NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	224.14
Volume:	243.309
LogP:	3.666
LogD:	3.851
LogS:	-3.166
# Rotatable Bonds:	5
TPSA:	50.44
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.782
Synthetic Accessibility Score:	2.49
Fsp3:	0.615
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.602
MDCK Permeability:	2.4734379621804692e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.218
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.122
30% Bioavailability (F30%):	0.382

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.213
Plasma Protein Binding (PPB):	97.02848052978516%
Volume Distribution (VD):	0.656
Pgp-substrate:	3.8495514392852783%

ADMET: Metabolism

CYP1A2-inhibitor:	0.952
CYP1A2-substrate:	0.911
CYP2C19-inhibitor:	0.939
CYP2C19-substrate:	0.711
CYP2C9-inhibitor:	0.907
CYP2C9-substrate:	0.971
CYP2D6-inhibitor:	0.152
CYP2D6-substrate:	0.77
CYP3A4-inhibitor:	0.167
CYP3A4-substrate:	0.206

ADMET: Excretion

Clearance (CL):	4.557
Half-life (T1/2):	0.483

ADMET: Toxicity

hERG Blockers:	0.023
Human Hepatotoxicity (H-HT):	0.286
Drug-inuced Liver Injury (DILI):	0.661
AMES Toxicity:	0.027
Rat Oral Acute Toxicity:	0.134
Maximum Recommended Daily Dose:	0.065
Skin Sensitization:	0.723
Carcinogencity:	0.144
Eye Corrosion:	0.847
Eye Irritation:	0.967
Respiratory Toxicity:	0.107

Download Data

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

Natural Product: NPC313444

Natural Product ID:	NPC313444
*Common Name:**	Violapyrone B
IUPAC Name:	4-hydroxy-3-methyl-6-(5-methylhexyl)pyran-2-one
Synonyms:
Standard InCHIKey:	ATVUDEORTZJYHL-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C13H20O3/c1-9(2)6-4-5-7-11-8-12(14)10(3)13(15)16-11/h8-9,14H,4-7H2,1-3H3
SMILES:	CC(C)CCCCc1cc(c(C)c(=O)o1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3087382
PubChem CID:	71607042
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000086] Pyrans [CHEMONTID:0000481] Pyranones and derivatives

*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
NPO11517	Streptomyces violascens	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24182355]
NPO11517	Streptomyces violascens	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[28206772]

☑ 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	5
MIC	2

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	2
Organism	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	>	200000.0	nM	PMID[554510]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	>	200000.0	nM	PMID[554510]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	>	200000.0	nM	PMID[554510]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	4.0	ug.mL-1	PMID[554510]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	4.0	ug.mL-1	PMID[554510]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	200000.0	nM	PMID[554510]

☑ 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 NPC313444 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	302
0.1-0.2	1896
0.2-0.3	4994
0.3-0.4	11084
0.4-0.5	7383
0.5-0.6	5720
0.6-0.7	7337
0.7-0.8	3625
0.8-0.85	267
0.85-0.9	53
0.9-0.95	11
0.95-1	25

