Structure

Physi-Chem Properties

Molecular Weight:  252.14
Volume:  266.759
LogP:  2.19
LogD:  0.791
LogS:  -1.875
# Rotatable Bonds:  4
TPSA:  67.51
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.894
Synthetic Accessibility Score:  3.769
Fsp3:  0.571
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.58
MDCK Permeability:  2.262380439788103e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.018
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.026
30% Bioavailability (F30%):  0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.602
Plasma Protein Binding (PPB):  96.33573150634766%
Volume Distribution (VD):  0.897
Pgp-substrate:  3.951512575149536%

ADMET: Metabolism

CYP1A2-inhibitor:  0.266
CYP1A2-substrate:  0.946
CYP2C19-inhibitor:  0.171
CYP2C19-substrate:  0.876
CYP2C9-inhibitor:  0.262
CYP2C9-substrate:  0.821
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.305
CYP3A4-inhibitor:  0.149
CYP3A4-substrate:  0.481

ADMET: Excretion

Clearance (CL):  4.844
Half-life (T1/2):  0.632

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.94
Drug-inuced Liver Injury (DILI):  0.964
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.81
Maximum Recommended Daily Dose:  0.034
Skin Sensitization:  0.477
Carcinogencity:  0.147
Eye Corrosion:  0.203
Eye Irritation:  0.228
Respiratory Toxicity:  0.395

Download Data

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

  Natural Product: NPC473277

Natural Product ID:  NPC473277
Common Name*:   Micropyrone
IUPAC Name:   4-hydroxy-3,5-dimethyl-6-(4-methyl-3-oxohexan-2-yl)pyran-2-one
Synonyms:   Micropyrone
Standard InCHIKey:  IJPRHCNTDLDONG-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H20O4/c1-6-7(2)11(15)8(3)13-9(4)12(16)10(5)14(17)18-13/h7-8,16H,6H2,1-5H3
SMILES:  CCC(C)C(=O)C(C)C1=C(C(=C(C(=O)O1)C)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL390585
PubChem CID:   54682570
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
NPO32653 helichrysum italicum ssp. microphyllum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[17315926]
NPO25148.1 Helichrysum italicum Under-species n.a. n.a. Flowered aerial parts Arzana, Sardinia 2010-Jul PMID[23265253]

☑ 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 128.0 ug.mL-1 PMID[482656]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 128.0 ug.mL-1 PMID[482656]

