Structure

Physi-Chem Properties

Molecular Weight:  208.07
Volume:  212.234
LogP:  1.087
LogD:  1.265
LogS:  -2.774
# Rotatable Bonds:  3
TPSA:  56.51
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.707
Synthetic Accessibility Score:  2.69
Fsp3:  0.273
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:  -4.627
MDCK Permeability:  1.7164364180644043e-05
Pgp-inhibitor:  0.136
Pgp-substrate:  0.259
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.935

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.078
Plasma Protein Binding (PPB):  79.84468841552734%
Volume Distribution (VD):  0.568
Pgp-substrate:  21.49927520751953%

ADMET: Metabolism

CYP1A2-inhibitor:  0.938
CYP1A2-substrate:  0.951
CYP2C19-inhibitor:  0.246
CYP2C19-substrate:  0.183
CYP2C9-inhibitor:  0.045
CYP2C9-substrate:  0.885
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.772
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.351

ADMET: Excretion

Clearance (CL):  5.499
Half-life (T1/2):  0.749

ADMET: Toxicity

hERG Blockers:  0.139
Human Hepatotoxicity (H-HT):  0.735
Drug-inuced Liver Injury (DILI):  0.817
AMES Toxicity:  0.096
Rat Oral Acute Toxicity:  0.037
Maximum Recommended Daily Dose:  0.115
Skin Sensitization:  0.704
Carcinogencity:  0.681
Eye Corrosion:  0.895
Eye Irritation:  0.974
Respiratory Toxicity:  0.114

Download Data

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

  Natural Product: NPC150717

Natural Product ID:  NPC150717
Common Name*:   Nigerapyrone E
IUPAC Name:   4-methoxy-3-methyl-6-[(E)-3-oxobut-1-enyl]pyran-2-one
Synonyms:   Nigerapyrone E
Standard InCHIKey:  ZYAUSSMPHVTIRL-SNAWJCMRSA-N
Standard InCHI:  InChI=1S/C11H12O4/c1-7(12)4-5-9-6-10(14-3)8(2)11(13)15-9/h4-6H,1-3H3/b5-4+
SMILES:  CC(=O)/C=C/c1cc(c(C)c(=O)o1)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1823133
PubChem CID:   53483954
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
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4039(01)88611-1]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np058103o]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/JR9620000040]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1080/00021369.1966.10858561]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1080/00021369.1972.10860562]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1080/00021369.1985.10867263]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. mycelium n.a. PMID[10695672]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[12458767]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[12542363]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15387655]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. sponge-derived n.a. PMID[15387655]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15556711]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15620260]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17653510]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17827758]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20014861]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20028011]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21176790]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21543515]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. mycelium n.a. PMID[21774474]
NPO33567 Aspergillus niger MA-132 Species Aspergillaceae Eukaryota obtained from the fresh tissue of the marine mangrove plant Avicennia marina n.a. n.a. PMID[21774474]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. latex n.a. PMID[21854017]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21854017]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22921072]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24684908]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[25044953]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[25062661]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[25293978]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[26040782]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[26132344]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[26414728]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[27245874]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[32159958]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[6073032]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. mycelium n.a. Database[Article]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota 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
NPT90 Cell Line DU-145 Homo sapiens IC50 = 86000.0 nM PMID[506721]
NPT65 Cell Line HepG2 Homo sapiens IC50 = 86000.0 nM PMID[506721]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 105000.0 nM PMID[506721]
NPT397 Cell Line NCI-H460 Homo sapiens IC50 = 43000.0 nM PMID[506721]
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 = 48000.0 nM PMID[506721]
NPT1312 Cell Line SW1990 Homo sapiens IC50 = 38000.0 nM PMID[506721]
NPT81 Cell Line A549 Homo sapiens IC50 = 43000.0 nM PMID[506721]