Similarity Score	Similarity Level	Natural Product ID
0.9692	High Similarity	NPC316029
0.9394	High Similarity	NPC315597
0.9375	High Similarity	NPC315115
0.9104	High Similarity	NPC315285
0.8873	High Similarity	NPC316324
0.8873	High Similarity	NPC315394
0.8636	High Similarity	NPC471556
0.8358	Intermediate Similarity	NPC471566
0.8143	Intermediate Similarity	NPC473277
0.8143	Intermediate Similarity	NPC232812
0.8088	Intermediate Similarity	NPC471565
0.8028	Intermediate Similarity	NPC64234
0.8028	Intermediate Similarity	NPC37929
0.8	Intermediate Similarity	NPC315765
0.7937	Intermediate Similarity	NPC218486
0.7887	Intermediate Similarity	NPC151481
0.7867	Intermediate Similarity	NPC54996
0.7857	Intermediate Similarity	NPC132286
0.7778	Intermediate Similarity	NPC59558
0.7761	Intermediate Similarity	NPC429928
0.7746	Intermediate Similarity	NPC238223
0.7714	Intermediate Similarity	NPC191233
0.7714	Intermediate Similarity	NPC142423
0.7714	Intermediate Similarity	NPC308294
0.7703	Intermediate Similarity	NPC470686
0.7692	Intermediate Similarity	NPC86948
0.7632	Intermediate Similarity	NPC471225
0.7571	Intermediate Similarity	NPC220766
0.7538	Intermediate Similarity	NPC173157
0.7536	Intermediate Similarity	NPC2328
0.7536	Intermediate Similarity	NPC155849
0.7531	Intermediate Similarity	NPC67081
0.7531	Intermediate Similarity	NPC471223
0.75	Intermediate Similarity	NPC475083
0.75	Intermediate Similarity	NPC475714
0.747	Intermediate Similarity	NPC473658
0.7436	Intermediate Similarity	NPC469617
0.7432	Intermediate Similarity	NPC181587
0.7407	Intermediate Similarity	NPC196487
0.7407	Intermediate Similarity	NPC14575
0.7407	Intermediate Similarity	NPC475706
0.7397	Intermediate Similarity	NPC470693
0.7397	Intermediate Similarity	NPC475004
0.7397	Intermediate Similarity	NPC265574
0.7381	Intermediate Similarity	NPC307092
0.7375	Intermediate Similarity	NPC474028
0.7375	Intermediate Similarity	NPC474439
0.7361	Intermediate Similarity	NPC472266
0.7353	Intermediate Similarity	NPC133600
0.7344	Intermediate Similarity	NPC191643
0.7317	Intermediate Similarity	NPC471185
0.7297	Intermediate Similarity	NPC4299
0.7297	Intermediate Similarity	NPC329904
0.7297	Intermediate Similarity	NPC473361
0.7297	Intermediate Similarity	NPC67183
0.7286	Intermediate Similarity	NPC217940
0.7262	Intermediate Similarity	NPC260343
0.7262	Intermediate Similarity	NPC26078
0.726	Intermediate Similarity	NPC474823
0.726	Intermediate Similarity	NPC310210
0.7229	Intermediate Similarity	NPC47220
0.7229	Intermediate Similarity	NPC234038
0.7229	Intermediate Similarity	NPC186332
0.7209	Intermediate Similarity	NPC2882
0.72	Intermediate Similarity	NPC288667
0.72	Intermediate Similarity	NPC316185
0.7179	Intermediate Similarity	NPC180290
0.7179	Intermediate Similarity	NPC473825
0.7176	Intermediate Similarity	NPC51358
0.7164	Intermediate Similarity	NPC221763
0.7162	Intermediate Similarity	NPC101622
0.716	Intermediate Similarity	NPC10080
0.716	Intermediate Similarity	NPC123908
0.7143	Intermediate Similarity	NPC113370
0.7143	Intermediate Similarity	NPC125925
0.7143	Intermediate Similarity	NPC103743
0.7143	Intermediate Similarity	NPC234084
0.7143	Intermediate Similarity	NPC329852
0.7143	Intermediate Similarity	NPC476079
0.7143	Intermediate Similarity	NPC126184
0.7143	Intermediate Similarity	NPC191283
0.7126	Intermediate Similarity	NPC472954
0.7125	Intermediate Similarity	NPC10636
0.7108	Intermediate Similarity	NPC307112
0.7108	Intermediate Similarity	NPC474424
0.7108	Intermediate Similarity	NPC242233
0.7089	Intermediate Similarity	NPC108816
0.7089	Intermediate Similarity	NPC93763
0.7083	Intermediate Similarity	NPC182794
0.7083	Intermediate Similarity	NPC470688
0.7073	Intermediate Similarity	NPC16488
0.7073	Intermediate Similarity	NPC44261
0.7067	Intermediate Similarity	NPC469660
0.7059	Intermediate Similarity	NPC165808
