Structure

Physi-Chem Properties

Molecular Weight:  262.16
Volume:  289.924
LogP:  3.431
LogD:  1.861
LogS:  -3.407
# Rotatable Bonds:  10
TPSA:  51.21
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.345
Synthetic Accessibility Score:  2.735
Fsp3:  0.562
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.678
MDCK Permeability:  2.760111055977177e-05
Pgp-inhibitor:  0.191
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.773
30% Bioavailability (F30%):  0.037

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.705
Plasma Protein Binding (PPB):  93.11128234863281%
Volume Distribution (VD):  0.383
Pgp-substrate:  2.2358651161193848%

ADMET: Metabolism

CYP1A2-inhibitor:  0.106
CYP1A2-substrate:  0.81
CYP2C19-inhibitor:  0.379
CYP2C19-substrate:  0.849
CYP2C9-inhibitor:  0.37
CYP2C9-substrate:  0.909
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.108
CYP3A4-inhibitor:  0.743
CYP3A4-substrate:  0.495

ADMET: Excretion

Clearance (CL):  0.814
Half-life (T1/2):  0.371

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.223
Drug-inuced Liver Injury (DILI):  0.572
AMES Toxicity:  0.309
Rat Oral Acute Toxicity:  0.234
Maximum Recommended Daily Dose:  0.447
Skin Sensitization:  0.941
Carcinogencity:  0.791
Eye Corrosion:  0.036
Eye Irritation:  0.518
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: NPC281230

Natural Product ID:  NPC281230
Common Name*:   Chrysotrione A
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MTCIZZXMWYIICP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H22O3/c1-2-3-4-5-6-7-8-9-10-13(17)16-14(18)11-12-15(16)19/h2,11-12,17H,1,3-10H2
SMILES:  C=CCCCCCCCCC(=C1C(=O)C=CC1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL218883
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0003889] Vinylogous acids

*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
NPO4182 Hygrophorus chrysodon Species Hygrophoraceae Eukaryota fruiting bodies n.a. n.a. PMID[17253868]
NPO4182 Hygrophorus chrysodon Species Hygrophoraceae 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
NPT2781 Organism Fusarium moniliforme Gibberella moniliformis IZ = 3.0 mm PMID[482782]
NPT2781 Organism Fusarium moniliforme Gibberella moniliformis IZ = 10.0 mm PMID[482782]
NPT2781 Organism Fusarium moniliforme Gibberella moniliformis IZ = 35.0 mm PMID[482782]

