Structure

Physi-Chem Properties

Molecular Weight:  186.09
Volume:  191.472
LogP:  1.191
LogD:  1.764
LogS:  -1.159
# Rotatable Bonds:  5
TPSA:  63.6
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.532
Synthetic Accessibility Score:  2.565
Fsp3:  0.556
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:  -4.869
MDCK Permeability:  3.20054023177363e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.081
Human Intestinal Absorption (HIA):  0.03
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.859

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.818
Plasma Protein Binding (PPB):  24.97905158996582%
Volume Distribution (VD):  0.266
Pgp-substrate:  73.3680191040039%

ADMET: Metabolism

CYP1A2-inhibitor:  0.046
CYP1A2-substrate:  0.184
CYP2C19-inhibitor:  0.044
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.028
CYP2C9-substrate:  0.484
CYP2D6-inhibitor:  0.163
CYP2D6-substrate:  0.197
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.175

ADMET: Excretion

Clearance (CL):  7.6
Half-life (T1/2):  0.942

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.068
Drug-inuced Liver Injury (DILI):  0.484
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.036
Maximum Recommended Daily Dose:  0.02
Skin Sensitization:  0.858
Carcinogencity:  0.221
Eye Corrosion:  0.88
Eye Irritation:  0.969
Respiratory Toxicity:  0.094

Download Data

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

  Natural Product: NPC473936

Natural Product ID:  NPC473936
Common Name*:   5-Methoxy-5-Oxo-2-Prop-1-En-2-Ylpentanoic Acid
IUPAC Name:   5-methoxy-5-oxo-2-prop-1-en-2-ylpentanoic acid
Synonyms:  
Standard InCHIKey:  KIINVCJXLPORTK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H14O4/c1-6(2)7(9(11)12)4-5-8(10)13-3/h7H,1,4-5H2,2-3H3,(H,11,12)
SMILES:  COC(=O)CCC(C(=O)O)C(=C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL455736
PubChem CID:   10932149
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0000338] Branched fatty acids
            • [CHEMONTID:0003544] Methyl-branched fatty 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
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[12444684]
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[16441074]
NPO32963 Acremonium sp. Species Eukaryota n.a. Australian n.a. PMID[18288804]
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[19199645]
NPO32963 Acremonium sp. Species Eukaryota n.a. Mangrove Rhizophora apiculata n.a. PMID[22524636]
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[22524636]
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[25689430]
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[26928174]

☑ 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = -8.6 % PMID[517657]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = -16.3 % PMID[517657]
NPT1 Others Radical scavenging activity Activity = 3.4 % PMID[517657]
NPT1 Others Radical scavenging activity Activity = 10.3 % PMID[517657]
NPT1 Others Radical scavenging activity Activity = 35.1 % PMID[517657]

