NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	226.08
Volume:	223.661
LogP:	-0.615
LogD:	-0.365
LogS:	-0.306
# Rotatable Bonds:	5
TPSA:	83.83
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.389
Synthetic Accessibility Score:	4.706
Fsp3:	0.455
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.688
MDCK Permeability:	3.394084342289716e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.58
20% Bioavailability (F20%):	0.101
30% Bioavailability (F30%):	0.933

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.768
Plasma Protein Binding (PPB):	21.75908851623535%
Volume Distribution (VD):	0.453
Pgp-substrate:	85.79429626464844%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.122
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.063
CYP2C9-inhibitor:	0.004
CYP2C9-substrate:	0.156
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.115
CYP3A4-inhibitor:	0.016
CYP3A4-substrate:	0.135

ADMET: Excretion

Clearance (CL):	2.802
Half-life (T1/2):	0.819

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.16
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.958
Rat Oral Acute Toxicity:	0.055
Maximum Recommended Daily Dose:	0.335
Skin Sensitization:	0.938
Carcinogencity:	0.034
Eye Corrosion:	0.014
Eye Irritation:	0.235
Respiratory Toxicity:	0.806

Download Data

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

Natural Product: NPC161038

Natural Product ID:	NPC161038
*Common Name:**	Eutypellin B
IUPAC Name:	(3E,4S,5R)-4-hydroxy-3-[(E)-4-hydroxybut-2-enylidene]-5-[(E)-3-hydroxyprop-1-enyl]oxolan-2-one
Synonyms:
Standard InCHIKey:	IKZVKSMJMBFFAC-ISKCKYDESA-N
Standard InCHI:	InChI=1S/C11H14O5/c12-6-2-1-4-8-10(14)9(5-3-7-13)16-11(8)15/h1-5,9-10,12-14H,6-7H2/b2-1+,5-3+,8-4+/t9-,10+/m1/s1
SMILES:	C(=CCO)/C=C/1[C@@H]([C@@H](/C=C/CO)OC1=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1077665
PubChem CID:	44479729
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
NPO32452	Eutypella sp.	Under-species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[19739600]

☑ 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
IC50	4

Activity Type	# Activity
Cell Line	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT639	Cell Line	NCI-H187	Homo sapiens	IC50	=	206000.0	nM	PMID[502958]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	221000.0	nM	PMID[502958]
NPT91	Cell Line	KB	Homo sapiens	IC50	=	144000.0	nM	PMID[502958]
NPT189	Cell Line	Vero	Chlorocebus aethiops	IC50	>	221000.0	nM	PMID[502958]

