (CL):	10.563
Half-life (T1/2):	0.865

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.252
Drug-inuced Liver Injury (DILI):	0.588
AMES Toxicity:	0.099
Rat Oral Acute Toxicity:	0.23
Maximum Recommended Daily Dose:	0.045
Skin Sensitization:	0.668
Carcinogencity:	0.904
Eye Corrosion:	0.09
Eye Irritation:	0.627
Respiratory Toxicity:	0.109

Download Data

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

Natural Product: NPC473737

Natural Product ID:	NPC473737
*Common Name:**	Bombardolide D
IUPAC Name:	4-[(E)-3-hydroxyprop-1-enyl]-2-propyl-2H-furan-5-one
Synonyms:	Bombardolide D
Standard InCHIKey:	WWJYPRXNKYXREE-HWKANZROSA-N
Standard InCHI:	InChI=1S/C10H14O3/c1-2-4-9-7-8(5-3-6-11)10(12)13-9/h3,5,7,9,11H,2,4,6H2,1H3/b5-3+
SMILES:	CCCC1C=C(C(=O)O1)C=CCO
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL450676
PubChem CID:	10375070
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

Activity Type	# Activity
Others	1

Activity Type	# Activity
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20	Organism	Candida albicans	Candida albicans	IZ	=	20.0	mm	PMID[502746]