☑ 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 NPC473936 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
0.7544 Intermediate Similarity NPC216407
0.7419 Intermediate Similarity NPC472328
0.7077 Intermediate Similarity NPC53642
0.7077 Intermediate Similarity NPC470325
0.7 Intermediate Similarity NPC154626
0.6949 Remote Similarity NPC170167
0.6912 Remote Similarity NPC476629
0.6885 Remote Similarity NPC49028
0.6818 Remote Similarity NPC234767
0.678 Remote Similarity NPC48162
0.678 Remote Similarity NPC244452
0.6731 Remote Similarity NPC325454
0.6667 Remote Similarity NPC248763
0.6667 Remote Similarity NPC325452
0.6667 Remote Similarity NPC48641
0.6613 Remote Similarity NPC67367
0.661 Remote Similarity NPC289388
0.661 Remote Similarity NPC142103
0.6575 Remote Similarity NPC217725
0.6538 Remote Similarity NPC188717
0.6538 Remote Similarity NPC252843
0.6538 Remote Similarity NPC211455
0.6538 Remote Similarity NPC206924
0.6522 Remote Similarity NPC60120
0.6522 Remote Similarity NPC472875
0.65 Remote Similarity NPC15129
0.6486 Remote Similarity NPC61863
0.6479 Remote Similarity NPC67183
0.6479 Remote Similarity NPC318766
0.6456 Remote Similarity NPC474776
0.6441 Remote Similarity NPC5413
0.6441 Remote Similarity NPC476469
0.6441 Remote Similarity NPC149821
0.6429 Remote Similarity NPC36616
0.6429 Remote Similarity NPC290445
0.6389 Remote Similarity NPC126061
0.6389 Remote Similarity NPC477087
0.6389 Remote Similarity NPC477086
0.6377 Remote Similarity NPC304665
0.6377 Remote Similarity NPC154728
0.6377 Remote Similarity NPC100719
0.6377 Remote Similarity NPC126899
0.6377 Remote Similarity NPC166791
0.6377 Remote Similarity NPC322035
0.6364 Remote Similarity NPC258965
0.6364 Remote Similarity NPC51507
0.6364 Remote Similarity NPC156658
0.6351 Remote Similarity NPC471491
0.6338 Remote Similarity NPC67608
0.6329 Remote Similarity NPC11620
0.6329 Remote Similarity NPC111409
0.6329 Remote Similarity NPC128246
0.6316 Remote Similarity NPC93763
0.6316 Remote Similarity NPC108816
0.6316 Remote Similarity NPC264391
0.6308 Remote Similarity NPC329819
0.6301 Remote Similarity NPC477085
0.6301 Remote Similarity NPC326024
0.6296 Remote Similarity NPC3531
0.6296 Remote Similarity NPC470242
0.6282 Remote Similarity NPC126248
0.6271 Remote Similarity NPC216130
0.6271 Remote Similarity NPC180534
0.6271 Remote Similarity NPC207292
0.6269 Remote Similarity NPC125312
0.6269 Remote Similarity NPC174560
0.6267 Remote Similarity NPC12740
0.6267 Remote Similarity NPC110461
0.625 Remote Similarity NPC472955
0.625 Remote Similarity NPC474780
0.625 Remote Similarity NPC151176
0.625 Remote Similarity NPC472958
0.625 Remote Similarity NPC472957
0.625 Remote Similarity NPC3464
0.625 Remote Similarity NPC475963
0.625 Remote Similarity NPC252860
0.625 Remote Similarity NPC91369
0.625 Remote Similarity NPC212363
0.6234 Remote Similarity NPC19841
0.623 Remote Similarity NPC470411
0.623 Remote Similarity NPC28205
0.622 Remote Similarity NPC474765
0.622 Remote Similarity NPC477959
0.622 Remote Similarity NPC118601
0.622 Remote Similarity NPC142583
0.622 Remote Similarity NPC186148
0.6216 Remote Similarity NPC472966
0.6207 Remote Similarity NPC314679
0.6207 Remote Similarity NPC308301
0.619 Remote Similarity NPC137538
0.6184 Remote Similarity NPC122847
0.6184 Remote Similarity NPC469867
0.6184 Remote Similarity NPC7563
0.6184 Remote Similarity NPC320630
0.6184 Remote Similarity NPC238227
0.6184 Remote Similarity NPC107668
0.6184 Remote Similarity NPC116177
0.6182 Remote Similarity NPC240109
0.6176 Remote Similarity NPC322457
0.6173 Remote Similarity NPC304509
0.6173 Remote Similarity NPC47958
0.6173 Remote Similarity NPC149725
0.6173 Remote Similarity NPC329749
0.6173 Remote Similarity NPC137033
0.6173 Remote Similarity NPC21469
0.6167 Remote Similarity NPC163345
0.6167 Remote Similarity NPC234597
0.6164 Remote Similarity NPC72343
0.6154 Remote Similarity NPC103634
0.6145 Remote Similarity NPC178875
0.6145 Remote Similarity NPC202672
0.6145 Remote Similarity NPC177629
0.6145 Remote Similarity NPC473715
0.6145 Remote Similarity NPC315911
0.6145 Remote Similarity NPC58219
0.6143 Remote Similarity NPC308294
0.6143 Remote Similarity NPC142423
0.6133 Remote Similarity NPC60718
0.6133 Remote Similarity NPC199445
0.6133 Remote Similarity NPC81052
0.6129 Remote Similarity NPC92114
0.6129 Remote Similarity NPC281245
0.6125 Remote Similarity NPC52609
0.6125 Remote Similarity NPC1761
0.6125 Remote Similarity NPC69469
0.6125 Remote Similarity NPC250315
0.6125 Remote Similarity NPC52923
0.6119 Remote Similarity NPC40206
0.6111 Remote Similarity NPC101622
0.6111 Remote Similarity NPC317583
0.6111 Remote Similarity NPC5714
0.6104 Remote Similarity NPC196653
0.6104 Remote Similarity NPC267231
0.6104 Remote Similarity NPC471465
0.6104 Remote Similarity NPC127526
0.6104 Remote Similarity NPC321514
0.6098 Remote Similarity NPC474949
0.6098 Remote Similarity NPC162071
0.6098 Remote Similarity NPC476015
0.6098 Remote Similarity NPC475019
0.6098 Remote Similarity NPC122502
0.6098 Remote Similarity NPC164393
0.6098 Remote Similarity NPC474762
0.6094 Remote Similarity NPC52264
0.6081 Remote Similarity NPC215745
0.6081 Remote Similarity NPC135703
0.6081 Remote Similarity NPC472813
0.6081 Remote Similarity NPC12815
0.6081 Remote Similarity NPC238948
0.6076 Remote Similarity NPC221647
0.6076 Remote Similarity NPC191711
0.6076 Remote Similarity NPC47635
0.6076 Remote Similarity NPC52861
0.6076 Remote Similarity NPC24417
0.6071 Remote Similarity NPC307411
0.6071 Remote Similarity NPC474032
0.6071 Remote Similarity NPC92974
0.6071 Remote Similarity NPC295312
0.6061 Remote Similarity NPC471619
0.6056 Remote Similarity NPC49863
0.6053 Remote Similarity NPC476601
0.6049 Remote Similarity NPC219966
0.6049 Remote Similarity NPC97505
0.6034 Remote Similarity NPC55023
0.6032 Remote Similarity NPC294548
0.6032 Remote Similarity NPC321062
0.6032 Remote Similarity NPC36061
0.6032 Remote Similarity NPC70387
0.6032 Remote Similarity NPC1813
0.6032 Remote Similarity NPC139029
0.6029 Remote Similarity NPC469923
0.6029 Remote Similarity NPC201939
0.6027 Remote Similarity NPC235586
0.6027 Remote Similarity NPC18543
0.6027 Remote Similarity NPC472017
0.6027 Remote Similarity NPC475310
0.6027 Remote Similarity NPC4299
0.6026 Remote Similarity NPC323472
0.6026 Remote Similarity NPC98557
0.6026 Remote Similarity NPC470239
0.6026 Remote Similarity NPC327674
0.6026 Remote Similarity NPC167881
0.6026 Remote Similarity NPC470244
0.6024 Remote Similarity NPC475773
0.6024 Remote Similarity NPC190753
0.6024 Remote Similarity NPC248602
0.6024 Remote Similarity NPC160138
0.6024 Remote Similarity NPC86005
0.6 Remote Similarity NPC140287
0.6 Remote Similarity NPC117596
0.6 Remote Similarity NPC324793
0.6 Remote Similarity NPC474304
0.6 Remote Similarity NPC474761
0.6 Remote Similarity NPC51004
0.6 Remote Similarity NPC473619
0.6 Remote Similarity NPC323477
0.6 Remote Similarity NPC313670
0.6 Remote Similarity NPC106510
0.6 Remote Similarity NPC71533
0.6 Remote Similarity NPC477878

