Structure

Physi-Chem Properties

Molecular Weight:  238.08
Volume:  232.401
LogP:  0.291
LogD:  0.73
LogS:  -0.757
# Rotatable Bonds:  3
TPSA:  65.74
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.788
Synthetic Accessibility Score:  3.516
Fsp3:  0.5
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:  -4.711
MDCK Permeability:  1.41420605359599e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.312
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.757

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.361
Plasma Protein Binding (PPB):  41.30769348144531%
Volume Distribution (VD):  0.663
Pgp-substrate:  59.64003372192383%

ADMET: Metabolism

CYP1A2-inhibitor:  0.186
CYP1A2-substrate:  0.868
CYP2C19-inhibitor:  0.075
CYP2C19-substrate:  0.753
CYP2C9-inhibitor:  0.026
CYP2C9-substrate:  0.196
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.495
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.421

ADMET: Excretion

Clearance (CL):  9.305
Half-life (T1/2):  0.762

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.951
Drug-inuced Liver Injury (DILI):  0.87
AMES Toxicity:  0.662
Rat Oral Acute Toxicity:  0.225
Maximum Recommended Daily Dose:  0.776
Skin Sensitization:  0.42
Carcinogencity:  0.91
Eye Corrosion:  0.007
Eye Irritation:  0.056
Respiratory Toxicity:  0.152

Download Data

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

  Natural Product: NPC133098

Natural Product ID:  NPC133098
Common Name*:   Pyrenocine K
IUPAC Name:   (7R)-4-methoxy-7-(2-oxopropyl)-7,8-dihydro-5H-pyrano[4,3-b]pyran-2-one
Synonyms:  
Standard InCHIKey:  GUGDAUYYWAEZBO-QMMMGPOBSA-N
Standard InCHI:  InChI=1S/C12H14O5/c1-7(13)3-8-4-11-9(6-16-8)10(15-2)5-12(14)17-11/h5,8H,3-4,6H2,1-2H3/t8-/m0/s1
SMILES:  COc1cc(=O)oc2c1CO[C@H](C2)CC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2288016
PubChem CID:   76334677
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
NPO32626 Phomopsis sp. Species Valsaceae Eukaryota n.a. n.a. n.a. PMID[18336005]
NPO32626 Phomopsis sp. Species Valsaceae Eukaryota n.a. n.a. n.a. PMID[22233864]
NPO40075 Clohesyomyces sp. Species Lindgomycetaceae Eukaryota n.a. n.a. n.a. PMID[27964996]
NPO32626 Phomopsis sp. Species Valsaceae Eukaryota n.a. n.a. n.a. PMID[32686414]

☑ 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
NPT825 Organism Phytophthora infestans Phytophthora infestans IZ = 0.0 mm PMID[570483]
NPT827 Organism Mycosphaerella graminicola Mycosphaerella graminicola IZ = 6.0 mm PMID[570483]
NPT826 Organism Magnaporthe oryzae Magnaporthe oryzae IZ = 0.0 mm PMID[570483]
NPT635 Organism Botryotinia fuckeliana Botryotinia fuckeliana IZ = 0.0 mm PMID[570483]
NPT1231 Organism Microbotryum violaceum Microbotryum violaceum IZ = 5.0 mm PMID[570483]
NPT1234 Organism Chlorella fusca Chlorella fusca IZ = 6.0 mm PMID[570483]
NPT1230 Organism Bacillus megaterium Bacillus megaterium IZ = 8.0 mm PMID[570483]
NPT19 Organism Escherichia coli Escherichia coli IZ = 6.0 mm PMID[570483]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MIC > 25.0 ug.mL-1 PMID[570484]

