Structure

Physi-Chem Properties

Molecular Weight:  489.31
Volume:  517.73
LogP:  3.733
LogD:  3.273
LogS:  -4.585
# Rotatable Bonds:  7
TPSA:  108.99
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.494
Synthetic Accessibility Score:  5.094
Fsp3:  0.714
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.891
MDCK Permeability:  1.2326976502663456e-05
Pgp-inhibitor:  0.807
Pgp-substrate:  0.992
Human Intestinal Absorption (HIA):  0.552
20% Bioavailability (F20%):  0.058
30% Bioavailability (F30%):  0.913

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.878
Plasma Protein Binding (PPB):  91.07849884033203%
Volume Distribution (VD):  1.91
Pgp-substrate:  3.3582632541656494%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.784
CYP2C19-inhibitor:  0.038
CYP2C19-substrate:  0.916
CYP2C9-inhibitor:  0.195
CYP2C9-substrate:  0.945
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.206
CYP3A4-inhibitor:  0.274
CYP3A4-substrate:  0.693

ADMET: Excretion

Clearance (CL):  10.075
Half-life (T1/2):  0.089

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.836
Drug-inuced Liver Injury (DILI):  0.267
AMES Toxicity:  0.04
Rat Oral Acute Toxicity:  0.882
Maximum Recommended Daily Dose:  0.965
Skin Sensitization:  0.16
Carcinogencity:  0.063
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.914

Download Data

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

  Natural Product: NPC477140

Natural Product ID:  NPC477140
Common Name*:   6-Epi-oxysporidinone
IUPAC Name:   5-[(1S,2R)-1,2-dihydroxy-4-oxocyclohexyl]-3-[(2S,5R,6R)-6-[(E)-4,6-dimethyloct-2-en-2-yl]-5-methyloxan-2-yl]-4-hydroxy-1-methylpyridin-2-one
Synonyms:   6-Epi-Oxysporidinone
Standard InCHIKey:  CYNJYGDSSURTLH-HYJFNEQJSA-N
Standard InCHI:  InChI=1S/C28H43NO6/c1-7-16(2)12-17(3)13-19(5)26-18(4)8-9-22(35-26)24-25(32)21(15-29(6)27(24)33)28(34)11-10-20(30)14-23(28)31/h13,15-18,22-23,26,31-32,34H,7-12,14H2,1-6H3/b19-13+/t16?,17?,18-,22+,23-,26-,28+/m1/s1
SMILES:  CCC(C)CC(C)/C=C(\C)/[C@H]1[C@@H](CC[C@H](O1)C2=C(C(=CN(C2=O)C)[C@]3(CCC(=O)C[C@H]3O)O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   54677669
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides

*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
NPO29266 Fusarium oxysporum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[16562855]
NPO29266 Fusarium oxysporum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[17286429]
NPO29266 Fusarium oxysporum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[9014349]
NPO29266 Fusarium oxysporum Species Nectriaceae 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
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus IC50 = 35 ug/ml PMID[16562855]

