Structure

Physi-Chem Properties

Molecular Weight:  192.04
Volume:  186.382
LogP:  1.182
LogD:  1.213
LogS:  -1.701
# Rotatable Bonds:  1
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.351
Synthetic Accessibility Score:  4.456
Fsp3:  0.2
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.823
MDCK Permeability:  1.5068981156218797e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.026
30% Bioavailability (F30%):  0.315

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.524
Plasma Protein Binding (PPB):  72.48194122314453%
Volume Distribution (VD):  1.78
Pgp-substrate:  28.786273956298828%

ADMET: Metabolism

CYP1A2-inhibitor:  0.982
CYP1A2-substrate:  0.272
CYP2C19-inhibitor:  0.455
CYP2C19-substrate:  0.247
CYP2C9-inhibitor:  0.173
CYP2C9-substrate:  0.066
CYP2D6-inhibitor:  0.104
CYP2D6-substrate:  0.082
CYP3A4-inhibitor:  0.306
CYP3A4-substrate:  0.211

ADMET: Excretion

Clearance (CL):  3.072
Half-life (T1/2):  0.812

ADMET: Toxicity

hERG Blockers:  0.042
Human Hepatotoxicity (H-HT):  0.39
Drug-inuced Liver Injury (DILI):  0.711
AMES Toxicity:  0.171
Rat Oral Acute Toxicity:  0.312
Maximum Recommended Daily Dose:  0.875
Skin Sensitization:  0.782
Carcinogencity:  0.998
Eye Corrosion:  0.004
Eye Irritation:  0.268
Respiratory Toxicity:  0.951

Download Data

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

  Natural Product: NPC477117

Natural Product ID:  NPC477117
Common Name*:   Fagraldehyde
IUPAC Name:   1-methyl-3-oxo-1H-pyrano[3,4-c]pyran-4-carbaldehyde
Synonyms:   Fagraldehyde
Standard InCHIKey:  STZFTMXKJRIOSV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H8O4/c1-6-9-5-13-3-2-7(9)8(4-11)10(12)14-6/h2-6H,1H3
SMILES:  CC1C2=COC=CC2=C(C(=O)O1)C=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   25147622
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones and derivatives
          • [CHEMONTID:0001211] Dihydropyranones

*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
NPO1905 Fagraea fragrans Species Gentianaceae Eukaryota bark and leaves Koh Kong Province, Cambodia 2005-DEC PMID[19053508]
NPO1905 Fagraea fragrans Species Gentianaceae 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
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 22.4 ug/ml PMID[19053508]