0.7059	Intermediate Similarity	NPC475739
0.7051	Intermediate Similarity	NPC469880
0.7037	Intermediate Similarity	NPC112868
0.7037	Intermediate Similarity	NPC325031
0.7037	Intermediate Similarity	NPC59994
0.7037	Intermediate Similarity	NPC315731
0.7037	Intermediate Similarity	NPC78677
0.7027	Intermediate Similarity	NPC276290
0.7027	Intermediate Similarity	NPC79220
0.7024	Intermediate Similarity	NPC316426
0.7024	Intermediate Similarity	NPC315395
0.7024	Intermediate Similarity	NPC122502
0.7015	Intermediate Similarity	NPC478117
0.7013	Intermediate Similarity	NPC315843
0.7	Intermediate Similarity	NPC471537
0.7	Intermediate Similarity	NPC19241
0.7	Intermediate Similarity	NPC139712
0.6986	Remote Similarity	NPC100719
0.6986	Remote Similarity	NPC470033
0.6986	Remote Similarity	NPC166791
0.6986	Remote Similarity	NPC322035
0.6986	Remote Similarity	NPC116013
0.6977	Remote Similarity	NPC225283
0.6977	Remote Similarity	NPC115179
0.6977	Remote Similarity	NPC212598
0.6977	Remote Similarity	NPC106040
0.6974	Remote Similarity	NPC477087
0.6974	Remote Similarity	NPC477086
0.6974	Remote Similarity	NPC472254
0.6962	Remote Similarity	NPC41780
0.6962	Remote Similarity	NPC7563
0.6962	Remote Similarity	NPC320630
0.6962	Remote Similarity	NPC187568
0.6962	Remote Similarity	NPC116177
0.6957	Remote Similarity	NPC189700
0.6951	Remote Similarity	NPC85772
0.6944	Remote Similarity	NPC150162
0.6944	Remote Similarity	NPC477456
0.6944	Remote Similarity	NPC477457
0.6941	Remote Similarity	NPC475678
0.6941	Remote Similarity	NPC313658
0.6941	Remote Similarity	NPC316138
0.6932	Remote Similarity	NPC59646
0.6923	Remote Similarity	NPC148056
0.6923	Remote Similarity	NPC315552
0.6923	Remote Similarity	NPC68624
0.6914	Remote Similarity	NPC268827
0.6914	Remote Similarity	NPC474510
0.6912	Remote Similarity	NPC150717
0.6912	Remote Similarity	NPC141699
0.6905	Remote Similarity	NPC474369
0.6901	Remote Similarity	NPC317025
0.6901	Remote Similarity	NPC15193
0.6901	Remote Similarity	NPC317177
0.6901	Remote Similarity	NPC326645
0.6901	Remote Similarity	NPC329416
0.6897	Remote Similarity	NPC182136
0.6897	Remote Similarity	NPC3436
0.6892	Remote Similarity	NPC21998
0.6883	Remote Similarity	NPC316851
0.6883	Remote Similarity	NPC477085
0.6875	Remote Similarity	NPC196653
0.6875	Remote Similarity	NPC184737
0.6875	Remote Similarity	NPC471220
0.6875	Remote Similarity	NPC267231
0.6875	Remote Similarity	NPC169095
0.6875	Remote Similarity	NPC471465
0.6867	Remote Similarity	NPC472377
0.6867	Remote Similarity	NPC288281
0.6867	Remote Similarity	NPC311070
0.6866	Remote Similarity	NPC478120
0.6866	Remote Similarity	NPC474127
0.686	Remote Similarity	NPC60765
0.686	Remote Similarity	NPC472302
0.686	Remote Similarity	NPC471956
0.6857	Remote Similarity	NPC22897
0.6857	Remote Similarity	NPC159650
0.6854	Remote Similarity	NPC470521
0.6842	Remote Similarity	NPC203819
0.6835	Remote Similarity	NPC473223
0.6835	Remote Similarity	NPC477202
0.6829	Remote Similarity	NPC8538
0.6829	Remote Similarity	NPC475944
0.6829	Remote Similarity	NPC42470
0.6829	Remote Similarity	NPC184208
0.6824	Remote Similarity	NPC116575
0.6824	Remote Similarity	NPC198314
0.6818	Remote Similarity	NPC151919
0.6818	Remote Similarity	NPC470520
0.6818	Remote Similarity	NPC45579
0.6818	Remote Similarity	NPC32494
0.6818	Remote Similarity	NPC166110
0.6818	Remote Similarity	NPC175842
0.6806	Remote Similarity	NPC473737
0.68	Remote Similarity	NPC287705
0.6795	Remote Similarity	NPC259599
0.6795	Remote Similarity	NPC15499
0.6795	Remote Similarity	NPC107654
0.6795	Remote Similarity	NPC476355
0.6795	Remote Similarity	NPC213223
0.6795	Remote Similarity	NPC474758
0.6795	Remote Similarity	NPC117746
0.6795	Remote Similarity	NPC294434
0.679	Remote Similarity	NPC264227
0.679	Remote Similarity	NPC271632
0.679	Remote Similarity	NPC472965