☑ 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 NPC477140 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
1.0 High Similarity NPC477143
0.7642 Intermediate Similarity NPC475642
0.754 Intermediate Similarity NPC475383
0.754 Intermediate Similarity NPC156379
0.7381 Intermediate Similarity NPC241050
0.7377 Intermediate Similarity NPC475608
0.7377 Intermediate Similarity NPC21713
0.7311 Intermediate Similarity NPC470073
0.7227 Intermediate Similarity NPC318544
0.7164 Intermediate Similarity NPC103605
0.7164 Intermediate Similarity NPC81092
0.7131 Intermediate Similarity NPC470072
0.6975 Remote Similarity NPC316730
0.6967 Remote Similarity NPC154601
0.6967 Remote Similarity NPC271269
0.696 Remote Similarity NPC44733
0.6934 Remote Similarity NPC120420
0.6911 Remote Similarity NPC251330
0.6891 Remote Similarity NPC35717
0.6891 Remote Similarity NPC306908
0.6884 Remote Similarity NPC99864
0.6875 Remote Similarity NPC30196
0.6822 Remote Similarity NPC6531
0.6822 Remote Similarity NPC476190
0.6769 Remote Similarity NPC120599
0.6769 Remote Similarity NPC200412
0.6769 Remote Similarity NPC156336
0.6767 Remote Similarity NPC316133
0.6767 Remote Similarity NPC318445
0.6767 Remote Similarity NPC314629
0.6765 Remote Similarity NPC315387
0.6765 Remote Similarity NPC316205
0.6748 Remote Similarity NPC133420
0.6741 Remote Similarity NPC314282
0.6724 Remote Similarity NPC469464
0.6716 Remote Similarity NPC314451
0.6716 Remote Similarity NPC313333
0.6716 Remote Similarity NPC313342
0.6716 Remote Similarity NPC314512
0.6695 Remote Similarity NPC477241
0.6667 Remote Similarity NPC474827
0.6667 Remote Similarity NPC239895
0.6667 Remote Similarity NPC316401
0.6667 Remote Similarity NPC68001
0.6667 Remote Similarity NPC199831
0.6667 Remote Similarity NPC474828
0.6643 Remote Similarity NPC315210
0.6643 Remote Similarity NPC315848
0.6641 Remote Similarity NPC474497
0.6641 Remote Similarity NPC275100
0.6641 Remote Similarity NPC476269
0.6641 Remote Similarity NPC1111
0.6641 Remote Similarity NPC261750
0.664 Remote Similarity NPC176773
0.6639 Remote Similarity NPC150041
0.6614 Remote Similarity NPC469603
0.6612 Remote Similarity NPC187761
0.6612 Remote Similarity NPC83895
0.6599 Remote Similarity NPC201899
0.6599 Remote Similarity NPC471674
0.6589 Remote Similarity NPC478212
0.6587 Remote Similarity NPC473807
0.6581 Remote Similarity NPC265856
0.656 Remote Similarity NPC469852
0.6549 Remote Similarity NPC185256
0.6538 Remote Similarity NPC145501
0.6535 Remote Similarity NPC218602
0.6529 Remote Similarity NPC40812
0.6529 Remote Similarity NPC476344
0.6519 Remote Similarity NPC16709
0.6515 Remote Similarity NPC108581
0.6515 Remote Similarity NPC478205
0.6515 Remote Similarity NPC478206
0.6512 Remote Similarity NPC60432
0.6508 Remote Similarity NPC469853
0.6504 Remote Similarity NPC472637
0.6504 Remote Similarity NPC77703
0.6489 Remote Similarity NPC64318
0.6484 Remote Similarity NPC195435
0.6484 Remote Similarity NPC476290
0.6484 Remote Similarity NPC196073
0.6475 Remote Similarity NPC308567
0.6475 Remote Similarity NPC261377
0.6475 Remote Similarity NPC255592
0.6466 Remote Similarity NPC476079
0.6466 Remote Similarity NPC103743
0.6466 Remote Similarity NPC113370
0.6462 Remote Similarity NPC469597
0.6457 Remote Similarity NPC474099
0.6446 Remote Similarity NPC135576
0.6446 Remote Similarity NPC93271
0.6441 Remote Similarity NPC316228
0.6439 Remote Similarity NPC98249
0.6439 Remote Similarity NPC53396
0.6439 Remote Similarity NPC478204
0.6434 Remote Similarity NPC100329
0.6434 Remote Similarity NPC132790
