Structure

Physi-Chem Properties

Molecular Weight:  254.12
Volume:  258.253
LogP:  -0.091
LogD:  0.531
LogS:  -1.717
# Rotatable Bonds:  9
TPSA:  83.97
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.279
Synthetic Accessibility Score:  4.532
Fsp3:  0.615
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.698
MDCK Permeability:  0.00017785899399314076
Pgp-inhibitor:  0.196
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.957
20% Bioavailability (F20%):  0.252
30% Bioavailability (F30%):  0.232

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.764
Plasma Protein Binding (PPB):  69.12466430664062%
Volume Distribution (VD):  0.463
Pgp-substrate:  54.72459030151367%

ADMET: Metabolism

CYP1A2-inhibitor:  0.025
CYP1A2-substrate:  0.125
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.315
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.053
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.117
CYP3A4-inhibitor:  0.055
CYP3A4-substrate:  0.226

ADMET: Excretion

Clearance (CL):  5.196
Half-life (T1/2):  0.791

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.076
Drug-inuced Liver Injury (DILI):  0.7
AMES Toxicity:  0.697
Rat Oral Acute Toxicity:  0.048
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.921
Carcinogencity:  0.103
Eye Corrosion:  0.013
Eye Irritation:  0.459
Respiratory Toxicity:  0.403

Download Data

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

  Natural Product: NPC474545

Natural Product ID:  NPC474545
Common Name*:   (2E,4E)-6,7-Dihydroxy-7-[(2S,3S)-3-(Hydroxymethyl)Oxiran-2-Yl]-2-[(E)-Prop-1-Enyl]Hepta-2,4-Dienal
IUPAC Name:   (2E,4E)-6,7-dihydroxy-7-[(2S,3S)-3-(hydroxymethyl)oxiran-2-yl]-2-[(E)-prop-1-enyl]hepta-2,4-dienal
Synonyms:  
Standard InCHIKey:  VAEGPTFYQCVMTP-KRQHTCOKSA-N
Standard InCHI:  InChI=1S/C13H18O5/c1-2-4-9(7-14)5-3-6-10(16)12(17)13-11(8-15)18-13/h2-7,10-13,15-17H,8H2,1H3/b4-2+,6-3+,9-5+/t10?,11-,12?,13+/m0/s1
SMILES:  CC=CC(=CC=CC(C(C1C(O1)CO)O)O)C=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL471676
PubChem CID:   44559140
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols

*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
NPO33429 menisporopsis theobromae bcc 3975 Species n.a. Eukaryota n.a. n.a. n.a. PMID[17067151]

☑ 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
NPT91 Cell Line KB Homo sapiens IC50 > 78700.0 nM PMID[469410]
NPT639 Cell Line NCI-H187 Homo sapiens IC50 > 78700.0 nM PMID[469410]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 78700.0 nM PMID[469410]
NPT485 Organism Plasmodium falciparum (isolate K1 / Thailand) Plasmodium falciparum K1 IC50 > 78700.0 nM PMID[469410]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC > 787400.0 nM PMID[469410]