☑ 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 NPC161038 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	206
0.1-0.2	1522
0.2-0.3	7299
0.3-0.4	17489
0.4-0.5	10695
0.5-0.6	3975
0.6-0.7	1200
0.7-0.8	280
0.8-0.85	25
0.85-0.9	4
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9718	High Similarity	NPC275530
0.8533	High Similarity	NPC209113
0.8533	High Similarity	NPC127118
0.8442	Intermediate Similarity	NPC99651
0.84	Intermediate Similarity	NPC478191
0.84	Intermediate Similarity	NPC478195
0.84	Intermediate Similarity	NPC478196
0.84	Intermediate Similarity	NPC478192
0.84	Intermediate Similarity	NPC478193
0.84	Intermediate Similarity	NPC478194
0.8356	Intermediate Similarity	NPC202011
0.8354	Intermediate Similarity	NPC475046
0.8354	Intermediate Similarity	NPC310450
0.8354	Intermediate Similarity	NPC474959
0.8354	Intermediate Similarity	NPC11383
0.8312	Intermediate Similarity	NPC473471
0.8289	Intermediate Similarity	NPC301207
0.825	Intermediate Similarity	NPC286770
0.825	Intermediate Similarity	NPC284472
0.825	Intermediate Similarity	NPC229799
0.8228	Intermediate Similarity	NPC150502
0.8219	Intermediate Similarity	NPC475982
0.8182	Intermediate Similarity	NPC474818
0.8182	Intermediate Similarity	NPC49302
0.8182	Intermediate Similarity	NPC51809
0.8182	Intermediate Similarity	NPC125365
0.8182	Intermediate Similarity	NPC176329
0.8077	Intermediate Similarity	NPC221095
0.8077	Intermediate Similarity	NPC279214
0.8052	Intermediate Similarity	NPC470705
0.8026	Intermediate Similarity	NPC114727
0.8026	Intermediate Similarity	NPC476590
0.8	Intermediate Similarity	NPC297440
0.7917	Intermediate Similarity	NPC470123
0.7887	Intermediate Similarity	NPC473737
0.7875	Intermediate Similarity	NPC121374
0.7838	Intermediate Similarity	NPC63873
0.7808	Intermediate Similarity	NPC37382
0.7808	Intermediate Similarity	NPC276299
0.7792	Intermediate Similarity	NPC107654
0.7792	Intermediate Similarity	NPC315843
0.7763	Intermediate Similarity	NPC293114
0.7692	Intermediate Similarity	NPC260396
0.7671	Intermediate Similarity	NPC273600
0.7671	Intermediate Similarity	NPC19769
0.7662	Intermediate Similarity	NPC284006
0.7625	Intermediate Similarity	NPC28049
0.7625	Intermediate Similarity	NPC318481
0.7595	Intermediate Similarity	NPC68819
0.7595	Intermediate Similarity	NPC203277
0.7568	Intermediate Similarity	NPC146811
0.7568	Intermediate Similarity	NPC201356
0.7532	Intermediate Similarity	NPC316185
0.7529	Intermediate Similarity	NPC469910
0.747	Intermediate Similarity	NPC8161
0.7468	Intermediate Similarity	NPC473948
0.7432	Intermediate Similarity	NPC478098
0.7432	Intermediate Similarity	NPC282760
0.7432	Intermediate Similarity	NPC96414
0.7432	Intermediate Similarity	NPC478099
0.7416	Intermediate Similarity	NPC469645
0.7416	Intermediate Similarity	NPC469692
0.7412	Intermediate Similarity	NPC470755
0.7407	Intermediate Similarity	NPC279532
0.7407	Intermediate Similarity	NPC182292
0.7397	Intermediate Similarity	NPC68110
0.7386	Intermediate Similarity	NPC474232
0.7375	Intermediate Similarity	NPC205615
0.7375	Intermediate Similarity	NPC16279
0.7375	Intermediate Similarity	NPC256640
0.7368	Intermediate Similarity	NPC474823
0.7368	Intermediate Similarity	NPC287705
0.7361	Intermediate Similarity	NPC98519
0.7356	Intermediate Similarity	NPC476803
0.7356	Intermediate Similarity	NPC287089
0.7342	Intermediate Similarity	NPC326504
0.7333	Intermediate Similarity	NPC121825
0.7333	Intermediate Similarity	NPC478101
0.7326	Intermediate Similarity	NPC279267
0.7326	Intermediate Similarity	NPC69082
0.7297	Intermediate Similarity	NPC470808
0.7294	Intermediate Similarity	NPC158756
0.7273	Intermediate Similarity	NPC476591
0.7273	Intermediate Similarity	NPC475004
0.7273	Intermediate Similarity	NPC14901
0.7273	Intermediate Similarity	NPC88877
0.7273	Intermediate Similarity	NPC130359
0.725	Intermediate Similarity	NPC473582
0.7241	Intermediate Similarity	NPC178215
0.7241	Intermediate Similarity	NPC45409
0.7237	Intermediate Similarity	NPC478100
0.7237	Intermediate Similarity	NPC25298
0.7237	Intermediate Similarity	NPC478097
0.7222	Intermediate Similarity	NPC302564
0.7222	Intermediate Similarity	NPC97570
0.7222	Intermediate Similarity	NPC318306
0.7215	Intermediate Similarity	NPC238948