☑ 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 NPC281230 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
0.963 High Similarity NPC192843
0.8197 Intermediate Similarity NPC477707
0.7903 Intermediate Similarity NPC477830
0.7705 Intermediate Similarity NPC274927
0.7705 Intermediate Similarity NPC106851
0.7619 Intermediate Similarity NPC143168
0.7619 Intermediate Similarity NPC53109
0.7581 Intermediate Similarity NPC174447
0.7581 Intermediate Similarity NPC122521
0.7581 Intermediate Similarity NPC251042
0.7581 Intermediate Similarity NPC235242
0.7576 Intermediate Similarity NPC476614
0.75 Intermediate Similarity NPC7029
0.7463 Intermediate Similarity NPC262673
0.746 Intermediate Similarity NPC40082
0.7455 Intermediate Similarity NPC100380
0.7353 Intermediate Similarity NPC291062
0.7353 Intermediate Similarity NPC318766
0.7353 Intermediate Similarity NPC94743
0.7344 Intermediate Similarity NPC322457
0.7258 Intermediate Similarity NPC320421
0.7241 Intermediate Similarity NPC477458
0.7213 Intermediate Similarity NPC325977
0.7213 Intermediate Similarity NPC477201
0.7206 Intermediate Similarity NPC236208
0.7206 Intermediate Similarity NPC67608
0.7193 Intermediate Similarity NPC145311
0.7188 Intermediate Similarity NPC260573
0.7167 Intermediate Similarity NPC322461
0.7164 Intermediate Similarity NPC243272
0.7143 Intermediate Similarity NPC38455
0.7143 Intermediate Similarity NPC471752
0.7121 Intermediate Similarity NPC474329
0.7121 Intermediate Similarity NPC474304
0.7091 Intermediate Similarity NPC471753
0.7069 Intermediate Similarity NPC225974
0.7069 Intermediate Similarity NPC20934
0.7069 Intermediate Similarity NPC288381
0.7059 Intermediate Similarity NPC146376
0.7059 Intermediate Similarity NPC263382
0.7059 Intermediate Similarity NPC125578
0.7042 Intermediate Similarity NPC227396
0.7042 Intermediate Similarity NPC264178
0.7015 Intermediate Similarity NPC197089
0.7015 Intermediate Similarity NPC16119
0.7 Intermediate Similarity NPC296311
0.7 Intermediate Similarity NPC294548
0.7 Intermediate Similarity NPC1813
0.7 Intermediate Similarity NPC217188
0.7 Intermediate Similarity NPC139029
0.7 Intermediate Similarity NPC36061
0.6984 Remote Similarity NPC34416
0.697 Remote Similarity NPC474400
0.697 Remote Similarity NPC34622
0.6964 Remote Similarity NPC191337
0.6957 Remote Similarity NPC94488
0.6957 Remote Similarity NPC469914
0.6923 Remote Similarity NPC174560
0.6923 Remote Similarity NPC125312
0.6912 Remote Similarity NPC474619
0.6885 Remote Similarity NPC261831
0.6885 Remote Similarity NPC6095
0.6885 Remote Similarity NPC154245
0.6885 Remote Similarity NPC424
0.6885 Remote Similarity NPC25417
0.6885 Remote Similarity NPC87564
0.6885 Remote Similarity NPC88966
0.6885 Remote Similarity NPC85813
0.6885 Remote Similarity NPC32467
0.6885 Remote Similarity NPC281972
0.6885 Remote Similarity NPC290563
0.6875 Remote Similarity NPC329550
0.6866 Remote Similarity NPC98897
0.6849 Remote Similarity NPC477708
0.6842 Remote Similarity NPC262558
0.6842 Remote Similarity NPC8610
0.6833 Remote Similarity NPC281245
0.6833 Remote Similarity NPC92114
0.6833 Remote Similarity NPC137396
0.6833 Remote Similarity NPC471751
0.6825 Remote Similarity NPC268185
0.6818 Remote Similarity NPC57463
0.6818 Remote Similarity NPC151728
0.6786 Remote Similarity NPC477686
0.678 Remote Similarity NPC59051
0.678 Remote Similarity NPC15325
0.6774 Remote Similarity NPC52264
0.6774 Remote Similarity NPC54766
0.6769 Remote Similarity NPC229252
0.6769 Remote Similarity NPC143857
0.6765 Remote Similarity NPC137163
0.6765 Remote Similarity NPC83965
0.6761 Remote Similarity NPC67076
0.6761 Remote Similarity NPC106309
