Structure

Physi-Chem Properties

Molecular Weight:  140.05
Volume:  133.613
LogP:  -0.096
LogD:  -0.972
LogS:  -1.1
# Rotatable Bonds:  0
TPSA:  46.67
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.442
Synthetic Accessibility Score:  4.3
Fsp3:  0.714
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.432
MDCK Permeability:  2.6028157662949525e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.806
Plasma Protein Binding (PPB):  25.436071395874023%
Volume Distribution (VD):  1.121
Pgp-substrate:  79.57074737548828%

ADMET: Metabolism

CYP1A2-inhibitor:  0.039
CYP1A2-substrate:  0.729
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.577
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.121
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.393
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.206

ADMET: Excretion

Clearance (CL):  9.17
Half-life (T1/2):  0.869

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.295
Drug-inuced Liver Injury (DILI):  0.917
AMES Toxicity:  0.031
Rat Oral Acute Toxicity:  0.858
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.312
Carcinogencity:  0.272
Eye Corrosion:  0.96
Eye Irritation:  0.91
Respiratory Toxicity:  0.07

Download Data

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

  Natural Product: NPC272267

Natural Product ID:  NPC272267
Common Name*:   (+)-Epiepoformin
IUPAC Name:   (1R,2S,6R)-2-hydroxy-4-methyl-7-oxabicyclo[4.1.0]hept-3-en-5-one
Synonyms:  
Standard InCHIKey:  WCZPXJJNPSYRIV-JHYUDYDFSA-N
Standard InCHI:  InChI=1S/C7H8O3/c1-3-2-4(8)6-7(10-6)5(3)9/h2,4,6-8H,1H3/t4-,6+,7-/m0/s1
SMILES:  O[C@H]1C=C(C)C(=O)[C@H]2[C@@H]1O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3337529
PubChem CID:   155055
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones
              • [CHEMONTID:0004325] Cyclohexenones

*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
NPO33084 Geosmithia langdonii Species Bionectriaceae Eukaryota n.a. n.a. n.a. PMID[25084548]
NPO33084 Geosmithia langdonii Species Bionectriaceae Eukaryota n.a. n.a. n.a. PMID[30298736]

☑ 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
NPT633 Organism Leishmania donovani Leishmania donovani IC50 = 6900.0 nM PMID[477565]
NPT633 Organism Leishmania donovani Leishmania donovani IC90 = 10800.0 nM PMID[477565]