☑ 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 NPC473277 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
0.8889 High Similarity NPC315765
0.8382 Intermediate Similarity NPC315115
0.8243 Intermediate Similarity NPC316324
0.8169 Intermediate Similarity NPC315597
0.8169 Intermediate Similarity NPC316029
0.8143 Intermediate Similarity NPC313444
0.8 Intermediate Similarity NPC315394
0.7917 Intermediate Similarity NPC315285
0.7895 Intermediate Similarity NPC264391
0.7746 Intermediate Similarity NPC132286
0.7714 Intermediate Similarity NPC471556
0.7714 Intermediate Similarity NPC471566
0.7639 Intermediate Similarity NPC238223
0.7639 Intermediate Similarity NPC79220
0.7465 Intermediate Similarity NPC471565
0.7432 Intermediate Similarity NPC59558
0.7432 Intermediate Similarity NPC203819
0.7407 Intermediate Similarity NPC16488
0.7407 Intermediate Similarity NPC475083
0.7349 Intermediate Similarity NPC315395
0.7349 Intermediate Similarity NPC316426
0.7333 Intermediate Similarity NPC133098
0.7262 Intermediate Similarity NPC103743
0.7262 Intermediate Similarity NPC476079
0.7262 Intermediate Similarity NPC113370
0.7241 Intermediate Similarity NPC282644
0.7241 Intermediate Similarity NPC29798
0.7237 Intermediate Similarity NPC12815
0.7237 Intermediate Similarity NPC215745
0.7237 Intermediate Similarity NPC238948
0.7229 Intermediate Similarity NPC307112
0.7176 Intermediate Similarity NPC473658
0.7176 Intermediate Similarity NPC26078
0.7143 Intermediate Similarity NPC470686
0.7111 Intermediate Similarity NPC478233
0.7093 Intermediate Similarity NPC307092
0.7093 Intermediate Similarity NPC51358
0.7067 Intermediate Similarity NPC470693
0.7051 Intermediate Similarity NPC315552
0.7015 Intermediate Similarity NPC218486
0.7013 Intermediate Similarity NPC287878
0.6986 Remote Similarity NPC220766
0.6977 Remote Similarity NPC260343
0.6974 Remote Similarity NPC67183
0.6962 Remote Similarity NPC51391
0.6962 Remote Similarity NPC4492
0.6944 Remote Similarity NPC2328
0.6941 Remote Similarity NPC47220
0.6941 Remote Similarity NPC186332
0.6941 Remote Similarity NPC291712
0.6932 Remote Similarity NPC32552
0.6923 Remote Similarity NPC177030
0.6912 Remote Similarity NPC173157
0.6897 Remote Similarity NPC225283
0.6892 Remote Similarity NPC470033
0.6892 Remote Similarity NPC191233
0.6883 Remote Similarity NPC316185
0.6882 Remote Similarity NPC469851
0.6875 Remote Similarity NPC473825
0.6867 Remote Similarity NPC85772
0.6842 Remote Similarity NPC232812
0.6842 Remote Similarity NPC151481
0.6835 Remote Similarity NPC260396
0.6829 Remote Similarity NPC160582
0.6824 Remote Similarity NPC471185
0.6824 Remote Similarity NPC242233
0.6824 Remote Similarity NPC471223
0.6824 Remote Similarity NPC261380
0.6824 Remote Similarity NPC67081
0.6818 Remote Similarity NPC3436
0.6812 Remote Similarity NPC86948
0.6812 Remote Similarity NPC221763
0.6795 Remote Similarity NPC316851
0.6795 Remote Similarity NPC144419
0.679 Remote Similarity NPC108816
0.679 Remote Similarity NPC127526
0.679 Remote Similarity NPC93763
0.6757 Remote Similarity NPC470688
0.6753 Remote Similarity NPC64234
0.6753 Remote Similarity NPC37929
0.675 Remote Similarity NPC238554
0.675 Remote Similarity NPC470705
0.675 Remote Similarity NPC225022
0.6747 Remote Similarity NPC78677
0.6747 Remote Similarity NPC59994
0.6744 Remote Similarity NPC234038
0.6742 Remote Similarity NPC470520
0.6742 Remote Similarity NPC166110
0.6742 Remote Similarity NPC2882
0.6712 Remote Similarity NPC322457
0.6709 Remote Similarity NPC476590
0.6709 Remote Similarity NPC114727
0.6709 Remote Similarity NPC315843
0.6707 Remote Similarity NPC63326
0.6707 Remote Similarity NPC265980
0.6707 Remote Similarity NPC469617
0.6706 Remote Similarity NPC475706
0.6705 Remote Similarity NPC142159
0.6705 Remote Similarity NPC95364
0.6667 Remote Similarity NPC54996
0.6667 Remote Similarity NPC125925
0.6667 Remote Similarity NPC142423
0.6667 Remote Similarity NPC26624
0.6667 Remote Similarity NPC24827
0.6667 Remote Similarity NPC228902
0.6667 Remote Similarity NPC308294
0.6667 Remote Similarity NPC10080
0.6667 Remote Similarity NPC471225
0.6667 Remote Similarity NPC191283
0.6667 Remote Similarity NPC288667
0.6667 Remote Similarity NPC248193
0.6667 Remote Similarity NPC126061
0.6667 Remote Similarity NPC429928
0.6667 Remote Similarity NPC123908
0.6667 Remote Similarity NPC178575
0.6667 Remote Similarity NPC59646
0.6629 Remote Similarity NPC145666
0.6629 Remote Similarity NPC77337
0.6629 Remote Similarity NPC475879
0.6628 Remote Similarity NPC92633
0.6628 Remote Similarity NPC281172
0.6628 Remote Similarity NPC470755
0.6625 Remote Similarity NPC329852
0.6625 Remote Similarity NPC478196
0.6625 Remote Similarity NPC478191
0.6625 Remote Similarity NPC478194
0.6625 Remote Similarity NPC166018
0.6625 Remote Similarity NPC68624
0.6625 Remote Similarity NPC478192
0.6625 Remote Similarity NPC478193
0.6625 Remote Similarity NPC478195
0.6625 Remote Similarity NPC225665
0.6625 Remote Similarity NPC169056
0.6623 Remote Similarity NPC494
0.6623 Remote Similarity NPC67608
0.6598 Remote Similarity NPC469852
0.6593 Remote Similarity NPC470521
0.6591 Remote Similarity NPC475819
0.6591 Remote Similarity NPC143025
0.6588 Remote Similarity NPC475714
0.6588 Remote Similarity NPC161045
0.6588 Remote Similarity NPC258985
0.6588 Remote Similarity NPC44261
0.6585 Remote Similarity NPC248624
0.6585 Remote Similarity NPC476627
0.6585 Remote Similarity NPC279532
0.6575 Remote Similarity NPC64985
0.6575 Remote Similarity NPC15193
0.6575 Remote Similarity NPC217537
0.6575 Remote Similarity NPC263732
0.6571 Remote Similarity NPC150717
0.6559 Remote Similarity NPC53844
0.6556 Remote Similarity NPC472705
0.6556 Remote Similarity NPC193396
0.6556 Remote Similarity NPC175842
0.6556 Remote Similarity NPC32494
0.6556 Remote Similarity NPC45579
0.6556 Remote Similarity NPC32944
0.6552 Remote Similarity NPC261721
0.6552 Remote Similarity NPC122502
0.6552 Remote Similarity NPC472009
0.6548 Remote Similarity NPC275766
0.6548 Remote Similarity NPC112868
0.6538 Remote Similarity NPC473361
0.6538 Remote Similarity NPC4299
0.6538 Remote Similarity NPC329904
0.6533 Remote Similarity NPC101670
0.6533 Remote Similarity NPC476589
0.6528 Remote Similarity NPC133600
0.6528 Remote Similarity NPC86789
0.6528 Remote Similarity NPC203233
0.6522 Remote Similarity NPC209355
0.6517 Remote Similarity NPC212598
0.6517 Remote Similarity NPC87306
0.6512 Remote Similarity NPC14575
0.6512 Remote Similarity NPC470918
0.6512 Remote Similarity NPC196487
0.6512 Remote Similarity NPC158756
0.6506 Remote Similarity NPC286816
0.6506 Remote Similarity NPC199134
0.6506 Remote Similarity NPC472013
0.6506 Remote Similarity NPC476624
0.6506 Remote Similarity NPC271632
0.65 Remote Similarity NPC122244
0.65 Remote Similarity NPC107654
0.65 Remote Similarity NPC294434
0.65 Remote Similarity NPC117746
0.65 Remote Similarity NPC15499
0.65 Remote Similarity NPC259599
0.6494 Remote Similarity NPC474823
0.6494 Remote Similarity NPC287705
0.6494 Remote Similarity NPC477117
0.6486 Remote Similarity NPC155849
0.6486 Remote Similarity NPC68110
0.6486 Remote Similarity NPC190049
0.6484 Remote Similarity NPC271652
0.6479 Remote Similarity NPC283502
0.6477 Remote Similarity NPC72513
0.6477 Remote Similarity NPC23622
0.6477 Remote Similarity NPC473248

