Structure

Physi-Chem Properties

Molecular Weight:  192.12
Volume:  214.586
LogP:  3.287
LogD:  3.802
LogS:  -3.972
# Rotatable Bonds:  3
TPSA:  30.21
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.736
Synthetic Accessibility Score:  2.768
Fsp3:  0.417
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.615
MDCK Permeability:  2.2854594135424122e-05
Pgp-inhibitor:  0.804
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.054
30% Bioavailability (F30%):  0.949

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.119
Plasma Protein Binding (PPB):  93.99695587158203%
Volume Distribution (VD):  3.01
Pgp-substrate:  8.33885383605957%

ADMET: Metabolism

CYP1A2-inhibitor:  0.982
CYP1A2-substrate:  0.943
CYP2C19-inhibitor:  0.935
CYP2C19-substrate:  0.377
CYP2C9-inhibitor:  0.729
CYP2C9-substrate:  0.626
CYP2D6-inhibitor:  0.278
CYP2D6-substrate:  0.444
CYP3A4-inhibitor:  0.16
CYP3A4-substrate:  0.271

ADMET: Excretion

Clearance (CL):  2.333
Half-life (T1/2):  0.319

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.113
Drug-inuced Liver Injury (DILI):  0.616
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.103
Maximum Recommended Daily Dose:  0.068
Skin Sensitization:  0.1
Carcinogencity:  0.73
Eye Corrosion:  0.421
Eye Irritation:  0.918
Respiratory Toxicity:  0.153

Download Data

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

  Natural Product: NPC173157

Natural Product ID:  NPC173157
Common Name*:   Nocapyrone E
IUPAC Name:   3-ethyl-6-[(E)-pent-2-en-2-yl]pyran-2-one
Synonyms:   Nocapyrone E
Standard InCHIKey:  MHYXYBIZEFPTAE-RMKNXTFCSA-N
Standard InCHI:  InChI=1S/C12H16O2/c1-4-6-9(3)11-8-7-10(5-2)12(13)14-11/h6-8H,4-5H2,1-3H3/b9-6+
SMILES:  CC/C=C(/c1ccc(c(=O)o1)CC)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1835443
PubChem CID:   53345949
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
NPO14429 0cardiopsis dassonvillei Species 0cardiopsaceae Bacteria isolated from marine sediments The estuary of Yellow River, Dongying, Shandong Province, China n.a. PMID[21958359]
NPO14429 0cardiopsis dassonvillei Species 0cardiopsaceae Bacteria n.a. spore n.a. PMID[21958359]
NPO14429 0cardiopsis dassonvillei Species 0cardiopsaceae Bacteria n.a. n.a. n.a. Database[UNPD]

☑ 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
NPT116 Cell Line HL-60 Homo sapiens IC50 >= 100000.0 nM PMID[575374]
NPT81 Cell Line A549 Homo sapiens IC5 >= 100.0 uM PMID[575374]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 26000.0 nM PMID[575374]