☑ 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 NPC272267 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
0.9211 High Similarity NPC159714
0.9211 High Similarity NPC221510
0.9103 High Similarity NPC469809
0.8846 High Similarity NPC253364
0.8592 High Similarity NPC472072
0.8415 Intermediate Similarity NPC196381
0.8235 Intermediate Similarity NPC477684
0.8148 Intermediate Similarity NPC47450
0.7647 Intermediate Similarity NPC187529
0.7553 Intermediate Similarity NPC39996
0.7531 Intermediate Similarity NPC473536
0.7474 Intermediate Similarity NPC104161
0.7474 Intermediate Similarity NPC118902
0.7474 Intermediate Similarity NPC469980
0.7442 Intermediate Similarity NPC77971
0.7407 Intermediate Similarity NPC474197
0.7273 Intermediate Similarity NPC472007
0.7245 Intermediate Similarity NPC266514
0.7229 Intermediate Similarity NPC318481
0.7209 Intermediate Similarity NPC477784
0.7209 Intermediate Similarity NPC477785
0.7209 Intermediate Similarity NPC477786
0.7159 Intermediate Similarity NPC472009
0.7108 Intermediate Similarity NPC141195
0.7108 Intermediate Similarity NPC47844
0.7105 Intermediate Similarity NPC475221
0.7079 Intermediate Similarity NPC23622
0.7065 Intermediate Similarity NPC327620
0.7059 Intermediate Similarity NPC91332
0.7059 Intermediate Similarity NPC162741
0.7051 Intermediate Similarity NPC251429
0.7021 Intermediate Similarity NPC279722
0.7 Intermediate Similarity NPC150063
0.7 Intermediate Similarity NPC287089
0.7 Intermediate Similarity NPC119740
0.7 Intermediate Similarity NPC202011
0.7 Intermediate Similarity NPC107848
0.7 Intermediate Similarity NPC472008
0.6989 Remote Similarity NPC121825
0.6988 Remote Similarity NPC205615
0.6988 Remote Similarity NPC256640
0.6988 Remote Similarity NPC301207
0.6988 Remote Similarity NPC16279
0.6977 Remote Similarity NPC150502
0.6962 Remote Similarity NPC309466
0.6951 Remote Similarity NPC326504
0.6951 Remote Similarity NPC474545
0.6931 Remote Similarity NPC87335
0.6907 Remote Similarity NPC207885
0.6905 Remote Similarity NPC97173
0.6905 Remote Similarity NPC49302
0.6905 Remote Similarity NPC125365
0.6905 Remote Similarity NPC474818
0.6905 Remote Similarity NPC176329
0.6905 Remote Similarity NPC82666
0.6905 Remote Similarity NPC51809
0.6897 Remote Similarity NPC475046
0.6897 Remote Similarity NPC310450
0.6897 Remote Similarity NPC474959
0.6897 Remote Similarity NPC11383
0.6882 Remote Similarity NPC469692
0.6882 Remote Similarity NPC469645
0.6875 Remote Similarity NPC130618
0.6875 Remote Similarity NPC475982
0.6875 Remote Similarity NPC306908
0.6867 Remote Similarity NPC161038
0.6867 Remote Similarity NPC473582
0.6848 Remote Similarity NPC471399
0.6842 Remote Similarity NPC269737
0.6837 Remote Similarity NPC478176
0.6832 Remote Similarity NPC264819
0.6824 Remote Similarity NPC478122
0.6824 Remote Similarity NPC221095
0.6824 Remote Similarity NPC279214
0.6824 Remote Similarity NPC231739
0.6824 Remote Similarity NPC473471
0.6818 Remote Similarity NPC229799
0.6818 Remote Similarity NPC286770
0.6818 Remote Similarity NPC284472
0.6796 Remote Similarity NPC317107
0.6795 Remote Similarity NPC101670
0.6786 Remote Similarity NPC127118
0.6786 Remote Similarity NPC209113
0.6782 Remote Similarity NPC474980
0.6774 Remote Similarity NPC476705
0.6774 Remote Similarity NPC475441
0.6771 Remote Similarity NPC471916
0.6747 Remote Similarity NPC24590
0.6747 Remote Similarity NPC473489
0.6744 Remote Similarity NPC291260
0.6742 Remote Similarity NPC474251
0.6735 Remote Similarity NPC112613
0.6733 Remote Similarity NPC469853
0.6731 Remote Similarity NPC317687
0.6709 Remote Similarity NPC83965
0.6706 Remote Similarity NPC275530
0.6703 Remote Similarity NPC471738
0.6701 Remote Similarity NPC281608
0.6701 Remote Similarity NPC475284
0.6699 Remote Similarity NPC89408
0.6667 Remote Similarity NPC68303
0.6667 Remote Similarity NPC307126
0.6667 Remote Similarity NPC94488
0.6667 Remote Similarity NPC131864
0.6667 Remote Similarity NPC121374
0.6634 Remote Similarity NPC469852
0.6629 Remote Similarity NPC185256
0.6625 Remote Similarity NPC106613
0.6625 Remote Similarity NPC269985
0.6625 Remote Similarity NPC25298
0.6622 Remote Similarity NPC40148
0.66 Remote Similarity NPC473624
0.66 Remote Similarity NPC131366
0.6598 Remote Similarity NPC20066
0.6596 Remote Similarity NPC32552
0.6596 Remote Similarity NPC6099
0.6596 Remote Similarity NPC114345
0.6596 Remote Similarity NPC303230
0.6596 Remote Similarity NPC327760
0.6596 Remote Similarity NPC142838
0.6591 Remote Similarity NPC67254
0.6591 Remote Similarity NPC297440
0.6579 Remote Similarity NPC473494
0.6566 Remote Similarity NPC185141
0.6566 Remote Similarity NPC133907
0.6566 Remote Similarity NPC474339
0.6566 Remote Similarity NPC46998
0.6566 Remote Similarity NPC128733
0.6566 Remote Similarity NPC164598
0.6566 Remote Similarity NPC110443
0.6556 Remote Similarity NPC316819
0.6548 Remote Similarity NPC227814
0.6548 Remote Similarity NPC144995
0.6548 Remote Similarity NPC122244
0.6533 Remote Similarity NPC268185
0.6531 Remote Similarity NPC300584
0.6531 Remote Similarity NPC35717
0.6512 Remote Similarity NPC471061
0.6505 Remote Similarity NPC322903
0.6505 Remote Similarity NPC327106
0.65 Remote Similarity NPC137163
0.6495 Remote Similarity NPC94337
0.6489 Remote Similarity NPC274075
0.6489 Remote Similarity NPC469464
0.6489 Remote Similarity NPC166554
0.6489 Remote Similarity NPC265856
0.6471 Remote Similarity NPC260396
0.6471 Remote Similarity NPC473948
0.6465 Remote Similarity NPC475949
0.6465 Remote Similarity NPC324667
0.6463 Remote Similarity NPC262673
0.6452 Remote Similarity NPC476706
0.6452 Remote Similarity NPC476707
0.6447 Remote Similarity NPC320421
0.6444 Remote Similarity NPC161045
0.6437 Remote Similarity NPC68119
0.6437 Remote Similarity NPC475699
0.6437 Remote Similarity NPC13823
0.6437 Remote Similarity NPC28049
0.6421 Remote Similarity NPC472010
0.642 Remote Similarity NPC243272
0.642 Remote Similarity NPC122627
0.6413 Remote Similarity NPC469910
0.6404 Remote Similarity NPC275766
0.64 Remote Similarity NPC224172
0.6395 Remote Similarity NPC477708
0.6395 Remote Similarity NPC49392
0.6395 Remote Similarity NPC190400
0.6395 Remote Similarity NPC470705
0.6386 Remote Similarity NPC291062
0.6386 Remote Similarity NPC94743
0.6383 Remote Similarity NPC14901
0.6383 Remote Similarity NPC130359
0.6375 Remote Similarity NPC296436
0.6375 Remote Similarity NPC176215
0.6374 Remote Similarity NPC32676
0.6364 Remote Similarity NPC159763
0.6364 Remote Similarity NPC278386
0.6364 Remote Similarity NPC161855
0.6364 Remote Similarity NPC99651
0.6364 Remote Similarity NPC473980
0.6364 Remote Similarity NPC19900
0.6364 Remote Similarity NPC124512
0.6364 Remote Similarity NPC473981
0.6354 Remote Similarity NPC165383
0.6354 Remote Similarity NPC282644
0.6354 Remote Similarity NPC29798
0.6353 Remote Similarity NPC114727
0.6353 Remote Similarity NPC160540
0.6353 Remote Similarity NPC476590
0.6344 Remote Similarity NPC266957
0.6344 Remote Similarity NPC300779
0.6341 Remote Similarity NPC477452
0.6341 Remote Similarity NPC263382
0.6341 Remote Similarity NPC146376
0.6341 Remote Similarity NPC125578
0.6337 Remote Similarity NPC471148
0.6333 Remote Similarity NPC477487
0.6329 Remote Similarity NPC57463
0.6329 Remote Similarity NPC151728

