Structure

Physi-Chem Properties

Molecular Weight:  210.09
Volume:  208.951
LogP:  1.404
LogD:  1.405
LogS:  -1.411
# Rotatable Bonds:  2
TPSA:  48.67
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.742
Synthetic Accessibility Score:  3.445
Fsp3:  0.545
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:  -4.64
MDCK Permeability:  2.3035754566080868e-05
Pgp-inhibitor:  0.007
Pgp-substrate:  0.083
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.256
Plasma Protein Binding (PPB):  39.27878952026367%
Volume Distribution (VD):  0.846
Pgp-substrate:  50.46719741821289%

ADMET: Metabolism

CYP1A2-inhibitor:  0.449
CYP1A2-substrate:  0.954
CYP2C19-inhibitor:  0.075
CYP2C19-substrate:  0.796
CYP2C9-inhibitor:  0.023
CYP2C9-substrate:  0.269
CYP2D6-inhibitor:  0.041
CYP2D6-substrate:  0.7
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.254

ADMET: Excretion

Clearance (CL):  11.083
Half-life (T1/2):  0.79

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.918
Drug-inuced Liver Injury (DILI):  0.694
AMES Toxicity:  0.636
Rat Oral Acute Toxicity:  0.283
Maximum Recommended Daily Dose:  0.631
Skin Sensitization:  0.264
Carcinogencity:  0.932
Eye Corrosion:  0.022
Eye Irritation:  0.145
Respiratory Toxicity:  0.883

Download Data

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

  Natural Product: NPC15193

Natural Product ID:  NPC15193
Common Name*:   Pyrenocine J
IUPAC Name:   (7S)-7-ethyl-4-methoxy-7,8-dihydro-5H-pyrano[4,3-b]pyran-2-one
Synonyms:  
Standard InCHIKey:  GBPMVIAHTDJTEZ-ZETCQYMHSA-N
Standard InCHI:  InChI=1S/C11H14O4/c1-3-7-4-10-8(6-14-7)9(13-2)5-11(12)15-10/h5,7H,3-4,6H2,1-2H3/t7-/m0/s1
SMILES:  CC[C@H]1Cc2c(CO1)c(cc(=O)o2)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2288015
PubChem CID:   76312966
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]
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[483650]
NPT827 Organism Mycosphaerella graminicola Mycosphaerella graminicola IZ = 8.0 mm PMID[483650]
NPT826 Organism Magnaporthe oryzae Magnaporthe oryzae IZ = 0.0 mm PMID[483650]
NPT635 Organism Botryotinia fuckeliana Botryotinia fuckeliana IZ = 0.0 mm PMID[483650]
NPT1231 Organism Microbotryum violaceum Microbotryum violaceum IZ = 0.0 mm PMID[483650]
NPT1234 Organism Chlorella fusca Chlorella fusca IZ = 8.0 mm PMID[483650]
NPT1230 Organism Bacillus megaterium Bacillus megaterium IZ = 9.0 mm PMID[483650]
NPT19 Organism Escherichia coli Escherichia coli IZ = 8.0 mm PMID[483650]