0.6761 Remote Similarity NPC29328
0.6761 Remote Similarity NPC288667
0.6761 Remote Similarity NPC319163
0.6724 Remote Similarity NPC207292
0.6721 Remote Similarity NPC321062
0.6721 Remote Similarity NPC70387
0.6719 Remote Similarity NPC281195
0.6714 Remote Similarity NPC10758
0.6714 Remote Similarity NPC250928
0.6714 Remote Similarity NPC143396
0.6712 Remote Similarity NPC251435
0.6712 Remote Similarity NPC474011
0.6667 Remote Similarity NPC474362
0.6667 Remote Similarity NPC187777
0.6667 Remote Similarity NPC192006
0.6667 Remote Similarity NPC40148
0.6667 Remote Similarity NPC474202
0.6667 Remote Similarity NPC179764
0.6667 Remote Similarity NPC18951
0.6615 Remote Similarity NPC278202
0.6615 Remote Similarity NPC473494
0.6613 Remote Similarity NPC137538
0.6613 Remote Similarity NPC189677
0.6613 Remote Similarity NPC300121
0.661 Remote Similarity NPC149821
0.661 Remote Similarity NPC5413
0.6607 Remote Similarity NPC301972
0.6604 Remote Similarity NPC130923
0.6571 Remote Similarity NPC218477
0.6562 Remote Similarity NPC283502
0.6562 Remote Similarity NPC225929
0.6522 Remote Similarity NPC308294
0.6522 Remote Similarity NPC142423
0.6515 Remote Similarity NPC243532
0.6508 Remote Similarity NPC473863
0.6508 Remote Similarity NPC274290
0.6508 Remote Similarity NPC317899
0.65 Remote Similarity NPC474391
0.65 Remote Similarity NPC224227
0.65 Remote Similarity NPC118788
0.6494 Remote Similarity NPC91332
0.6494 Remote Similarity NPC162741
0.6491 Remote Similarity NPC145755
0.6491 Remote Similarity NPC267514
0.6481 Remote Similarity NPC217923
0.6479 Remote Similarity NPC265574
0.6479 Remote Similarity NPC475004
0.6452 Remote Similarity NPC284224
0.6452 Remote Similarity NPC45283
0.6452 Remote Similarity NPC474141
0.6447 Remote Similarity NPC19443
0.6447 Remote Similarity NPC189485
0.6441 Remote Similarity NPC180534
0.6441 Remote Similarity NPC91495
0.6441 Remote Similarity NPC471958
0.6438 Remote Similarity NPC238948
0.6438 Remote Similarity NPC300940
0.6438 Remote Similarity NPC12815
0.6438 Remote Similarity NPC215745
0.6429 Remote Similarity NPC106613
0.6429 Remote Similarity NPC278895
0.6429 Remote Similarity NPC476626
0.6429 Remote Similarity NPC60120
0.6429 Remote Similarity NPC96962
0.6418 Remote Similarity NPC64971
0.6418 Remote Similarity NPC321838
0.6418 Remote Similarity NPC328776
0.6418 Remote Similarity NPC320305
0.6418 Remote Similarity NPC64985
0.6418 Remote Similarity NPC201939
0.6418 Remote Similarity NPC97322
0.6415 Remote Similarity NPC24833
0.64 Remote Similarity NPC469646
0.6393 Remote Similarity NPC48162
0.6393 Remote Similarity NPC262968
0.6389 Remote Similarity NPC477455
0.6389 Remote Similarity NPC67183
0.6389 Remote Similarity NPC203819
0.6379 Remote Similarity NPC76976
0.6379 Remote Similarity NPC117572
0.6377 Remote Similarity NPC176215
0.6377 Remote Similarity NPC61473
0.6377 Remote Similarity NPC470688
0.6377 Remote Similarity NPC296436
0.6351 Remote Similarity NPC7382
0.6351 Remote Similarity NPC474321
0.6351 Remote Similarity NPC144995
0.6351 Remote Similarity NPC160540
0.6351 Remote Similarity NPC227814
0.6351 Remote Similarity NPC147438
0.6349 Remote Similarity NPC474127
0.6349 Remote Similarity NPC87394
0.6338 Remote Similarity NPC134385
0.6338 Remote Similarity NPC474823
0.6338 Remote Similarity NPC477452
0.6333 Remote Similarity NPC267110
0.6324 Remote Similarity NPC190049
0.6316 Remote Similarity NPC476007
0.6316 Remote Similarity NPC276769
0.6316 Remote Similarity NPC86917
0.6316 Remote Similarity NPC216921
0.6316 Remote Similarity NPC473536
0.6316 Remote Similarity NPC471061
0.6316 Remote Similarity NPC472014
0.6316 Remote Similarity NPC252978
0.6308 Remote Similarity NPC71755