  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 NPC473936 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
0.6721 Remote Similarity NPD9298 Approved
0.6441 Remote Similarity NPD3173 Approved
0.6296 Remote Similarity NPD77 Approved
0.6296 Remote Similarity NPD9450 Approved
0.6271 Remote Similarity NPD622 Approved
0.6271 Remote Similarity NPD2266 Phase 2
0.6226 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6207 Remote Similarity NPD634 Phase 3
0.6182 Remote Similarity NPD9635 Discontinued
0.6056 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6032 Remote Similarity NPD3172 Approved
0.6 Remote Similarity NPD9201 Clinical (unspecified phase)
0.5938 Remote Similarity NPD4266 Approved
0.5938 Remote Similarity NPD3195 Phase 2
0.5938 Remote Similarity NPD3196 Approved
0.5938 Remote Similarity NPD3194 Approved
0.5932 Remote Similarity NPD4222 Approved
0.5932 Remote Similarity NPD3174 Discontinued
0.593 Remote Similarity NPD7983 Approved
0.5926 Remote Similarity NPD7154 Phase 3
0.5926 Remote Similarity NPD5362 Discontinued
0.5875 Remote Similarity NPD5369 Approved
0.5862 Remote Similarity NPD8975 Clinical (unspecified phase)
0.5857 Remote Similarity NPD7909 Approved
0.5849 Remote Similarity NPD9447 Approved
0.5814 Remote Similarity NPD6698 Approved
0.5814 Remote Similarity NPD46 Approved
0.5802 Remote Similarity NPD6435 Approved
0.5763 Remote Similarity NPD8974 Clinical (unspecified phase)
0.575 Remote Similarity NPD5368 Approved
0.575 Remote Similarity NPD4252 Approved
0.575 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6422 Discontinued
0.5714 Remote Similarity NPD4249 Approved
0.5714 Remote Similarity NPD5786 Approved
0.5698 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5698 Remote Similarity NPD6101 Approved
0.5696 Remote Similarity NPD4271 Approved
0.5696 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5696 Remote Similarity NPD4268 Approved
0.5694 Remote Similarity NPD7331 Phase 2
0.5682 Remote Similarity NPD5778 Approved
0.5682 Remote Similarity NPD5779 Approved
0.5667 Remote Similarity NPD39 Approved
0.5647 Remote Similarity NPD4251 Approved
0.5647 Remote Similarity NPD4250 Approved
0.5625 Remote Similarity NPD3186 Phase 1
0.561 Remote Similarity NPD4269 Approved
0.561 Remote Similarity NPD4270 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