☑ 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 NPC474545 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
0.7895 Intermediate Similarity NPC24590
0.7887 Intermediate Similarity NPC475221
0.7625 Intermediate Similarity NPC291260
0.7625 Intermediate Similarity NPC1180
0.7595 Intermediate Similarity NPC233071
0.7595 Intermediate Similarity NPC475711
0.7534 Intermediate Similarity NPC19769
0.75 Intermediate Similarity NPC476037
0.7468 Intermediate Similarity NPC188860
0.7467 Intermediate Similarity NPC63873
0.7465 Intermediate Similarity NPC258788
0.7436 Intermediate Similarity NPC315843
0.7436 Intermediate Similarity NPC107654
0.7381 Intermediate Similarity NPC469809
0.7375 Intermediate Similarity NPC275530
0.7308 Intermediate Similarity NPC329890
0.7284 Intermediate Similarity NPC318481
0.7284 Intermediate Similarity NPC248775
0.7273 Intermediate Similarity NPC476012
0.7262 Intermediate Similarity NPC142111
0.7262 Intermediate Similarity NPC473315
0.725 Intermediate Similarity NPC326661
0.7246 Intermediate Similarity NPC317899
0.7229 Intermediate Similarity NPC159714
0.7229 Intermediate Similarity NPC221510
0.7215 Intermediate Similarity NPC227814
0.7215 Intermediate Similarity NPC144995
0.7209 Intermediate Similarity NPC61527
0.72 Intermediate Similarity NPC201356
0.72 Intermediate Similarity NPC276299
0.72 Intermediate Similarity NPC146811
0.7195 Intermediate Similarity NPC180725
0.7195 Intermediate Similarity NPC470149
0.7195 Intermediate Similarity NPC470148
0.7179 Intermediate Similarity NPC316185
0.7176 Intermediate Similarity NPC161670
0.7176 Intermediate Similarity NPC475035
0.7176 Intermediate Similarity NPC473308
0.716 Intermediate Similarity NPC474026
0.7143 Intermediate Similarity NPC251026
0.7143 Intermediate Similarity NPC475982
0.7126 Intermediate Similarity NPC475186
0.7126 Intermediate Similarity NPC118077
0.7125 Intermediate Similarity NPC478192
0.7125 Intermediate Similarity NPC478191
0.7125 Intermediate Similarity NPC478194
0.7125 Intermediate Similarity NPC478195
0.7125 Intermediate Similarity NPC478196
0.7125 Intermediate Similarity NPC161038
0.7125 Intermediate Similarity NPC478193
0.7108 Intermediate Similarity NPC133226
0.7108 Intermediate Similarity NPC470147
0.7105 Intermediate Similarity NPC25298
0.7093 Intermediate Similarity NPC475034
0.7089 Intermediate Similarity NPC284006
0.7089 Intermediate Similarity NPC329914
0.7079 Intermediate Similarity NPC3952
0.7073 Intermediate Similarity NPC477314
0.7067 Intermediate Similarity NPC96414
0.7067 Intermediate Similarity NPC273600
0.7067 Intermediate Similarity NPC470123
0.7051 Intermediate Similarity NPC202011
0.7045 Intermediate Similarity NPC470137
0.7037 Intermediate Similarity NPC170148
0.7013 Intermediate Similarity NPC238223
0.7013 Intermediate Similarity NPC474823
0.7011 Intermediate Similarity NPC208473
0.6977 Remote Similarity NPC186155
0.6977 Remote Similarity NPC160517
0.6977 Remote Similarity NPC78673
0.6974 Remote Similarity NPC83965
0.6962 Remote Similarity NPC293114
0.6951 Remote Similarity NPC272267
0.6941 Remote Similarity NPC253364
0.6933 Remote Similarity NPC470808
0.6932 Remote Similarity NPC475037
0.6923 Remote Similarity NPC130618
0.6923 Remote Similarity NPC475004
0.6914 Remote Similarity NPC473582
0.6901 Remote Similarity NPC324224
0.6901 Remote Similarity NPC472808
0.6897 Remote Similarity NPC470124
0.6892 Remote Similarity NPC26810
0.6889 Remote Similarity NPC327253
0.6883 Remote Similarity NPC132286
0.6883 Remote Similarity NPC122627
0.6867 Remote Similarity NPC68119
0.6867 Remote Similarity NPC13823
0.686 Remote Similarity NPC44261
0.686 Remote Similarity NPC315559
0.6854 Remote Similarity NPC476704
0.6842 Remote Similarity NPC475053
0.6829 Remote Similarity NPC470705
0.6824 Remote Similarity NPC315731
0.6824 Remote Similarity NPC280367
0.6824 Remote Similarity NPC474894
0.6824 Remote Similarity NPC297440
0.6818 Remote Similarity NPC69082
0.6818 Remote Similarity NPC279267
0.6813 Remote Similarity NPC476705
0.6806 Remote Similarity NPC71755
0.6804 Remote Similarity NPC104161
0.6804 Remote Similarity NPC469980
0.6804 Remote Similarity NPC118902
0.68 Remote Similarity NPC473737
0.679 Remote Similarity NPC190859
0.679 Remote Similarity NPC473489
0.679 Remote Similarity NPC326504
0.679 Remote Similarity NPC474321
0.6786 Remote Similarity NPC471537
0.6786 Remote Similarity NPC136033
0.6782 Remote Similarity NPC266718
0.6782 Remote Similarity NPC163093
0.6778 Remote Similarity NPC285588
0.6753 Remote Similarity NPC124586
0.6753 Remote Similarity NPC37382
0.6747 Remote Similarity NPC476703
0.6744 Remote Similarity NPC477385
0.6744 Remote Similarity NPC477390
0.6744 Remote Similarity NPC310450
0.6744 Remote Similarity NPC47450
0.6744 Remote Similarity NPC11383
0.6744 Remote Similarity NPC313677
0.6744 Remote Similarity NPC474959
0.6744 Remote Similarity NPC475046
0.6742 Remote Similarity NPC178215
0.6739 Remote Similarity NPC320552
0.6737 Remote Similarity NPC161855
0.6711 Remote Similarity NPC308457
0.6709 Remote Similarity NPC236208
0.6707 Remote Similarity NPC260396
0.6705 Remote Similarity NPC82795
0.6705 Remote Similarity NPC110710
0.6705 Remote Similarity NPC103284
0.6705 Remote Similarity NPC473669
0.6705 Remote Similarity NPC473478
0.6705 Remote Similarity NPC182383
0.6705 Remote Similarity NPC322529
0.6705 Remote Similarity NPC283085
0.6705 Remote Similarity NPC477014
0.6705 Remote Similarity NPC223871
0.6705 Remote Similarity NPC120398
0.6705 Remote Similarity NPC231009
0.6705 Remote Similarity NPC477013
0.6705 Remote Similarity NPC107986
0.6705 Remote Similarity NPC298595
0.6705 Remote Similarity NPC286338
0.6705 Remote Similarity NPC471567
0.6705 Remote Similarity NPC1083
0.6705 Remote Similarity NPC132496
0.6705 Remote Similarity NPC66346
0.6705 Remote Similarity NPC473651
0.6703 Remote Similarity NPC473311
0.6702 Remote Similarity NPC473291
0.6702 Remote Similarity NPC477921
0.6667 Remote Similarity NPC185186
0.6667 Remote Similarity NPC473471
0.6667 Remote Similarity NPC327383
0.6667 Remote Similarity NPC48338
0.6667 Remote Similarity NPC40376
0.6667 Remote Similarity NPC161045
0.6667 Remote Similarity NPC21208
0.6667 Remote Similarity NPC253801
0.6667 Remote Similarity NPC284472
0.6667 Remote Similarity NPC229799
0.6667 Remote Similarity NPC280621
0.6667 Remote Similarity NPC279532
0.6667 Remote Similarity NPC233551
0.6667 Remote Similarity NPC49863
0.6667 Remote Similarity NPC325627
0.6667 Remote Similarity NPC477303
0.6667 Remote Similarity NPC20339
0.6667 Remote Similarity NPC470435
0.6667 Remote Similarity NPC116543
0.6667 Remote Similarity NPC286770
0.6667 Remote Similarity NPC477311
0.663 Remote Similarity NPC473321
0.663 Remote Similarity NPC110072
0.663 Remote Similarity NPC158061
0.6629 Remote Similarity NPC308412
0.6629 Remote Similarity NPC171174
0.6629 Remote Similarity NPC107717
0.6629 Remote Similarity NPC477015
0.6629 Remote Similarity NPC134885
0.6629 Remote Similarity NPC311163
0.6629 Remote Similarity NPC47937
0.6629 Remote Similarity NPC112685
0.6629 Remote Similarity NPC232555
0.6629 Remote Similarity NPC240695
0.6629 Remote Similarity NPC231096
0.6629 Remote Similarity NPC134807
0.6629 Remote Similarity NPC219498
0.6629 Remote Similarity NPC473687
0.6629 Remote Similarity NPC114694
0.6629 Remote Similarity NPC142117
0.6629 Remote Similarity NPC134865
0.6629 Remote Similarity NPC475581
0.6629 Remote Similarity NPC62118
0.6629 Remote Similarity NPC103523
0.6629 Remote Similarity NPC204686