☑ 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 NPC15193 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 NPC133098
0.8462 Intermediate Similarity NPC238223
0.8462 Intermediate Similarity NPC477117
0.8438 Intermediate Similarity NPC470033
0.8308 Intermediate Similarity NPC132286
0.8281 Intermediate Similarity NPC476589
0.8182 Intermediate Similarity NPC280374
0.8088 Intermediate Similarity NPC178575
0.7879 Intermediate Similarity NPC469446
0.7778 Intermediate Similarity NPC133600
0.7746 Intermediate Similarity NPC206507
0.7746 Intermediate Similarity NPC210258
0.7746 Intermediate Similarity NPC147621
0.7705 Intermediate Similarity NPC25038
0.7656 Intermediate Similarity NPC309408
0.7656 Intermediate Similarity NPC429928
0.7647 Intermediate Similarity NPC470032
0.7586 Intermediate Similarity NPC234084
0.7581 Intermediate Similarity NPC221763
0.7581 Intermediate Similarity NPC150717
0.7581 Intermediate Similarity NPC86948
0.7538 Intermediate Similarity NPC68044
0.75 Intermediate Similarity NPC191643
0.7463 Intermediate Similarity NPC471566
0.7463 Intermediate Similarity NPC471565
0.7463 Intermediate Similarity NPC182794
0.7463 Intermediate Similarity NPC471556
0.7429 Intermediate Similarity NPC59558
0.7424 Intermediate Similarity NPC2328
0.7419 Intermediate Similarity NPC173157
0.7385 Intermediate Similarity NPC26223
0.7353 Intermediate Similarity NPC37382
0.7333 Intermediate Similarity NPC271632
0.7313 Intermediate Similarity NPC25747
0.7313 Intermediate Similarity NPC308457
0.7313 Intermediate Similarity NPC148233
0.7258 Intermediate Similarity NPC218486
0.7231 Intermediate Similarity NPC22897
0.7231 Intermediate Similarity NPC159650
0.7206 Intermediate Similarity NPC470123
0.7206 Intermediate Similarity NPC282760
0.7183 Intermediate Similarity NPC315285
0.7167 Intermediate Similarity NPC275316
0.7164 Intermediate Similarity NPC473737
0.7143 Intermediate Similarity NPC79220
0.7121 Intermediate Similarity NPC79756
0.7101 Intermediate Similarity NPC124586
0.7101 Intermediate Similarity NPC146811
0.7101 Intermediate Similarity NPC315115
0.7083 Intermediate Similarity NPC316185
0.7067 Intermediate Similarity NPC315394
0.7059 Intermediate Similarity NPC477457
0.7059 Intermediate Similarity NPC477456
0.7051 Intermediate Similarity NPC10080
0.7051 Intermediate Similarity NPC123908
0.7042 Intermediate Similarity NPC151481
0.7027 Intermediate Similarity NPC478193
0.7027 Intermediate Similarity NPC478192
0.7027 Intermediate Similarity NPC478195
0.7027 Intermediate Similarity NPC478194
0.7027 Intermediate Similarity NPC478196
0.7027 Intermediate Similarity NPC478191
0.7015 Intermediate Similarity NPC151648
0.7 Intermediate Similarity NPC203335
0.6984 Remote Similarity NPC478120
0.697 Remote Similarity NPC286189
0.6957 Remote Similarity NPC131174
0.6957 Remote Similarity NPC96414
0.6957 Remote Similarity NPC220766
0.6944 Remote Similarity NPC202011
0.6944 Remote Similarity NPC315597
0.6933 Remote Similarity NPC470705
0.6912 Remote Similarity NPC210303
0.6912 Remote Similarity NPC179087
0.6912 Remote Similarity NPC44343
0.6901 Remote Similarity NPC313444
0.6901 Remote Similarity NPC287705
0.6901 Remote Similarity NPC475760
0.6901 Remote Similarity NPC63873
0.6901 Remote Similarity NPC474823
0.6892 Remote Similarity NPC470686
0.6892 Remote Similarity NPC107654
0.6892 Remote Similarity NPC315843
0.6885 Remote Similarity NPC236338
0.6875 Remote Similarity NPC474913
0.6866 Remote Similarity NPC98519
0.6866 Remote Similarity NPC476585
0.6866 Remote Similarity NPC130953
0.6857 Remote Similarity NPC191233
0.6857 Remote Similarity NPC248125
0.6857 Remote Similarity NPC201356
0.6849 Remote Similarity NPC112983
0.6849 Remote Similarity NPC162571
0.6842 Remote Similarity NPC68156
0.6842 Remote Similarity NPC473825
0.6842 Remote Similarity NPC471225
0.6818 Remote Similarity NPC189700
0.6812 Remote Similarity NPC471611
0.6806 Remote Similarity NPC494
0.6806 Remote Similarity NPC88877
0.6806 Remote Similarity NPC475004
0.6806 Remote Similarity NPC476591
0.6806 Remote Similarity NPC470693
0.678 Remote Similarity NPC270706