☑ 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 NPC477117 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
0.8462 Intermediate Similarity NPC15193
0.8169 Intermediate Similarity NPC133098
0.8088 Intermediate Similarity NPC476589
0.7761 Intermediate Similarity NPC309408
0.7692 Intermediate Similarity NPC150717
0.7692 Intermediate Similarity NPC221763
0.7612 Intermediate Similarity NPC133600
0.7534 Intermediate Similarity NPC59558
0.7465 Intermediate Similarity NPC470033
0.7344 Intermediate Similarity NPC191643
0.7324 Intermediate Similarity NPC471565
0.7324 Intermediate Similarity NPC471566
0.7324 Intermediate Similarity NPC182794
0.7286 Intermediate Similarity NPC473737
0.7286 Intermediate Similarity NPC2328
0.7273 Intermediate Similarity NPC173157
0.7273 Intermediate Similarity NPC25038
0.726 Intermediate Similarity NPC238223
0.726 Intermediate Similarity NPC280374
0.7222 Intermediate Similarity NPC469446
0.72 Intermediate Similarity NPC178575
0.7164 Intermediate Similarity NPC86948
0.7143 Intermediate Similarity NPC125925
0.7143 Intermediate Similarity NPC234084
0.7123 Intermediate Similarity NPC132286
0.7121 Intermediate Similarity NPC218486
0.7121 Intermediate Similarity NPC478120
0.7108 Intermediate Similarity NPC281172
0.7093 Intermediate Similarity NPC274075
0.7083 Intermediate Similarity NPC471556
0.7051 Intermediate Similarity NPC470705
0.7042 Intermediate Similarity NPC179087
0.7042 Intermediate Similarity NPC44343
0.7042 Intermediate Similarity NPC210303
0.7031 Intermediate Similarity NPC275316
0.7024 Intermediate Similarity NPC291712
0.7 Intermediate Similarity NPC130953
0.7 Intermediate Similarity NPC429928
0.7 Intermediate Similarity NPC98519
0.7 Intermediate Similarity NPC26223
0.6974 Remote Similarity NPC293114
0.6962 Remote Similarity NPC275530
0.6957 Remote Similarity NPC189700
0.6923 Remote Similarity NPC147621
0.6923 Remote Similarity NPC210258
0.6923 Remote Similarity NPC206507
0.6912 Remote Similarity NPC51846
0.6901 Remote Similarity NPC68044
0.6857 Remote Similarity NPC22897
0.6857 Remote Similarity NPC159650
0.6857 Remote Similarity NPC286189
0.6857 Remote Similarity NPC82465
0.6849 Remote Similarity NPC7940
0.6849 Remote Similarity NPC273600
0.6849 Remote Similarity NPC131174
0.6842 Remote Similarity NPC315285
0.6818 Remote Similarity NPC32552
0.68 Remote Similarity NPC474823
0.68 Remote Similarity NPC470032
0.679 Remote Similarity NPC271632
0.6769 Remote Similarity NPC236338
0.6769 Remote Similarity NPC15789
0.6765 Remote Similarity NPC478117
0.6765 Remote Similarity NPC474913
0.6761 Remote Similarity NPC79756
0.6757 Remote Similarity NPC475675
0.6757 Remote Similarity NPC475555
0.6757 Remote Similarity NPC37382
0.6757 Remote Similarity NPC315115
0.675 Remote Similarity NPC315394
0.675 Remote Similarity NPC473825
0.675 Remote Similarity NPC68156
0.6742 Remote Similarity NPC29798
0.6742 Remote Similarity NPC282644
0.6714 Remote Similarity NPC21946
0.6712 Remote Similarity NPC477457
0.6712 Remote Similarity NPC25747
0.6712 Remote Similarity NPC308457
0.6712 Remote Similarity NPC148233
0.6712 Remote Similarity NPC477456
0.6711 Remote Similarity NPC151481
0.6711 Remote Similarity NPC475004
0.6709 Remote Similarity NPC478194
0.6709 Remote Similarity NPC478193
0.6709 Remote Similarity NPC478191
0.6709 Remote Similarity NPC478195
0.6709 Remote Similarity NPC161038
0.6709 Remote Similarity NPC478196
0.6709 Remote Similarity NPC478192
0.6667 Remote Similarity NPC470442
0.6667 Remote Similarity NPC151648
0.6667 Remote Similarity NPC287878
0.6667 Remote Similarity NPC16488
0.6667 Remote Similarity NPC225272
0.6667 Remote Similarity NPC316851
0.6667 Remote Similarity NPC264391
0.6667 Remote Similarity NPC203335
0.6629 Remote Similarity NPC32944
0.6629 Remote Similarity NPC193396
0.6623 Remote Similarity NPC202011
0.6623 Remote Similarity NPC315597
0.6622 Remote Similarity NPC220766
0.6622 Remote Similarity NPC96414
0.6622 Remote Similarity NPC133904