0.6434 Remote Similarity NPC97939
0.6434 Remote Similarity NPC247031
0.6429 Remote Similarity NPC478052
0.6412 Remote Similarity NPC147912
0.6412 Remote Similarity NPC67259
0.6406 Remote Similarity NPC24389
0.6406 Remote Similarity NPC478210
0.6406 Remote Similarity NPC137911
0.6406 Remote Similarity NPC228477
0.64 Remote Similarity NPC473624
0.6397 Remote Similarity NPC280498
0.6397 Remote Similarity NPC315783
0.6393 Remote Similarity NPC52820
0.6391 Remote Similarity NPC284707
0.6387 Remote Similarity NPC314500
0.6387 Remote Similarity NPC472010
0.6385 Remote Similarity NPC66108
0.6385 Remote Similarity NPC314550
0.6383 Remote Similarity NPC314361
0.6379 Remote Similarity NPC315395
0.6379 Remote Similarity NPC316426
0.6371 Remote Similarity NPC133907
0.6371 Remote Similarity NPC244456
0.6371 Remote Similarity NPC471401
0.6371 Remote Similarity NPC469657
0.6371 Remote Similarity NPC46998
0.6371 Remote Similarity NPC469851
0.6371 Remote Similarity NPC316250
0.6371 Remote Similarity NPC110443
0.6371 Remote Similarity NPC128733
0.6371 Remote Similarity NPC185141
0.637 Remote Similarity NPC315915
0.6364 Remote Similarity NPC478216
0.6357 Remote Similarity NPC478209
0.6357 Remote Similarity NPC477997
0.6357 Remote Similarity NPC478211
0.6356 Remote Similarity NPC307092
0.635 Remote Similarity NPC476729
0.635 Remote Similarity NPC469494
0.6349 Remote Similarity NPC469604
0.6349 Remote Similarity NPC472616
0.6349 Remote Similarity NPC309190
0.6348 Remote Similarity NPC243618
0.6348 Remote Similarity NPC70424
0.6343 Remote Similarity NPC477515
0.6343 Remote Similarity NPC67917
0.6343 Remote Similarity NPC313802
0.6343 Remote Similarity NPC314268
0.6336 Remote Similarity NPC471204
0.6336 Remote Similarity NPC469496
0.6336 Remote Similarity NPC469454
0.6336 Remote Similarity NPC475966
0.6336 Remote Similarity NPC469463
0.6328 Remote Similarity NPC193765
0.6325 Remote Similarity NPC86005
0.6324 Remote Similarity NPC269642
0.6316 Remote Similarity NPC55296
0.6316 Remote Similarity NPC470959
0.6316 Remote Similarity NPC476965
0.6316 Remote Similarity NPC469684
0.6312 Remote Similarity NPC120335
0.6308 Remote Similarity NPC474411
0.6308 Remote Similarity NPC474431
0.6304 Remote Similarity NPC293112
0.6303 Remote Similarity NPC471399
0.6303 Remote Similarity NPC166554
0.6303 Remote Similarity NPC473056
0.6299 Remote Similarity NPC32006
0.6299 Remote Similarity NPC472615
0.6299 Remote Similarity NPC476738
0.6299 Remote Similarity NPC85529
0.6299 Remote Similarity NPC476740
0.6296 Remote Similarity NPC478051
0.6293 Remote Similarity NPC307112
0.6288 Remote Similarity NPC284915
0.6288 Remote Similarity NPC80650
0.6286 Remote Similarity NPC110294
0.6281 Remote Similarity NPC472977
0.6281 Remote Similarity NPC71589
0.6281 Remote Similarity NPC472976
0.6279 Remote Similarity NPC38154
0.6279 Remote Similarity NPC87335
0.6279 Remote Similarity NPC475065
0.6279 Remote Similarity NPC471400
0.6279 Remote Similarity NPC315836
0.6279 Remote Similarity NPC313668
0.6277 Remote Similarity NPC105926
0.6277 Remote Similarity NPC67251
0.6277 Remote Similarity NPC265557
0.6277 Remote Similarity NPC469789
0.6277 Remote Similarity NPC91693
0.6277 Remote Similarity NPC18945
0.6271 Remote Similarity NPC472008
0.6271 Remote Similarity NPC473658
0.6271 Remote Similarity NPC106051
0.627 Remote Similarity NPC472755
0.627 Remote Similarity NPC309398
0.6269 Remote Similarity NPC186525
0.6269 Remote Similarity NPC201889
0.6269 Remote Similarity NPC106791
0.6269 Remote Similarity NPC251310
0.6269 Remote Similarity NPC709
0.6269 Remote Similarity NPC50774