☑ 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 NPC150717 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
0.9623 High Similarity NPC221763
0.9231 High Similarity NPC191643
0.8727 High Similarity NPC173157
0.8654 High Similarity NPC234084
0.8545 High Similarity NPC218486
0.8305 Intermediate Similarity NPC309408
0.8276 Intermediate Similarity NPC189700
0.8033 Intermediate Similarity NPC2328
0.8 Intermediate Similarity NPC130953
0.8 Intermediate Similarity NPC98519
0.7931 Intermediate Similarity NPC86948
0.7931 Intermediate Similarity NPC51846
0.7833 Intermediate Similarity NPC133600
0.7818 Intermediate Similarity NPC15789
0.7692 Intermediate Similarity NPC477117
0.7636 Intermediate Similarity NPC126184
0.7586 Intermediate Similarity NPC478120
0.7581 Intermediate Similarity NPC15193
0.75 Intermediate Similarity NPC471566
0.75 Intermediate Similarity NPC471565
0.75 Intermediate Similarity NPC275316
0.75 Intermediate Similarity NPC236338
0.75 Intermediate Similarity NPC476589
0.7463 Intermediate Similarity NPC59558
0.7458 Intermediate Similarity NPC25038
0.7455 Intermediate Similarity NPC128520
0.7419 Intermediate Similarity NPC429928
0.7419 Intermediate Similarity NPC79756
0.7385 Intermediate Similarity NPC475675
0.7385 Intermediate Similarity NPC475555
0.7313 Intermediate Similarity NPC470693
0.7231 Intermediate Similarity NPC471556
0.7231 Intermediate Similarity NPC273600
0.7206 Intermediate Similarity NPC315285
0.7193 Intermediate Similarity NPC221467
0.7188 Intermediate Similarity NPC473737
0.7188 Intermediate Similarity NPC132243
0.7188 Intermediate Similarity NPC44343
0.7188 Intermediate Similarity NPC179087
0.7188 Intermediate Similarity NPC210303
0.7167 Intermediate Similarity NPC478117
0.7143 Intermediate Similarity NPC90490
0.7121 Intermediate Similarity NPC470033
0.7121 Intermediate Similarity NPC315115
0.7101 Intermediate Similarity NPC133098
0.7097 Intermediate Similarity NPC254095
0.7091 Intermediate Similarity NPC270706
0.7069 Intermediate Similarity NPC43053
0.7018 Intermediate Similarity NPC82446
0.7015 Intermediate Similarity NPC132286
0.7 Intermediate Similarity NPC129710
0.6984 Remote Similarity NPC82465
0.697 Remote Similarity NPC133904
0.697 Remote Similarity NPC182794
0.697 Remote Similarity NPC220766
0.697 Remote Similarity NPC7940
0.6964 Remote Similarity NPC128280
0.6957 Remote Similarity NPC315597
0.6944 Remote Similarity NPC470705
0.6935 Remote Similarity NPC294938
0.6935 Remote Similarity NPC129150
0.6935 Remote Similarity NPC293437
0.6935 Remote Similarity NPC474825
0.6935 Remote Similarity NPC135863
0.6935 Remote Similarity NPC249850
0.6912 Remote Similarity NPC238223
0.6912 Remote Similarity NPC280374
0.6912 Remote Similarity NPC313444
0.6912 Remote Similarity NPC287705
0.6875 Remote Similarity NPC26223
0.6866 Remote Similarity NPC191233
0.6852 Remote Similarity NPC57923
0.6825 Remote Similarity NPC21946
0.6825 Remote Similarity NPC223679
0.6818 Remote Similarity NPC475618
0.6818 Remote Similarity NPC471611
0.6792 Remote Similarity NPC281043
0.6786 Remote Similarity NPC47946
0.6786 Remote Similarity NPC26600
0.678 Remote Similarity NPC22329
0.6769 Remote Similarity NPC151648
0.6765 Remote Similarity NPC225272
0.6765 Remote Similarity NPC470442
0.6765 Remote Similarity NPC203335
0.6761 Remote Similarity NPC287878
0.6761 Remote Similarity NPC316851
0.6724 Remote Similarity NPC135698
0.6721 Remote Similarity NPC151761
0.6721 Remote Similarity NPC159535
0.6719 Remote Similarity NPC302564
0.6719 Remote Similarity NPC22897
0.6719 Remote Similarity NPC159650
0.6716 Remote Similarity NPC131174
0.6714 Remote Similarity NPC316029
0.6667 Remote Similarity NPC197467
0.6667 Remote Similarity NPC475073
0.6622 Remote Similarity NPC315394
0.6622 Remote Similarity NPC473825
0.6622 Remote Similarity NPC316324
0.662 Remote Similarity NPC178575
0.662 Remote Similarity NPC181587
0.6618 Remote Similarity NPC469446
0.6613 Remote Similarity NPC474913
0.661 Remote Similarity NPC220191
0.661 Remote Similarity NPC27264
0.6575 Remote Similarity NPC315552
0.6575 Remote Similarity NPC478196