☑ 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 NPC473737 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	147
0.1-0.2	2103
0.2-0.3	11017
0.3-0.4	19072
0.4-0.5	6556
0.5-0.6	2758
0.6-0.7	854
0.7-0.8	163
0.8-0.85	17
0.85-0.9	9
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9	High Similarity	NPC130953
0.8689	High Similarity	NPC98519
0.8615	High Similarity	NPC474823
0.8594	High Similarity	NPC37382
0.8485	Intermediate Similarity	NPC475004
0.8413	Intermediate Similarity	NPC44343
0.8413	Intermediate Similarity	NPC210303
0.8413	Intermediate Similarity	NPC179087
0.8361	Intermediate Similarity	NPC189700
0.8154	Intermediate Similarity	NPC182794
0.8154	Intermediate Similarity	NPC470123
0.8154	Intermediate Similarity	NPC282760
0.8143	Intermediate Similarity	NPC478195
0.8143	Intermediate Similarity	NPC478193
0.8143	Intermediate Similarity	NPC478192
0.8143	Intermediate Similarity	NPC478196
0.8143	Intermediate Similarity	NPC478194
0.8143	Intermediate Similarity	NPC478191
0.8125	Intermediate Similarity	NPC2328
0.806	Intermediate Similarity	NPC287705
0.803	Intermediate Similarity	NPC146811
0.7971	Intermediate Similarity	NPC316185
0.7969	Intermediate Similarity	NPC151648
0.7937	Intermediate Similarity	NPC97570
0.7937	Intermediate Similarity	NPC133600
0.7937	Intermediate Similarity	NPC286189
0.791	Intermediate Similarity	NPC225272
0.7903	Intermediate Similarity	NPC129150
0.7903	Intermediate Similarity	NPC135863
0.7887	Intermediate Similarity	NPC161038
0.7879	Intermediate Similarity	NPC131174
0.7879	Intermediate Similarity	NPC273600
0.7869	Intermediate Similarity	NPC478117
0.7846	Intermediate Similarity	NPC68110
0.7826	Intermediate Similarity	NPC59558
0.7794	Intermediate Similarity	NPC63873
0.7778	Intermediate Similarity	NPC254095
0.7778	Intermediate Similarity	NPC223679
0.7761	Intermediate Similarity	NPC276299
0.7746	Intermediate Similarity	NPC470686
0.7746	Intermediate Similarity	NPC315843
0.7742	Intermediate Similarity	NPC324224
0.7742	Intermediate Similarity	NPC472808
0.7727	Intermediate Similarity	NPC470808
0.7714	Intermediate Similarity	NPC293114
0.7692	Intermediate Similarity	NPC26810
0.7671	Intermediate Similarity	NPC275530
0.7656	Intermediate Similarity	NPC82465
0.7656	Intermediate Similarity	NPC302564
0.7647	Intermediate Similarity	NPC122627
0.7627	Intermediate Similarity	NPC236338
0.7627	Intermediate Similarity	NPC15789
0.7619	Intermediate Similarity	NPC249850
0.7619	Intermediate Similarity	NPC293437
0.7619	Intermediate Similarity	NPC294938
0.7612	Intermediate Similarity	NPC133904
0.7612	Intermediate Similarity	NPC96414
0.7612	Intermediate Similarity	NPC471566
0.7612	Intermediate Similarity	NPC19769
0.7612	Intermediate Similarity	NPC471565
0.7606	Intermediate Similarity	NPC284006
0.7571	Intermediate Similarity	NPC476037
0.7571	Intermediate Similarity	NPC202011
0.7538	Intermediate Similarity	NPC309408
0.7536	Intermediate Similarity	NPC238223
0.75	Intermediate Similarity	NPC248125
0.75	Intermediate Similarity	NPC475555
0.75	Intermediate Similarity	NPC201356
0.75	Intermediate Similarity	NPC107654
0.75	Intermediate Similarity	NPC21946
0.75	Intermediate Similarity	NPC476590
0.75	Intermediate Similarity	NPC114727
0.75	Intermediate Similarity	NPC474084
0.75	Intermediate Similarity	NPC475675
0.7463	Intermediate Similarity	NPC475618
0.746	Intermediate Similarity	NPC230296
0.7429	Intermediate Similarity	NPC475982
0.7429	Intermediate Similarity	NPC151481
0.7424	Intermediate Similarity	NPC55376
0.7419	Intermediate Similarity	NPC218486
0.7419	Intermediate Similarity	NPC478120
0.7397	Intermediate Similarity	NPC260396
0.7391	Intermediate Similarity	NPC132286
0.7391	Intermediate Similarity	NPC203335
0.7385	Intermediate Similarity	NPC222852
0.7361	Intermediate Similarity	NPC329890
0.7353	Intermediate Similarity	NPC471556
0.7353	Intermediate Similarity	NPC476589
0.7344	Intermediate Similarity	NPC44542
0.7344	Intermediate Similarity	NPC71755
0.7344	Intermediate Similarity	NPC472445
0.7333	Intermediate Similarity	NPC275316
0.7333	Intermediate Similarity	NPC221467
0.7333	Intermediate Similarity	NPC473471
0.7324	Intermediate Similarity	NPC476012
0.7313	Intermediate Similarity	NPC475073
0.7297	Intermediate Similarity	NPC209113
0.7297	Intermediate Similarity	NPC127118
0.7297	Intermediate Similarity	NPC203277
0.7297	Intermediate Similarity	NPC301207
0.7286	Intermediate Similarity	NPC218477
0.7286	Intermediate Similarity	NPC477117
0.72	Intermediate Similarity	NPC125365
0.72	Intermediate Similarity	NPC474818
0.72	Intermediate Similarity	NPC51809
0.72	Intermediate Similarity	NPC176329
0.72	Intermediate Similarity	NPC49302
0.7188	Intermediate Similarity	NPC51846
0.7188	Intermediate Similarity	NPC245002
0.7188	Intermediate Similarity	NPC150717
0.7183	Intermediate Similarity	NPC236208
0.7167	Intermediate Similarity	NPC135698
0.7164	Intermediate Similarity	NPC15193
0.7143	Intermediate Similarity	NPC151761
0.7143	Intermediate Similarity	NPC474127
0.7143	Intermediate Similarity	NPC159535
0.7123	Intermediate Similarity	NPC329914
0.7121	Intermediate Similarity	NPC159650
0.7121	Intermediate Similarity	NPC322186
0.7121	Intermediate Similarity	NPC22897
0.7105	Intermediate Similarity	NPC279532
0.7105	Intermediate Similarity	NPC279214
0.7105	Intermediate Similarity	NPC221095
0.7101	Intermediate Similarity	NPC7940
0.7101	Intermediate Similarity	NPC220766
0.7101	Intermediate Similarity	NPC478099
0.7101	Intermediate Similarity	NPC478098
0.7097	Intermediate Similarity	NPC191643
0.7083	Intermediate Similarity	NPC329904
0.7083	Intermediate Similarity	NPC473361
0.7077	Intermediate Similarity	NPC265551
0.7077	Intermediate Similarity	NPC212730
0.7067	Intermediate Similarity	NPC470705
0.7067	Intermediate Similarity	NPC68819
0.7067	Intermediate Similarity	NPC225022
0.7067	Intermediate Similarity	NPC238554
0.7067	Intermediate Similarity	NPC188860
0.7059	Intermediate Similarity	NPC132243
0.7059	Intermediate Similarity	NPC474658
0.7051	Intermediate Similarity	NPC325031
0.7042	Intermediate Similarity	NPC470256
0.7031	Intermediate Similarity	NPC173157
0.7031	Intermediate Similarity	NPC474913
0.7027	Intermediate Similarity	NPC177030
0.7015	Intermediate Similarity	NPC26223
0.7015	Intermediate Similarity	NPC79756
0.7013	Intermediate Similarity	NPC99651
0.7	Intermediate Similarity	NPC191233
0.7	Intermediate Similarity	NPC315115
0.7	Intermediate Similarity	NPC161670
0.6986	Remote Similarity	NPC178575
0.6974	Remote Similarity	NPC24827
0.6974	Remote Similarity	NPC228902
0.6974	Remote Similarity	NPC475711
0.6974	Remote Similarity	NPC233071
0.6974	Remote Similarity	NPC7563
0.6974	Remote Similarity	NPC262747
0.6974	Remote Similarity	NPC116177
0.6974	Remote Similarity	NPC320630
0.6974	Remote Similarity	NPC315394
0.6957	Remote Similarity	NPC471611
0.6951	Remote Similarity	NPC45409
0.6949	Remote Similarity	NPC47946
0.6949	Remote Similarity	NPC26600
0.6949	Remote Similarity	NPC270706
0.6944	Remote Similarity	NPC470693
0.6944	Remote Similarity	NPC476591
0.6944	Remote Similarity	NPC88877
0.6935	Remote Similarity	NPC43053
0.6933	Remote Similarity	NPC469414
0.6933	Remote Similarity	NPC329826
0.6933	Remote Similarity	NPC329852
0.6923	Remote Similarity	NPC221763
0.6923	Remote Similarity	NPC86948
0.6905	Remote Similarity	NPC182136
0.6901	Remote Similarity	NPC21998
0.6901	Remote Similarity	NPC194871
0.6901	Remote Similarity	NPC478097
0.6892	Remote Similarity	NPC474705
0.6892	Remote Similarity	NPC215745
0.6892	Remote Similarity	NPC316851
0.6892	Remote Similarity	NPC287878
0.6892	Remote Similarity	NPC12815
0.6892	Remote Similarity	NPC238948
0.6883	Remote Similarity	NPC93763
0.6883	Remote Similarity	NPC28049
0.6883	Remote Similarity	NPC209135
0.6883	Remote Similarity	NPC108816
0.6883	Remote Similarity	NPC471465
0.6883	Remote Similarity	NPC267231
0.6883	Remote Similarity	NPC474816
0.6883	Remote Similarity	NPC196653
0.6883	Remote Similarity	NPC182292
0.6875	Remote Similarity	NPC16488
0.6866	Remote Similarity	NPC318306
0.6866	Remote Similarity	NPC322002
0.6857	Remote Similarity	NPC470688
0.6835	Remote Similarity	NPC150502
0.6835	Remote Similarity	NPC315731
0.6833	Remote Similarity	NPC128280