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 NPC313444 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	280
0.1-0.2	1011
0.2-0.3	1753
0.3-0.4	2727
0.4-0.5	1871
0.5-0.6	1097
0.6-0.7	315
0.7-0.8	83
0.8-0.85	10
0.85-0.9	2
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7083	Intermediate Similarity	NPD2685	Clinical (unspecified phase)
0.6962	Remote Similarity	NPD4756	Discovery
0.6901	Remote Similarity	NPD4191	Approved
0.6901	Remote Similarity	NPD4192	Approved
0.6901	Remote Similarity	NPD4194	Approved
0.6901	Remote Similarity	NPD4193	Approved
0.6709	Remote Similarity	NPD8039	Approved
0.6615	Remote Similarity	NPD4220	Pre-registration
0.6562	Remote Similarity	NPD5909	Discontinued
0.6517	Remote Similarity	NPD7838	Discovery
0.6486	Remote Similarity	NPD5325	Clinical (unspecified phase)
0.6471	Remote Similarity	NPD7154	Phase 3
0.6395	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.6383	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6353	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.6353	Remote Similarity	NPD5209	Approved
0.6333	Remote Similarity	NPD46	Approved
0.6333	Remote Similarity	NPD6698	Approved
0.6301	Remote Similarity	NPD4246	Clinical (unspecified phase)
0.6176	Remote Similarity	NPD6927	Phase 3
0.6146	Remote Similarity	NPD6648	Approved
0.6136	Remote Similarity	NPD1694	Approved
0.6136	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.6104	Remote Similarity	NPD7331	Phase 2
0.6056	Remote Similarity	NPD342	Phase 1
0.6042	Remote Similarity	NPD4225	Approved
0.6022	Remote Similarity	NPD5779	Approved
0.6022	Remote Similarity	NPD5778	Approved
0.6	Remote Similarity	NPD368	Approved
0.5979	Remote Similarity	NPD7640	Approved
0.5979	Remote Similarity	NPD7639	Approved
0.5978	Remote Similarity	NPD5785	Approved
0.593	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.5914	Remote Similarity	NPD7983	Approved
0.5914	Remote Similarity	NPD7637	Suspended
0.5909	Remote Similarity	NPD5362	Discontinued
0.5889	Remote Similarity	NPD4249	Approved
0.5876	Remote Similarity	NPD7638	Approved
0.5833	Remote Similarity	NPD7839	Suspended
0.5824	Remote Similarity	NPD1282	Approved
0.5824	Remote Similarity	NPD4250	Approved
0.5824	Remote Similarity	NPD4251	Approved
0.5778	Remote Similarity	NPD1733	Clinical (unspecified phase)
0.5778	Remote Similarity	NPD5363	Approved
0.5775	Remote Similarity	NPD3172	Approved
0.5769	Remote Similarity	NPD7341	Phase 2
0.5758	Remote Similarity	NPD5344	Discontinued
0.5747	Remote Similarity	NPD4819	Approved
0.5747	Remote Similarity	NPD4822	Approved
0.5747	Remote Similarity	NPD4820	Approved
0.5747	Remote Similarity	NPD4821	Approved
0.5745	Remote Similarity	NPD5693	Phase 1
0.573	Remote Similarity	NPD5331	Approved
0.573	Remote Similarity	NPD6110	Phase 1
0.573	Remote Similarity	NPD5332	Approved
0.5729	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD2664	Clinical (unspecified phase)
0.5699	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.5699	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.5699	Remote Similarity	NPD6101	Approved
0.5698	Remote Similarity	NPD4271	Approved
0.5698	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.5698	Remote Similarity	NPD4268	Approved
0.5696	Remote Similarity	NPD6108	Clinical (unspecified phase)
0.5694	Remote Similarity	NPD4266	Approved
0.5694	Remote Similarity	NPD3196	Approved
0.5694	Remote Similarity	NPD3194	Approved
0.5694	Remote Similarity	NPD3195	Phase 2
0.5682	Remote Similarity	NPD4790	Discontinued
0.566	Remote Similarity	NPD6053	Discontinued
0.5652	Remote Similarity	NPD3173	Approved
0.5644	Remote Similarity	NPD6647	Phase 2
0.5638	Remote Similarity	NPD5207	Approved
0.5638	Remote Similarity	NPD5692	Phase 3
0.5625	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.5618	Remote Similarity	NPD4269	Approved
0.5618	Remote Similarity	NPD4270	Approved
0.5606	Remote Similarity	NPD9411	Phase 1
0.5604	Remote Similarity	NPD1696	Phase 3

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