  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 NPC281230 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
0.7619 Intermediate Similarity NPD2664 Clinical (unspecified phase)
0.7015 Intermediate Similarity NPD7331 Phase 2
0.7015 Intermediate Similarity NPD6108 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD3172 Approved
0.6885 Remote Similarity NPD3194 Approved
0.6885 Remote Similarity NPD3195 Phase 2
0.6885 Remote Similarity NPD3196 Approved
0.6885 Remote Similarity NPD4266 Approved
0.661 Remote Similarity NPD3173 Approved
0.6533 Remote Similarity NPD4756 Discovery
0.6522 Remote Similarity NPD3704 Approved
0.6441 Remote Similarity NPD622 Approved
0.6393 Remote Similarity NPD28 Approved
0.6393 Remote Similarity NPD29 Approved
0.6379 Remote Similarity NPD39 Approved
0.6379 Remote Similarity NPD4222 Approved
0.6377 Remote Similarity NPD7341 Phase 2
0.6282 Remote Similarity NPD4695 Discontinued
0.6232 Remote Similarity NPD3197 Phase 1
0.6182 Remote Similarity NPD5783 Phase 3
0.6154 Remote Similarity NPD4195 Approved
0.6102 Remote Similarity NPD3174 Discontinued
0.6061 Remote Similarity NPD8779 Phase 3
0.6034 Remote Similarity NPD5326 Phase 3
0.6029 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6024 Remote Similarity NPD4519 Discontinued
0.6024 Remote Similarity NPD5690 Phase 2
0.6024 Remote Similarity NPD4623 Approved
0.6 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5926 Remote Similarity NPD4223 Phase 3
0.5926 Remote Similarity NPD4800 Clinical (unspecified phase)
0.5926 Remote Similarity NPD4221 Approved
0.5904 Remote Similarity NPD5363 Approved
0.5854 Remote Similarity NPD7154 Phase 3
0.5846 Remote Similarity NPD539 Approved
0.5823 Remote Similarity NPD3617 Approved
0.5806 Remote Similarity NPD4220 Pre-registration
0.5783 Remote Similarity NPD3666 Approved
0.5783 Remote Similarity NPD4197 Approved
0.5783 Remote Similarity NPD3665 Phase 1
0.5783 Remote Similarity NPD3133 Approved
0.5753 Remote Similarity NPD3709 Clinical (unspecified phase)
0.5732 Remote Similarity NPD5209 Approved
0.573 Remote Similarity NPD5282 Discontinued
0.5714 Remote Similarity NPD1696 Phase 3
0.5714 Remote Similarity NPD5329 Approved
0.5698 Remote Similarity NPD4518 Approved
0.5682 Remote Similarity NPD6079 Approved
0.5679 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5679 Remote Similarity NPD5368 Approved
0.5663 Remote Similarity NPD5362 Discontinued
0.5647 Remote Similarity NPD4693 Phase 3
0.5647 Remote Similarity NPD5205 Approved
0.5647 Remote Similarity NPD4138 Approved
0.5647 Remote Similarity NPD4690 Approved
0.5647 Remote Similarity NPD4694 Approved
0.5647 Remote Similarity NPD5279 Phase 3
0.5647 Remote Similarity NPD3618 Phase 1
0.5647 Remote Similarity NPD3574 Clinical (unspecified phase)
0.5647 Remote Similarity NPD4689 Approved
0.5647 Remote Similarity NPD4688 Approved
0.5647 Remote Similarity NPD5280 Approved
0.5625 Remote Similarity NPD4268 Approved
0.5625 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5625 Remote Similarity NPD4271 Approved
0.561 Remote Similarity NPD4790 Discontinued
0.561 Remote Similarity NPD5369 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