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 NPC473737 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	124
0.1-0.2	2400
0.2-0.3	4493
0.3-0.4	1759
0.4-0.5	280
0.5-0.6	74
0.6-0.7	18
0.7-0.8	2
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7167	Intermediate Similarity	NPD4220	Pre-registration
0.6935	Remote Similarity	NPD6927	Phase 3
0.6765	Remote Similarity	NPD4246	Clinical (unspecified phase)
0.6471	Remote Similarity	NPD69	Approved
0.6471	Remote Similarity	NPD9119	Approved
0.6438	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.6389	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.6386	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.6341	Remote Similarity	NPD5209	Approved
0.6324	Remote Similarity	NPD9118	Approved
0.6322	Remote Similarity	NPD7838	Discovery
0.6232	Remote Similarity	NPD585	Clinical (unspecified phase)
0.6125	Remote Similarity	NPD4756	Discovery
0.6066	Remote Similarity	NPD9411	Phase 1
0.6027	Remote Similarity	NPD5325	Clinical (unspecified phase)
0.6022	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6	Remote Similarity	NPD6109	Phase 1
0.5972	Remote Similarity	NPD4194	Approved
0.5972	Remote Similarity	NPD4193	Approved
0.5972	Remote Similarity	NPD4192	Approved
0.5972	Remote Similarity	NPD4191	Approved
0.5968	Remote Similarity	NPD6096	Approved
0.5968	Remote Similarity	NPD6097	Approved
0.5955	Remote Similarity	NPD5785	Approved
0.5938	Remote Similarity	NPD5343	Approved
0.5904	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.5882	Remote Similarity	NPD539	Approved
0.5882	Remote Similarity	NPD7154	Phase 3
0.5873	Remote Similarity	NPD4265	Approved
0.5843	Remote Similarity	NPD689	Discontinued
0.5747	Remote Similarity	NPD5363	Approved
0.5714	Remote Similarity	NPD7637	Suspended
0.5699	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.5698	Remote Similarity	NPD5362	Discontinued
0.5684	Remote Similarity	NPD4225	Approved
0.5679	Remote Similarity	NPD8039	Approved
0.5679	Remote Similarity	NPD1452	Discontinued
0.5663	Remote Similarity	NPD4268	Approved
0.5663	Remote Similarity	NPD4271	Approved
0.5625	Remote Similarity	NPD4222	Approved
0.5625	Remote Similarity	NPD39	Approved
0.5625	Remote Similarity	NPD6648	Approved
0.5618	Remote Similarity	NPD1282	Approved
0.5604	Remote Similarity	NPD46	Approved
0.5604	Remote Similarity	NPD6698	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