  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 NPC477140 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
0.6957 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6884 Remote Similarity NPD8415 Approved
0.6791 Remote Similarity NPD8451 Approved
0.6791 Remote Similarity NPD8273 Phase 1
0.6767 Remote Similarity NPD7642 Approved
0.6741 Remote Similarity NPD8448 Approved
0.6716 Remote Similarity NPD8341 Approved
0.6716 Remote Similarity NPD8340 Approved
0.6716 Remote Similarity NPD8342 Approved
0.6716 Remote Similarity NPD8299 Approved
0.6715 Remote Similarity NPD8392 Approved
0.6715 Remote Similarity NPD8391 Approved
0.6715 Remote Similarity NPD8390 Approved
0.6667 Remote Similarity NPD7260 Phase 2
0.6641 Remote Similarity NPD7641 Discontinued
0.656 Remote Similarity NPD7333 Discontinued
0.65 Remote Similarity NPD6845 Suspended
0.6493 Remote Similarity NPD6921 Approved
0.6397 Remote Similarity NPD7830 Approved
0.6397 Remote Similarity NPD7829 Approved
0.637 Remote Similarity NPD8384 Approved
0.6324 Remote Similarity NPD7624 Clinical (unspecified phase)
0.6324 Remote Similarity NPD7623 Phase 3
0.6324 Remote Similarity NPD8080 Discontinued
0.6296 Remote Similarity NPD7299 Clinical (unspecified phase)
0.6259 Remote Similarity NPD8074 Phase 3
0.625 Remote Similarity NPD8513 Phase 3
0.625 Remote Similarity NPD7983 Approved
0.625 Remote Similarity NPD8444 Approved
0.6212 Remote Similarity NPD1376 Discontinued
0.6194 Remote Similarity NPD7115 Discovery
0.6194 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6183 Remote Similarity NPD7116 Clinical (unspecified phase)
0.6179 Remote Similarity NPD7839 Suspended
0.6167 Remote Similarity NPD6698 Approved
0.6167 Remote Similarity NPD46 Approved
0.6143 Remote Similarity NPD7747 Phase 1
0.6143 Remote Similarity NPD7746 Phase 1
0.6131 Remote Similarity NPD7739 Clinical (unspecified phase)
0.6131 Remote Similarity NPD8516 Approved
0.6131 Remote Similarity NPD8517 Approved
0.6131 Remote Similarity NPD8515 Approved
0.6131 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6083 Remote Similarity NPD6101 Approved
0.6083 Remote Similarity NPD5764 Clinical (unspecified phase)
0.6074 Remote Similarity NPD7500 Approved
0.6066 Remote Similarity NPD5778 Approved
0.6066 Remote Similarity NPD5779 Approved
0.6061 Remote Similarity NPD2204 Approved
0.6 Remote Similarity NPD8389 Clinical (unspecified phase)
0.5984 Remote Similarity NPD6411 Approved
0.5952 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5952 Remote Similarity NPD4225 Approved
0.5899 Remote Similarity NPD6908 Approved
0.5899 Remote Similarity NPD6909 Approved
0.5865 Remote Similarity NPD6371 Approved
0.5857 Remote Similarity NPD2838 Clinical (unspecified phase)
0.5849 Remote Similarity NPD8414 Discontinued
0.584 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5833 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5821 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5821 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5794 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5793 Remote Similarity NPD6914 Discontinued
0.5786 Remote Similarity NPD8269 Approved
0.5786 Remote Similarity NPD8267 Approved
0.5786 Remote Similarity NPD8268 Approved
0.5786 Remote Similarity NPD8266 Approved
0.5778 Remote Similarity NPD6053 Discontinued
0.5772 Remote Similarity NPD5785 Approved
0.576 Remote Similarity NPD5282 Discontinued
0.5741 Remote Similarity NPD6844 Discontinued
0.5714 Remote Similarity NPD6686 Approved
0.5702 Remote Similarity NPD5786 Approved
0.5694 Remote Similarity NPD5157 Phase 1
0.5694 Remote Similarity NPD5158 Clinical (unspecified phase)
0.5694 Remote Similarity NPD5159 Phase 2
0.5692 Remote Similarity NPD8085 Approved
0.5692 Remote Similarity NPD8138 Approved
0.5692 Remote Similarity NPD8084 Approved
0.5692 Remote Similarity NPD8139 Approved
0.5692 Remote Similarity NPD8083 Approved
0.5692 Remote Similarity NPD8086 Approved
0.5692 Remote Similarity NPD8082 Approved
0.5664 Remote Similarity NPD3131 Approved
0.5664 Remote Similarity NPD2609 Approved
0.5664 Remote Similarity NPD2611 Approved
0.5664 Remote Similarity NPD2612 Approved
0.5664 Remote Similarity NPD4217 Approved
0.5664 Remote Similarity NPD4218 Approved
0.5664 Remote Similarity NPD2608 Approved
0.5664 Remote Similarity NPD2610 Approved
0.5664 Remote Similarity NPD3132 Approved
0.5664 Remote Similarity NPD4215 Approved
0.5664 Remote Similarity NPD4216 Approved
0.5649 Remote Similarity NPD8275 Approved
0.5649 Remote Similarity NPD8276 Approved
0.5645 Remote Similarity NPD790 Approved
0.5645 Remote Similarity NPD7838 Discovery
0.5641 Remote Similarity NPD2575 Approved
0.5639 Remote Similarity NPD7899 Clinical (unspecified phase)
0.563 Remote Similarity NPD6421 Discontinued
0.562 Remote Similarity NPD5363 Approved
0.5616 Remote Similarity NPD7319 Approved
0.5615 Remote Similarity NPD5344 Discontinued
0.5612 Remote Similarity NPD7505 Discontinued
0.5608 Remote Similarity NPD8338 Approved
0.5608 Remote Similarity NPD2613 Approved
0.5606 Remote Similarity NPD8081 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