☑ 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 NPC133098 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
0.8636 High Similarity NPC15193
0.8169 Intermediate Similarity NPC477117
0.8 Intermediate Similarity NPC476589
0.7917 Intermediate Similarity NPC238223
0.7895 Intermediate Similarity NPC271986
0.7778 Intermediate Similarity NPC132286
0.7647 Intermediate Similarity NPC274075
0.7639 Intermediate Similarity NPC469446
0.76 Intermediate Similarity NPC162571
0.76 Intermediate Similarity NPC112983
0.7571 Intermediate Similarity NPC68044
0.7568 Intermediate Similarity NPC494
0.75 Intermediate Similarity NPC146583
0.7468 Intermediate Similarity NPC264391
0.7397 Intermediate Similarity NPC470033
0.7333 Intermediate Similarity NPC473277
0.7317 Intermediate Similarity NPC123908
0.7317 Intermediate Similarity NPC10080
0.7308 Intermediate Similarity NPC469414
0.7308 Intermediate Similarity NPC329826
0.7297 Intermediate Similarity NPC203335
0.7262 Intermediate Similarity NPC281172
0.726 Intermediate Similarity NPC131174
0.72 Intermediate Similarity NPC79220
0.72 Intermediate Similarity NPC280374
0.7183 Intermediate Similarity NPC309408
0.7183 Intermediate Similarity NPC429928
0.7162 Intermediate Similarity NPC248125
0.7159 Intermediate Similarity NPC32552
0.7143 Intermediate Similarity NPC178575
0.7126 Intermediate Similarity NPC95364
0.7126 Intermediate Similarity NPC142159
0.7125 Intermediate Similarity NPC68156
0.7101 Intermediate Similarity NPC221763
0.7101 Intermediate Similarity NPC86948
0.7101 Intermediate Similarity NPC150717
0.7089 Intermediate Similarity NPC260396
0.7083 Intermediate Similarity NPC151648
0.7051 Intermediate Similarity NPC287878
0.7042 Intermediate Similarity NPC133600
0.7037 Intermediate Similarity NPC475699
0.7027 Intermediate Similarity NPC471556
0.7027 Intermediate Similarity NPC182794
0.7024 Intermediate Similarity NPC16488
0.7013 Intermediate Similarity NPC315285
0.7 Intermediate Similarity NPC238554
0.7 Intermediate Similarity NPC225022
0.7 Intermediate Similarity NPC470705
0.6986 Remote Similarity NPC2328
0.6986 Remote Similarity NPC132243
0.6986 Remote Similarity NPC474774
0.6977 Remote Similarity NPC186332
0.6977 Remote Similarity NPC291712
0.6977 Remote Similarity NPC47220
0.6974 Remote Similarity NPC287705
0.6966 Remote Similarity NPC32944
0.6966 Remote Similarity NPC193396
0.6966 Remote Similarity NPC166110
0.6962 Remote Similarity NPC177030
0.6957 Remote Similarity NPC173157
0.6957 Remote Similarity NPC25038
0.6951 Remote Similarity NPC473980
0.6951 Remote Similarity NPC271632
0.6951 Remote Similarity NPC473981
0.6944 Remote Similarity NPC79756
0.6933 Remote Similarity NPC315115
0.6915 Remote Similarity NPC469851
0.6914 Remote Similarity NPC24827
0.6914 Remote Similarity NPC228902
0.6914 Remote Similarity NPC316324
0.6914 Remote Similarity NPC315394
0.6914 Remote Similarity NPC471225
0.6892 Remote Similarity NPC477457
0.6892 Remote Similarity NPC477456
0.6889 Remote Similarity NPC248193
0.6883 Remote Similarity NPC476591
0.6883 Remote Similarity NPC88877
0.6875 Remote Similarity NPC478195
0.6875 Remote Similarity NPC210258
0.6875 Remote Similarity NPC206507
0.6875 Remote Similarity NPC161038
0.6875 Remote Similarity NPC478194
0.6875 Remote Similarity NPC478193
0.6875 Remote Similarity NPC147621
0.6875 Remote Similarity NPC478192
0.6875 Remote Similarity NPC478196
0.6875 Remote Similarity NPC478191
0.686 Remote Similarity NPC130030
0.6829 Remote Similarity NPC182292
0.6829 Remote Similarity NPC315765
0.6824 Remote Similarity NPC475083
0.6806 Remote Similarity NPC22897
0.6806 Remote Similarity NPC159650
0.68 Remote Similarity NPC471566
0.68 Remote Similarity NPC133904
0.68 Remote Similarity NPC471565
0.6795 Remote Similarity NPC202011
0.6795 Remote Similarity NPC59558
0.6795 Remote Similarity NPC315597
0.6795 Remote Similarity NPC475113
0.6795 Remote Similarity NPC299932
0.6786 Remote Similarity NPC275507
0.6786 Remote Similarity NPC297440
0.6782 Remote Similarity NPC316426
0.6782 Remote Similarity NPC315395
0.6778 Remote Similarity NPC327760
0.6778 Remote Similarity NPC6099
0.6778 Remote Similarity NPC114345
0.6778 Remote Similarity NPC303230
0.6765 Remote Similarity NPC191643
0.6753 Remote Similarity NPC474823
0.6753 Remote Similarity NPC313444
0.6753 Remote Similarity NPC470032
0.6753 Remote Similarity NPC470256
0.6747 Remote Similarity NPC199134
0.6747 Remote Similarity NPC286816
0.6742 Remote Similarity NPC280833
0.6739 Remote Similarity NPC471698
0.6712 Remote Similarity NPC26223
0.6711 Remote Similarity NPC284447
0.6711 Remote Similarity NPC37382
0.6709 Remote Similarity NPC124072
0.6709 Remote Similarity NPC269103
0.6709 Remote Similarity NPC293114
0.6707 Remote Similarity NPC275530
0.6707 Remote Similarity NPC473825
0.6706 Remote Similarity NPC475690
0.6703 Remote Similarity NPC29798
0.6703 Remote Similarity NPC282644
0.6667 Remote Similarity NPC53136
0.6667 Remote Similarity NPC121374
0.6667 Remote Similarity NPC475004
0.6667 Remote Similarity NPC47653
0.6667 Remote Similarity NPC139056
0.6667 Remote Similarity NPC173409
0.6667 Remote Similarity NPC307112
0.6667 Remote Similarity NPC473948
0.6667 Remote Similarity NPC148233
0.6667 Remote Similarity NPC107130
0.6667 Remote Similarity NPC308457
0.6667 Remote Similarity NPC25747
0.6667 Remote Similarity NPC242233
0.6633 Remote Similarity NPC469852
0.663 Remote Similarity NPC143210
0.6629 Remote Similarity NPC472008
0.6628 Remote Similarity NPC185256
0.6625 Remote Similarity NPC144419
0.6623 Remote Similarity NPC194871
0.6623 Remote Similarity NPC298249
0.6622 Remote Similarity NPC217537
0.6591 Remote Similarity NPC472009
0.6585 Remote Similarity NPC16279
0.6585 Remote Similarity NPC205615
0.6585 Remote Similarity NPC256640
0.6582 Remote Similarity NPC316029
0.6582 Remote Similarity NPC69462
0.6582 Remote Similarity NPC472017
0.6575 Remote Similarity NPC286189
0.6571 Remote Similarity NPC218486
0.6571 Remote Similarity NPC478120
0.6567 Remote Similarity NPC234084
0.6562 Remote Similarity NPC471699
0.6559 Remote Similarity NPC170204
0.6559 Remote Similarity NPC12727
0.6552 Remote Similarity NPC163615
0.6552 Remote Similarity NPC38569
0.6552 Remote Similarity NPC474251
0.6548 Remote Similarity NPC178277
0.6548 Remote Similarity NPC270126
0.6548 Remote Similarity NPC150646
0.6548 Remote Similarity NPC471299
0.6543 Remote Similarity NPC188354
0.6543 Remote Similarity NPC474758
0.6543 Remote Similarity NPC476355
0.6543 Remote Similarity NPC114727
0.6543 Remote Similarity NPC474551
0.6543 Remote Similarity NPC476590
0.6543 Remote Similarity NPC117746
0.6543 Remote Similarity NPC15499
0.6543 Remote Similarity NPC294434
0.6543 Remote Similarity NPC259599
0.6538 Remote Similarity NPC134385
0.6538 Remote Similarity NPC218477
0.6538 Remote Similarity NPC475760
0.6533 Remote Similarity NPC179087
0.6533 Remote Similarity NPC474658
0.6533 Remote Similarity NPC210303
0.6533 Remote Similarity NPC473737
0.6533 Remote Similarity NPC44343
0.6531 Remote Similarity NPC272528
0.6526 Remote Similarity NPC35717
0.6517 Remote Similarity NPC472007
0.6517 Remote Similarity NPC476079
0.6517 Remote Similarity NPC113370
0.6517 Remote Similarity NPC103743
0.6517 Remote Similarity NPC125925
0.6512 Remote Similarity NPC8161
0.6506 Remote Similarity NPC10572
0.65 Remote Similarity NPC327106
0.65 Remote Similarity NPC320119