0.7215	Intermediate Similarity	NPC12815
0.7215	Intermediate Similarity	NPC215745
0.7209	Intermediate Similarity	NPC107986
0.7209	Intermediate Similarity	NPC132496
0.7209	Intermediate Similarity	NPC223871
0.7209	Intermediate Similarity	NPC66346
0.7209	Intermediate Similarity	NPC21469
0.7209	Intermediate Similarity	NPC473651
0.7209	Intermediate Similarity	NPC82795
0.7209	Intermediate Similarity	NPC286338
0.7209	Intermediate Similarity	NPC103284
0.7209	Intermediate Similarity	NPC473478
0.7209	Intermediate Similarity	NPC1083
0.7209	Intermediate Similarity	NPC473669
0.7209	Intermediate Similarity	NPC110710
0.7209	Intermediate Similarity	NPC283085
0.7209	Intermediate Similarity	NPC231009
0.72	Intermediate Similarity	NPC476589
0.7195	Intermediate Similarity	NPC108816
0.7195	Intermediate Similarity	NPC93763
0.7195	Intermediate Similarity	NPC475699
0.7191	Intermediate Similarity	NPC274075
0.7191	Intermediate Similarity	NPC475879
0.7179	Intermediate Similarity	NPC476037
0.7176	Intermediate Similarity	NPC161045
0.7176	Intermediate Similarity	NPC116543
0.7176	Intermediate Similarity	NPC169575
0.7176	Intermediate Similarity	NPC40746
0.7176	Intermediate Similarity	NPC16488
0.7176	Intermediate Similarity	NPC253801
0.7174	Intermediate Similarity	NPC477921
0.716	Intermediate Similarity	NPC474197
0.716	Intermediate Similarity	NPC225022
0.716	Intermediate Similarity	NPC190400
0.716	Intermediate Similarity	NPC238554
0.716	Intermediate Similarity	NPC49392
0.7159	Intermediate Similarity	NPC150063
0.7159	Intermediate Similarity	NPC21208
0.7159	Intermediate Similarity	NPC119740
0.7159	Intermediate Similarity	NPC233551
0.7159	Intermediate Similarity	NPC280621
0.7159	Intermediate Similarity	NPC48338
0.7159	Intermediate Similarity	NPC20339
0.7159	Intermediate Similarity	NPC476805
0.7159	Intermediate Similarity	NPC40376
0.7159	Intermediate Similarity	NPC475819
0.7143	Intermediate Similarity	NPC238223
0.7143	Intermediate Similarity	NPC24417
0.7143	Intermediate Similarity	NPC309466
0.7143	Intermediate Similarity	NPC474980
0.7126	Intermediate Similarity	NPC232555
0.7126	Intermediate Similarity	NPC308412
0.7126	Intermediate Similarity	NPC103523
0.7126	Intermediate Similarity	NPC210218
0.7126	Intermediate Similarity	NPC204686
0.7126	Intermediate Similarity	NPC316426
0.7126	Intermediate Similarity	NPC107717
0.7126	Intermediate Similarity	NPC62118
0.7126	Intermediate Similarity	NPC134807
0.7126	Intermediate Similarity	NPC231096
0.7126	Intermediate Similarity	NPC219498
0.7126	Intermediate Similarity	NPC134885
0.7126	Intermediate Similarity	NPC134865
0.7126	Intermediate Similarity	NPC473687
0.7126	Intermediate Similarity	NPC114694
0.7126	Intermediate Similarity	NPC478112
0.7126	Intermediate Similarity	NPC475581
0.7126	Intermediate Similarity	NPC171174
0.7126	Intermediate Similarity	NPC315395
0.7126	Intermediate Similarity	NPC112685
0.7126	Intermediate Similarity	NPC240695
0.7126	Intermediate Similarity	NPC142117
0.7125	Intermediate Similarity	NPC177030
0.7125	Intermediate Similarity	NPC474545
0.7125	Intermediate Similarity	NPC473489
0.7123	Intermediate Similarity	NPC130953
0.7111	Intermediate Similarity	NPC473321
0.7111	Intermediate Similarity	NPC303230
0.7111	Intermediate Similarity	NPC327760
0.7111	Intermediate Similarity	NPC6099
0.7111	Intermediate Similarity	NPC114345
0.7108	Intermediate Similarity	NPC473980
0.7108	Intermediate Similarity	NPC473981
0.7108	Intermediate Similarity	NPC1180
0.7108	Intermediate Similarity	NPC475210
0.7105	Intermediate Similarity	NPC475675
0.7105	Intermediate Similarity	NPC475555
0.7093	Intermediate Similarity	NPC163093
0.7093	Intermediate Similarity	NPC161670
0.7093	Intermediate Similarity	NPC32676
0.7079	Intermediate Similarity	NPC139418
0.7079	Intermediate Similarity	NPC79027
0.7073	Intermediate Similarity	NPC228902
0.7073	Intermediate Similarity	NPC7563
0.7073	Intermediate Similarity	NPC320630
0.7073	Intermediate Similarity	NPC116177
0.7073	Intermediate Similarity	NPC474278
0.7073	Intermediate Similarity	NPC24827
0.7073	Intermediate Similarity	NPC475711
0.7065	Intermediate Similarity	NPC471142
0.7065	Intermediate Similarity	NPC477922
0.7059	Intermediate Similarity	NPC145914
0.7059	Intermediate Similarity	NPC11332