0.678 Remote Similarity NPC26600
0.678 Remote Similarity NPC47946
0.6769 Remote Similarity NPC51846
0.6757 Remote Similarity NPC16349
0.6757 Remote Similarity NPC222244
0.6757 Remote Similarity NPC146583
0.6721 Remote Similarity NPC135698
0.6716 Remote Similarity NPC97570
0.6714 Remote Similarity NPC273600
0.6714 Remote Similarity NPC476586
0.6714 Remote Similarity NPC7940
0.6712 Remote Similarity NPC476037
0.6712 Remote Similarity NPC316029
0.6712 Remote Similarity NPC476012
0.6711 Remote Similarity NPC271986
0.6707 Remote Similarity NPC186332
0.6707 Remote Similarity NPC47220
0.6667 Remote Similarity NPC128280
0.6667 Remote Similarity NPC474774
0.6667 Remote Similarity NPC132243
0.6667 Remote Similarity NPC197467
0.6667 Remote Similarity NPC475073
0.6667 Remote Similarity NPC217940
0.6622 Remote Similarity NPC181587
0.6622 Remote Similarity NPC475762
0.6622 Remote Similarity NPC293114
0.662 Remote Similarity NPC475555
0.662 Remote Similarity NPC276299
0.662 Remote Similarity NPC475675
0.6618 Remote Similarity NPC19241
0.6615 Remote Similarity NPC478117
0.6613 Remote Similarity NPC15789
0.6588 Remote Similarity NPC274075
0.6585 Remote Similarity NPC281172
0.6579 Remote Similarity NPC329826
0.6579 Remote Similarity NPC161038
0.6579 Remote Similarity NPC469414
0.6575 Remote Similarity NPC232812
0.6575 Remote Similarity NPC473277
0.6571 Remote Similarity NPC470808
0.6538 Remote Similarity NPC264391
0.6533 Remote Similarity NPC329890
0.6533 Remote Similarity NPC185186
0.6533 Remote Similarity NPC329914
0.6533 Remote Similarity NPC316851
0.6533 Remote Similarity NPC284006
0.6533 Remote Similarity NPC327383
0.6528 Remote Similarity NPC225272
0.6528 Remote Similarity NPC194871
0.6522 Remote Similarity NPC55376
0.6522 Remote Similarity NPC26810
0.6512 Remote Similarity NPC32552
0.6506 Remote Similarity NPC291712
0.6486 Remote Similarity NPC469660
0.6486 Remote Similarity NPC37929
0.6486 Remote Similarity NPC473361
0.6486 Remote Similarity NPC64234
0.6486 Remote Similarity NPC329904
0.6479 Remote Similarity NPC19769
0.6479 Remote Similarity NPC133904
0.6471 Remote Similarity NPC302564
0.6462 Remote Similarity NPC129710
0.6452 Remote Similarity NPC126184
0.6447 Remote Similarity NPC476590
0.6447 Remote Similarity NPC114727
0.6438 Remote Similarity NPC470256
0.6429 Remote Similarity NPC476584
0.6429 Remote Similarity NPC286608
0.6429 Remote Similarity NPC68110
0.6429 Remote Similarity NPC474723
0.6429 Remote Similarity NPC169050
0.6429 Remote Similarity NPC474729
0.6429 Remote Similarity NPC474658
0.642 Remote Similarity NPC313677
0.6418 Remote Similarity NPC249850
0.6418 Remote Similarity NPC135863
0.6418 Remote Similarity NPC293437
0.6418 Remote Similarity NPC129150
0.6418 Remote Similarity NPC294938
0.641 Remote Similarity NPC275530
0.641 Remote Similarity NPC475711
0.641 Remote Similarity NPC316324
0.6386 Remote Similarity NPC130030
0.6386 Remote Similarity NPC242233
0.6375 Remote Similarity NPC121374
0.6364 Remote Similarity NPC285840
0.6364 Remote Similarity NPC315552
0.6364 Remote Similarity NPC327041
0.6341 Remote Similarity NPC315559
0.6341 Remote Similarity NPC44261
0.6341 Remote Similarity NPC16488
0.6338 Remote Similarity NPC173409
0.6338 Remote Similarity NPC53136
0.6338 Remote Similarity NPC475618
0.6329 Remote Similarity NPC474816
0.6329 Remote Similarity NPC28049

  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 NPC15193 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
0.6508 Remote Similarity NPD6927 Phase 3
0.6479 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6429 Remote Similarity NPD1282 Approved
0.6265 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6087 Remote Similarity NPD69 Approved
0.6087 Remote Similarity NPD9119 Approved
0.6 Remote Similarity NPD4756 Discovery
0.5942 Remote Similarity NPD9118 Approved
0.5942 Remote Similarity NPD8779 Phase 3
0.5938 Remote Similarity NPD4220 Pre-registration
0.589 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5833 Remote Similarity NPD5209 Approved
0.5667 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