  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 NPC133098 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
0.6706 Remote Similarity NPD5209 Approved
0.6506 Remote Similarity NPD4756 Discovery
0.6154 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6143 Remote Similarity NPD6927 Phase 3
0.6 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6 Remote Similarity NPD5778 Approved
0.6 Remote Similarity NPD5779 Approved
0.5978 Remote Similarity NPD1282 Approved
0.5934 Remote Similarity NPD1694 Approved
0.5882 Remote Similarity NPD8039 Approved
0.5876 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5867 Remote Similarity NPD8779 Phase 3
0.5851 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5851 Remote Similarity NPD6101 Approved
0.5844 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5824 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5789 Remote Similarity NPD46 Approved
0.5789 Remote Similarity NPD6698 Approved
0.5778 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5729 Remote Similarity NPD7983 Approved
0.5729 Remote Similarity NPD7637 Suspended
0.5729 Remote Similarity NPD6411 Approved
0.5714 Remote Similarity NPD7154 Phase 3
0.57 Remote Similarity NPD4225 Approved
0.5679 Remote Similarity NPD3704 Approved
0.5679 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5657 Remote Similarity NPD7839 Suspended
0.5648 Remote Similarity NPD6053 Discontinued
0.5625 Remote Similarity NPD5785 Approved
0.5625 Remote Similarity NPD7838 Discovery

  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