  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 NPC474545 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
0.7471 Intermediate Similarity NPD7838 Discovery
0.6944 Remote Similarity NPD585 Clinical (unspecified phase)
0.6703 Remote Similarity NPD46 Approved
0.6703 Remote Similarity NPD6698 Approved
0.6667 Remote Similarity NPD4247 Clinical (unspecified phase)
0.663 Remote Similarity NPD7983 Approved
0.6429 Remote Similarity NPD5344 Discontinued
0.6392 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6327 Remote Similarity NPD6648 Approved
0.6316 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6292 Remote Similarity NPD6110 Phase 1
0.6071 Remote Similarity NPD4732 Discontinued
0.5977 Remote Similarity NPD4756 Discovery
0.5955 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5938 Remote Similarity NPD7637 Suspended
0.5914 Remote Similarity NPD4249 Approved
0.5876 Remote Similarity NPD5779 Approved
0.5876 Remote Similarity NPD5778 Approved
0.5851 Remote Similarity NPD4251 Approved
0.5851 Remote Similarity NPD4250 Approved
0.5851 Remote Similarity NPD7524 Approved
0.5844 Remote Similarity NPD6109 Phase 1
0.5802 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5794 Remote Similarity NPD6371 Approved
0.5761 Remote Similarity NPD7154 Phase 3
0.5743 Remote Similarity NPD4225 Approved
0.573 Remote Similarity NPD4268 Approved
0.573 Remote Similarity NPD4271 Approved
0.5714 Remote Similarity NPD6902 Approved
0.5714 Remote Similarity NPD4265 Approved
0.57 Remote Similarity NPD7839 Suspended
0.5699 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5694 Remote Similarity NPD4220 Pre-registration
0.5682 Remote Similarity NPD819 Approved
0.5682 Remote Similarity NPD818 Approved
0.5652 Remote Similarity NPD5209 Approved
0.5641 Remote Similarity NPD69 Approved
0.5641 Remote Similarity NPD9119 Approved
0.5638 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5625 Remote Similarity NPD368 Approved
0.5604 Remote Similarity NPD4821 Approved
0.5604 Remote Similarity NPD7514 Phase 3
0.5604 Remote Similarity NPD4822 Approved
0.5604 Remote Similarity NPD4820 Approved
0.5604 Remote Similarity NPD4819 Approved
0.5604 Remote Similarity NPD7332 Phase 2

  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