  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 NPC272267 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
0.6818 Remote Similarity NPD6110 Phase 1
0.6588 Remote Similarity NPD819 Approved
0.6588 Remote Similarity NPD818 Approved
0.6512 Remote Similarity NPD4756 Discovery
0.6364 Remote Similarity NPD4225 Approved
0.6304 Remote Similarity NPD1696 Phase 3
0.6296 Remote Similarity NPD3704 Approved
0.6182 Remote Similarity NPD7115 Discovery
0.6168 Remote Similarity NPD7601 Clinical (unspecified phase)
0.6146 Remote Similarity NPD6698 Approved
0.6146 Remote Similarity NPD46 Approved
0.6125 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6098 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5934 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5823 Remote Similarity NPD6109 Phase 1
0.5823 Remote Similarity NPD585 Clinical (unspecified phase)
0.5816 Remote Similarity NPD7838 Discovery
0.5789 Remote Similarity NPD5363 Approved
0.578 Remote Similarity NPD6371 Approved
0.5769 Remote Similarity NPD5344 Discontinued
0.5758 Remote Similarity NPD7983 Approved
0.57 Remote Similarity NPD5778 Approved
0.57 Remote Similarity NPD5779 Approved
0.5696 Remote Similarity NPD8779 Phase 3
0.5679 Remote Similarity NPD9120 Clinical (unspecified phase)
0.5679 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5663 Remote Similarity NPD3197 Phase 1
0.5657 Remote Similarity NPD5785 Approved
0.5648 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5644 Remote Similarity NPD5282 Discontinued

  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