0.6615 Remote Similarity NPC135698
0.6593 Remote Similarity NPC471698
0.6591 Remote Similarity NPC95364
0.6591 Remote Similarity NPC142159
0.6582 Remote Similarity NPC470686
0.6579 Remote Similarity NPC287705
0.6579 Remote Similarity NPC79220
0.6579 Remote Similarity NPC313444
0.6575 Remote Similarity NPC132243
0.6548 Remote Similarity NPC10080
0.6548 Remote Similarity NPC123908
0.6543 Remote Similarity NPC471225
0.6538 Remote Similarity NPC162571
0.6538 Remote Similarity NPC316185
0.6538 Remote Similarity NPC112983
0.6533 Remote Similarity NPC191233
0.6533 Remote Similarity NPC124586
0.6533 Remote Similarity NPC248125
0.6533 Remote Similarity NPC201356
0.6533 Remote Similarity NPC146811
0.65 Remote Similarity NPC469414
0.65 Remote Similarity NPC260396
0.65 Remote Similarity NPC315552
0.65 Remote Similarity NPC329826
0.6494 Remote Similarity NPC494
0.6494 Remote Similarity NPC473277
0.6494 Remote Similarity NPC470693
0.6486 Remote Similarity NPC475618
0.6484 Remote Similarity NPC143210
0.6479 Remote Similarity NPC254095
0.6456 Remote Similarity NPC146583
0.6444 Remote Similarity NPC166110
0.6437 Remote Similarity NPC316426
0.6437 Remote Similarity NPC315395
0.642 Remote Similarity NPC271986
0.642 Remote Similarity NPC203277
0.6413 Remote Similarity NPC12727
0.641 Remote Similarity NPC316029
0.6406 Remote Similarity NPC47946
0.6406 Remote Similarity NPC270706
0.6406 Remote Similarity NPC26600
0.64 Remote Similarity NPC470123
0.64 Remote Similarity NPC282760
0.6389 Remote Similarity NPC97570
0.6389 Remote Similarity NPC302564
0.6389 Remote Similarity NPC203233
0.6377 Remote Similarity NPC129710
0.6375 Remote Similarity NPC315843
0.6375 Remote Similarity NPC107654
0.6374 Remote Similarity NPC248193
0.6364 Remote Similarity NPC475760
0.6364 Remote Similarity NPC63873
0.6364 Remote Similarity NPC126184
0.6351 Remote Similarity NPC474774
0.6351 Remote Similarity NPC475073
0.6351 Remote Similarity NPC474723
0.6351 Remote Similarity NPC474729
0.6341 Remote Similarity NPC475711
0.6338 Remote Similarity NPC294938
0.6338 Remote Similarity NPC129150
0.6338 Remote Similarity NPC293437
0.6338 Remote Similarity NPC249850
0.6338 Remote Similarity NPC135863
0.6333 Remote Similarity NPC224270
0.6329 Remote Similarity NPC181587
0.6322 Remote Similarity NPC130030
0.6316 Remote Similarity NPC284447
0.631 Remote Similarity NPC121374
0.6308 Remote Similarity NPC197467
0.6308 Remote Similarity NPC128280
0.6282 Remote Similarity NPC476591
0.6282 Remote Similarity NPC88877
0.6279 Remote Similarity NPC475083
0.6269 Remote Similarity NPC27264
0.6267 Remote Similarity NPC470808
0.6267 Remote Similarity NPC471611
0.6265 Remote Similarity NPC473471
0.6265 Remote Similarity NPC182292
0.6265 Remote Similarity NPC279532
0.625 Remote Similarity NPC284006
0.625 Remote Similarity NPC186332
0.625 Remote Similarity NPC478096
0.625 Remote Similarity NPC223679
0.625 Remote Similarity NPC47220
0.6234 Remote Similarity NPC194871
0.6234 Remote Similarity NPC122627
0.622 Remote Similarity NPC301207
0.622 Remote Similarity NPC127118
0.622 Remote Similarity NPC209113
0.6216 Remote Similarity NPC55376
0.6216 Remote Similarity NPC263732
0.6216 Remote Similarity NPC26810
0.6212 Remote Similarity NPC128520
0.6207 Remote Similarity NPC161670
0.6203 Remote Similarity NPC469660
0.6203 Remote Similarity NPC476037

  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 NPC477117 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
0.6418 Remote Similarity NPD6927 Phase 3
0.618 Remote Similarity NPD1282 Approved
0.6163 Remote Similarity NPD5209 Approved
0.5974 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5882 Remote Similarity NPD4220 Pre-registration
0.5844 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5765 Remote Similarity NPD4756 Discovery
0.5676 Remote Similarity NPD8779 Phase 3
0.5667 Remote Similarity NPD6400 Clinical (unspecified phase)

  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