☑ 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 NPC173157 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
0.9412 High Similarity NPC191643
0.8824 High Similarity NPC234084
0.8793 High Similarity NPC2328
0.8727 High Similarity NPC150717
0.8727 High Similarity NPC221763
0.8704 High Similarity NPC218486
0.8136 Intermediate Similarity NPC309408
0.807 Intermediate Similarity NPC86948
0.7966 Intermediate Similarity NPC133600
0.7903 Intermediate Similarity NPC471565
0.7903 Intermediate Similarity NPC471556
0.7903 Intermediate Similarity NPC471566
0.7797 Intermediate Similarity NPC189700
0.7778 Intermediate Similarity NPC126184
0.7778 Intermediate Similarity NPC315115
0.7636 Intermediate Similarity NPC236338
0.7636 Intermediate Similarity NPC15789
0.7586 Intermediate Similarity NPC25038
0.7541 Intermediate Similarity NPC429928
0.7541 Intermediate Similarity NPC79756
0.7541 Intermediate Similarity NPC130953
0.7538 Intermediate Similarity NPC313444
0.7455 Intermediate Similarity NPC135698
0.7419 Intermediate Similarity NPC15193
0.7344 Intermediate Similarity NPC476589
0.7313 Intermediate Similarity NPC315597
0.7313 Intermediate Similarity NPC316029
0.7313 Intermediate Similarity NPC315285
0.7302 Intermediate Similarity NPC132243
0.7288 Intermediate Similarity NPC478117
0.7286 Intermediate Similarity NPC470705
0.7273 Intermediate Similarity NPC287705
0.7273 Intermediate Similarity NPC477117
0.7273 Intermediate Similarity NPC128520
0.7258 Intermediate Similarity NPC98519
0.7222 Intermediate Similarity NPC270706
0.7167 Intermediate Similarity NPC51846
0.7143 Intermediate Similarity NPC151648
0.7121 Intermediate Similarity NPC470442
0.7121 Intermediate Similarity NPC132286
0.7119 Intermediate Similarity NPC478120
0.7091 Intermediate Similarity NPC128280
0.7077 Intermediate Similarity NPC182794
0.7077 Intermediate Similarity NPC220766
0.7069 Intermediate Similarity NPC151919
0.7059 Intermediate Similarity NPC59558
0.7031 Intermediate Similarity NPC210303
0.7031 Intermediate Similarity NPC44343
0.7031 Intermediate Similarity NPC179087
0.7031 Intermediate Similarity NPC473737
0.7031 Intermediate Similarity NPC155849
0.7018 Intermediate Similarity NPC275316
0.7018 Intermediate Similarity NPC221467
0.7018 Intermediate Similarity NPC27264
0.7015 Intermediate Similarity NPC238223
0.7015 Intermediate Similarity NPC79220
0.697 Remote Similarity NPC191233
0.697 Remote Similarity NPC470033
0.6964 Remote Similarity NPC90490
0.6957 Remote Similarity NPC133098
0.6944 Remote Similarity NPC316324
0.6912 Remote Similarity NPC470693
0.6912 Remote Similarity NPC473277
0.6909 Remote Similarity NPC47946
0.6909 Remote Similarity NPC26600
0.6901 Remote Similarity NPC478193
0.6901 Remote Similarity NPC478192
0.6901 Remote Similarity NPC478195
0.6901 Remote Similarity NPC478194
0.6901 Remote Similarity NPC478191
0.6901 Remote Similarity NPC478196
0.6897 Remote Similarity NPC43053
0.6897 Remote Similarity NPC148056
0.6866 Remote Similarity NPC21998
0.6866 Remote Similarity NPC203335
0.6842 Remote Similarity NPC82446
0.6842 Remote Similarity NPC15912
0.6825 Remote Similarity NPC22897
0.6825 Remote Similarity NPC159650
0.6825 Remote Similarity NPC286189
0.6825 Remote Similarity NPC203233
0.6818 Remote Similarity NPC131174
0.6818 Remote Similarity NPC133904
0.6818 Remote Similarity NPC273600
0.6818 Remote Similarity NPC470688
0.6786 Remote Similarity NPC197467
0.6774 Remote Similarity NPC293437
0.6774 Remote Similarity NPC135863
0.6774 Remote Similarity NPC474825
0.6774 Remote Similarity NPC249850
0.6769 Remote Similarity NPC68110
0.6769 Remote Similarity NPC474658
0.6765 Remote Similarity NPC280374
0.6719 Remote Similarity NPC26223
0.6716 Remote Similarity NPC475675
0.6716 Remote Similarity NPC475555
0.6716 Remote Similarity NPC248125
0.6714 Remote Similarity NPC181587
0.6712 Remote Similarity NPC315394
0.6712 Remote Similarity NPC68156
0.6667 Remote Similarity NPC53136
0.6667 Remote Similarity NPC254095
0.6667 Remote Similarity NPC329826
0.6667 Remote Similarity NPC21946
0.6667 Remote Similarity NPC232812
0.6667 Remote Similarity NPC469414
0.6667 Remote Similarity NPC475618
0.6667 Remote Similarity NPC173409
0.662 Remote Similarity NPC287878