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 NPC161038 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	160
0.1-0.2	2152
0.2-0.3	4247
0.3-0.4	1898
0.4-0.5	583
0.5-0.6	83
0.6-0.7	27
0.7-0.8	0
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
0.6842	Remote Similarity	NPD4225	Approved
0.663	Remote Similarity	NPD7838	Discovery
0.6622	Remote Similarity	NPD69	Approved
0.6622	Remote Similarity	NPD9119	Approved
0.6559	Remote Similarity	NPD7983	Approved
0.6526	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.6486	Remote Similarity	NPD9118	Approved
0.6477	Remote Similarity	NPD5209	Approved
0.6452	Remote Similarity	NPD5785	Approved
0.6447	Remote Similarity	NPD4246	Clinical (unspecified phase)
0.64	Remote Similarity	NPD585	Clinical (unspecified phase)
0.6375	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.6327	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6277	Remote Similarity	NPD6698	Approved
0.6277	Remote Similarity	NPD46	Approved
0.6264	Remote Similarity	NPD5363	Approved
0.6214	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.619	Remote Similarity	NPD6371	Approved
0.6184	Remote Similarity	NPD6109	Phase 1
0.6092	Remote Similarity	NPD4756	Discovery
0.6067	Remote Similarity	NPD4252	Approved
0.6067	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.6044	Remote Similarity	NPD7154	Phase 3
0.6042	Remote Similarity	NPD7637	Suspended
0.6	Remote Similarity	NPD7115	Discovery
0.5979	Remote Similarity	NPD5779	Approved
0.5979	Remote Similarity	NPD5778	Approved
0.5978	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.5934	Remote Similarity	NPD4270	Approved
0.5934	Remote Similarity	NPD4269	Approved
0.5914	Remote Similarity	NPD1733	Clinical (unspecified phase)
0.589	Remote Similarity	NPD6927	Phase 3
0.5851	Remote Similarity	NPD5786	Approved
0.5851	Remote Similarity	NPD4249	Approved
0.5843	Remote Similarity	NPD4268	Approved
0.5843	Remote Similarity	NPD4271	Approved
0.5833	Remote Similarity	NPD4220	Pre-registration
0.58	Remote Similarity	NPD7839	Suspended
0.5789	Remote Similarity	NPD8515	Approved
0.5789	Remote Similarity	NPD4250	Approved
0.5789	Remote Similarity	NPD8513	Phase 3
0.5789	Remote Similarity	NPD4251	Approved
0.5789	Remote Similarity	NPD8517	Approved
0.5789	Remote Similarity	NPD8516	Approved
0.5728	Remote Similarity	NPD5344	Discontinued
0.5714	Remote Similarity	NPD4819	Approved
0.5714	Remote Similarity	NPD4821	Approved
0.5714	Remote Similarity	NPD4820	Approved
0.5714	Remote Similarity	NPD4822	Approved
0.5699	Remote Similarity	NPD5362	Discontinued
0.5699	Remote Similarity	NPD6110	Phase 1
0.5688	Remote Similarity	NPD7601	Clinical (unspecified phase)
0.5688	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.567	Remote Similarity	NPD5370	Suspended
0.567	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.567	Remote Similarity	NPD6101	Approved
0.5652	Remote Similarity	NPD5369	Approved
0.5652	Remote Similarity	NPD4790	Discontinued
0.5631	Remote Similarity	NPD6648	Approved
0.5625	Remote Similarity	NPD9120	Clinical (unspecified phase)
0.561	Remote Similarity	NPD3197	Phase 1

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