0.6575 Remote Similarity NPC478193
0.6575 Remote Similarity NPC478192
0.6575 Remote Similarity NPC478194
0.6575 Remote Similarity NPC478195
0.6575 Remote Similarity NPC478191
0.6571 Remote Similarity NPC151481
0.6571 Remote Similarity NPC473277
0.6567 Remote Similarity NPC477457
0.6567 Remote Similarity NPC308457
0.6567 Remote Similarity NPC477456
0.6567 Remote Similarity NPC25747
0.6567 Remote Similarity NPC148233
0.6528 Remote Similarity NPC276336
0.6515 Remote Similarity NPC263732
0.6515 Remote Similarity NPC14437
0.6515 Remote Similarity NPC270412
0.6515 Remote Similarity NPC68044
0.6508 Remote Similarity NPC245002
0.65 Remote Similarity NPC148056
0.65 Remote Similarity NPC291712
0.6481 Remote Similarity NPC111474
0.6481 Remote Similarity NPC297608
0.6479 Remote Similarity NPC202011
0.6471 Remote Similarity NPC96414
0.6471 Remote Similarity NPC470688
0.6462 Remote Similarity NPC203233
0.6462 Remote Similarity NPC286189
0.6462 Remote Similarity NPC97570
0.6462 Remote Similarity NPC86789
0.6447 Remote Similarity NPC271632
0.6441 Remote Similarity NPC15912
0.6438 Remote Similarity NPC470686
0.6429 Remote Similarity NPC470032
0.6429 Remote Similarity NPC474823
0.6429 Remote Similarity NPC79220
0.6418 Remote Similarity NPC155849
0.6418 Remote Similarity NPC474658
0.6418 Remote Similarity NPC474774
0.6418 Remote Similarity NPC474729
0.6418 Remote Similarity NPC474723
0.6418 Remote Similarity NPC68110
0.6406 Remote Similarity NPC283502
0.64 Remote Similarity NPC471225
0.64 Remote Similarity NPC68156
0.6393 Remote Similarity NPC106531
0.6393 Remote Similarity NPC151919
0.6389 Remote Similarity NPC316185
0.6377 Remote Similarity NPC201356
0.6377 Remote Similarity NPC146811
0.6377 Remote Similarity NPC248125
0.6377 Remote Similarity NPC37382
0.6377 Remote Similarity NPC124586
0.6375 Remote Similarity NPC281172
0.6364 Remote Similarity NPC159773
0.6351 Remote Similarity NPC147621
0.6351 Remote Similarity NPC206507
0.6351 Remote Similarity NPC210258
0.6338 Remote Similarity NPC476591
0.6338 Remote Similarity NPC232812
0.6338 Remote Similarity NPC88877
0.6338 Remote Similarity NPC475004
0.6329 Remote Similarity NPC16488
0.6316 Remote Similarity NPC106547
0.629 Remote Similarity NPC474805
0.6286 Remote Similarity NPC21998
0.6286 Remote Similarity NPC122627
0.6269 Remote Similarity NPC26810
0.625 Remote Similarity NPC64234
0.625 Remote Similarity NPC187922
0.625 Remote Similarity NPC37929
0.625 Remote Similarity NPC230296
0.625 Remote Similarity NPC41409
0.622 Remote Similarity NPC163016
0.622 Remote Similarity NPC75315
0.6216 Remote Similarity NPC315843
0.6216 Remote Similarity NPC107654
0.6207 Remote Similarity NPC110396
0.6197 Remote Similarity NPC218477
0.6197 Remote Similarity NPC63873
0.6197 Remote Similarity NPC470256
0.6197 Remote Similarity NPC475760
0.619 Remote Similarity NPC224270
0.619 Remote Similarity NPC317796
0.619 Remote Similarity NPC269615
0.619 Remote Similarity NPC135537
0.619 Remote Similarity NPC474127
0.6184 Remote Similarity NPC475711
0.6182 Remote Similarity NPC250954
0.6182 Remote Similarity NPC8270
0.6182 Remote Similarity NPC123357
0.6173 Remote Similarity NPC296589
0.6164 Remote Similarity NPC293114
0.6154 Remote Similarity NPC269641

  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 NPC150717 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
0.6538 Remote Similarity NPD9115 Approved
0.6515 Remote Similarity NPD9418 Clinical (unspecified phase)
0.65 Remote Similarity NPD6927 Phase 3
0.6441 Remote Similarity NPD4220 Pre-registration
0.625 Remote Similarity NPD9091 Suspended
0.625 Remote Similarity NPD9297 Discontinued
0.6184 Remote Similarity NPD4756 Discovery
0.6087 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6 Remote Similarity NPD5209 Approved
0.5932 Remote Similarity NPD9090 Phase 3
0.5909 Remote Similarity NPD8779 Phase 3
0.5862 Remote Similarity NPD9411 Phase 1
0.5775 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5763 Remote Similarity NPD6097 Approved
0.5763 Remote Similarity NPD6096 Approved
0.5647 Remote Similarity NPD1282 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