  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 NPC473277 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 NPD4756 Discovery
0.6667 Remote Similarity NPD5209 Approved
0.625 Remote Similarity NPD9411 Phase 1
0.6104 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6087 Remote Similarity NPD5785 Approved
0.6023 Remote Similarity NPD6110 Phase 1
0.6023 Remote Similarity NPD7154 Phase 3
0.6022 Remote Similarity NPD7637 Suspended
0.5979 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5979 Remote Similarity NPD4225 Approved
0.5957 Remote Similarity NPD5778 Approved
0.5957 Remote Similarity NPD5779 Approved
0.5955 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5921 Remote Similarity NPD4193 Approved
0.5921 Remote Similarity NPD4192 Approved
0.5921 Remote Similarity NPD4191 Approved
0.5921 Remote Similarity NPD4194 Approved
0.5914 Remote Similarity NPD7838 Discovery
0.5914 Remote Similarity NPD6698 Approved
0.5914 Remote Similarity NPD46 Approved
0.5897 Remote Similarity NPD7341 Phase 2
0.5889 Remote Similarity NPD5363 Approved
0.5862 Remote Similarity NPD4252 Approved
0.5851 Remote Similarity NPD7983 Approved
0.5842 Remote Similarity NPD5909 Discontinued
0.5833 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5833 Remote Similarity NPD8039 Approved
0.5823 Remote Similarity NPD3704 Approved
0.5797 Remote Similarity NPD4220 Pre-registration
0.5789 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5773 Remote Similarity NPD7839 Suspended
0.573 Remote Similarity NPD4800 Clinical (unspecified phase)
0.573 Remote Similarity NPD4270 Approved
0.573 Remote Similarity NPD4269 Approved
0.573 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5714 Remote Similarity NPD1694 Approved
0.5682 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5652 Remote Similarity NPD5786 Approved
0.5652 Remote Similarity NPD4249 Approved
0.5641 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5638 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5638 Remote Similarity NPD7285 Clinical (unspecified phase)
0.5638 Remote Similarity NPD6101 Approved
0.5634 Remote Similarity NPD6927 Phase 3
0.5632 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5625 Remote Similarity NPD7331 Phase 2
0.56 Remote Similarity NPD7640 Approved
0.56 Remote Similarity NPD7639 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