0.6618 Remote Similarity NPC225272
0.6615 Remote Similarity NPC217537
0.6571 Remote Similarity NPC64234
0.6571 Remote Similarity NPC202011
0.6571 Remote Similarity NPC37929
0.6562 Remote Similarity NPC82465
0.6557 Remote Similarity NPC474127
0.6557 Remote Similarity NPC159535
0.6557 Remote Similarity NPC151761
0.6533 Remote Similarity NPC271632
0.6522 Remote Similarity NPC474823
0.6522 Remote Similarity NPC470256
0.6522 Remote Similarity NPC218477
0.6515 Remote Similarity NPC475073
0.6508 Remote Similarity NPC129150
0.6508 Remote Similarity NPC283502
0.6508 Remote Similarity NPC294938
0.6491 Remote Similarity NPC87137
0.6486 Remote Similarity NPC473825
0.6486 Remote Similarity NPC54996
0.6479 Remote Similarity NPC178575
0.6471 Remote Similarity NPC469446
0.6452 Remote Similarity NPC474913
0.6441 Remote Similarity NPC220191
0.6438 Remote Similarity NPC206507
0.6438 Remote Similarity NPC147621
0.6438 Remote Similarity NPC210258
0.6429 Remote Similarity NPC151481
0.6429 Remote Similarity NPC477686
0.6429 Remote Similarity NPC6963
0.6429 Remote Similarity NPC265574
0.6429 Remote Similarity NPC88877
0.6429 Remote Similarity NPC475004
0.6429 Remote Similarity NPC476591
0.6429 Remote Similarity NPC304079
0.6418 Remote Similarity NPC471611
0.6418 Remote Similarity NPC148233
0.6418 Remote Similarity NPC308457
0.6418 Remote Similarity NPC477456
0.6418 Remote Similarity NPC25747
0.6418 Remote Similarity NPC477457
0.6406 Remote Similarity NPC223679
0.6393 Remote Similarity NPC474805
0.6389 Remote Similarity NPC276336
0.6377 Remote Similarity NPC194871
0.6375 Remote Similarity NPC291712
0.6364 Remote Similarity NPC68044
0.6364 Remote Similarity NPC57923
0.6364 Remote Similarity NPC270412
0.6364 Remote Similarity NPC14437
0.6349 Remote Similarity NPC245002
0.6333 Remote Similarity NPC22329
0.6324 Remote Similarity NPC96414
0.6324 Remote Similarity NPC7940
0.6316 Remote Similarity NPC191337
0.6308 Remote Similarity NPC302564
0.6301 Remote Similarity NPC470686
0.6296 Remote Similarity NPC111474
0.629 Remote Similarity NPC129710
0.629 Remote Similarity NPC317796
0.629 Remote Similarity NPC322461
0.6286 Remote Similarity NPC470032
0.6269 Remote Similarity NPC474774
0.6269 Remote Similarity NPC217940
0.6267 Remote Similarity NPC471225
0.6267 Remote Similarity NPC180290
0.625 Remote Similarity NPC186531
0.625 Remote Similarity NPC316185
0.625 Remote Similarity NPC296589
0.625 Remote Similarity NPC84038
0.625 Remote Similarity NPC257618
0.6232 Remote Similarity NPC201356
0.6232 Remote Similarity NPC146811
0.6232 Remote Similarity NPC37382
0.6232 Remote Similarity NPC124586
0.623 Remote Similarity NPC106531
0.6216 Remote Similarity NPC315552
0.6212 Remote Similarity NPC19241
0.6212 Remote Similarity NPC476585
0.6207 Remote Similarity NPC308331
0.6203 Remote Similarity NPC16488
0.6184 Remote Similarity NPC315765
0.6164 Remote Similarity NPC284006
0.6164 Remote Similarity NPC316851
0.6164 Remote Similarity NPC474705
0.6154 Remote Similarity NPC478096
0.6154 Remote Similarity NPC474084
0.6154 Remote Similarity NPC471619
0.614 Remote Similarity NPC312547
0.614 Remote Similarity NPC12907
0.6133 Remote Similarity NPC27205

  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 NPC173157 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
0.7193 Intermediate Similarity NPD6927 Phase 3
0.6552 Remote Similarity NPD4220 Pre-registration
0.6364 Remote Similarity NPD9418 Clinical (unspecified phase)
0.6267 Remote Similarity NPD4756 Discovery
0.625 Remote Similarity NPD9411 Phase 1
0.614 Remote Similarity NPD6096 Approved
0.614 Remote Similarity NPD6097 Approved
0.6087 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6 Remote Similarity NPD8779 Phase 3
0.5942 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5875 Remote Similarity NPD5209 Approved
0.5833 Remote Similarity NPD5343 Approved
0.5789 Remote Similarity NPD1452 Discontinued
0.5789 Remote Similarity NPD8039 Approved
0.5741 Remote Similarity NPD9115 Approved
0.569 Remote Similarity NPD5326 Phase 3
0.5652 Remote Similarity NPD4194 Approved
0.5652 Remote Similarity NPD4192 Approved
0.5652 Remote Similarity NPD4191 Approved
0.5652 Remote Similarity NPD4193 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