Structure

Physi-Chem Properties

Molecular Weight:  226.16
Volume:  245.946
LogP:  2.668
LogD:  2.121
LogS:  -2.963
# Rotatable Bonds:  7
TPSA:  43.37
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.516
Synthetic Accessibility Score:  3.083
Fsp3:  0.846
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.546
MDCK Permeability:  2.8948436010978185e-05
Pgp-inhibitor:  0.48
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.539
30% Bioavailability (F30%):  0.763

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.985
Plasma Protein Binding (PPB):  80.40966033935547%
Volume Distribution (VD):  0.388
Pgp-substrate:  17.608482360839844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.363
CYP1A2-substrate:  0.785
CYP2C19-inhibitor:  0.353
CYP2C19-substrate:  0.864
CYP2C9-inhibitor:  0.251
CYP2C9-substrate:  0.684
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.607
CYP3A4-inhibitor:  0.166
CYP3A4-substrate:  0.267

ADMET: Excretion

Clearance (CL):  11.237
Half-life (T1/2):  0.867

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.521
Drug-inuced Liver Injury (DILI):  0.435
AMES Toxicity:  0.035
Rat Oral Acute Toxicity:  0.07
Maximum Recommended Daily Dose:  0.406
Skin Sensitization:  0.096
Carcinogencity:  0.195
Eye Corrosion:  0.428
Eye Irritation:  0.667
Respiratory Toxicity:  0.053

Download Data

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

  Natural Product: NPC319589

Natural Product ID:  NPC319589
Common Name*:   Dihydrojasmonic Acid, Methyl Ester
IUPAC Name:   methyl 2-(3-oxo-2-pentylcyclopentyl)acetate
Synonyms:  
Standard InCHIKey:  KVWWIYGFBYDJQC-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H22O3/c1-3-4-5-6-11-10(7-8-12(11)14)9-13(15)16-2/h10-11H,3-9H2,1-2H3
SMILES:  CCCCCC1C(CCC1=O)CC(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1530328
PubChem CID:   102861
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000504] Lineolic acids and derivatives
          • [CHEMONTID:0000512] Jasmonic 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
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[16309325]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. Seoul, Korea 2000-Jun PMID[16643034]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[18505286]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[19650637]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[23305920]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[32141747]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9518 Gardenia jasminoides Species Rubiaceae 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
NPT160 Individual Protein TAR DNA-binding protein 43 Homo sapiens Potency n.a. 2818.4 nM PMID[523448]
NPT106 Individual Protein Peroxisome proliferator-activated receptor delta Homo sapiens Potency n.a. 54.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency = 15848.9 nM PMID[523447]
NPT73 Individual Protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 109.53 % PMID[523449]
NPT72 Individual Protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 82.72 % PMID[523449]
NPT2 Others Unspecified Potency n.a. 19496.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 13665.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 108.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68490.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 4364.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 3467 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 53.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 42837.4 nM PubChem BioAssay data set

☑ 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 NPC319589 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
0.7903 Intermediate Similarity NPC304665
0.7903 Intermediate Similarity NPC126899
0.7903 Intermediate Similarity NPC154728
0.7778 Intermediate Similarity NPC305182
0.7742 Intermediate Similarity NPC157518
0.7463 Intermediate Similarity NPC248567
0.7358 Intermediate Similarity NPC314679
0.7321 Intermediate Similarity NPC314084
0.7231 Intermediate Similarity NPC60120
0.717 Intermediate Similarity NPC55023
0.7115 Intermediate Similarity NPC18397
0.7091 Intermediate Similarity NPC13105
0.7091 Intermediate Similarity NPC477878
0.7091 Intermediate Similarity NPC324793
0.7059 Intermediate Similarity NPC470243
0.7042 Intermediate Similarity NPC475932
0.7042 Intermediate Similarity NPC169389
0.7037 Intermediate Similarity NPC282440
0.7015 Intermediate Similarity NPC98711
0.7 Intermediate Similarity NPC201622
0.7 Intermediate Similarity NPC305660
0.7 Intermediate Similarity NPC132064
0.7 Intermediate Similarity NPC472311
0.7 Intermediate Similarity NPC22903
0.7 Intermediate Similarity NPC54980
0.7 Intermediate Similarity NPC223315
0.6923 Remote Similarity NPC469791
0.6909 Remote Similarity NPC21844
0.6909 Remote Similarity NPC249754
0.6866 Remote Similarity NPC319007
0.6863 Remote Similarity NPC31551
0.6863 Remote Similarity NPC219536
0.6857 Remote Similarity NPC215030
0.6825 Remote Similarity NPC478126
0.6812 Remote Similarity NPC472309
0.6786 Remote Similarity NPC20017
0.678 Remote Similarity NPC72722
0.6765 Remote Similarity NPC475062
0.6765 Remote Similarity NPC5714
0.6761 Remote Similarity NPC179922
0.6731 Remote Similarity NPC256163
0.6731 Remote Similarity NPC149299
0.6731 Remote Similarity NPC250028
0.6731 Remote Similarity NPC40597
0.6731 Remote Similarity NPC161097
0.6731 Remote Similarity NPC28598
0.6727 Remote Similarity NPC105329
0.6727 Remote Similarity NPC63182
0.6727 Remote Similarity NPC52700
0.6727 Remote Similarity NPC145045
0.6727 Remote Similarity NPC308301
0.6719 Remote Similarity NPC306750
0.6719 Remote Similarity NPC469922
0.6667 Remote Similarity NPC476469
0.6667 Remote Similarity NPC317128
0.6667 Remote Similarity NPC226602
0.6667 Remote Similarity NPC472019
0.6667 Remote Similarity NPC472020
0.662 Remote Similarity NPC469643
0.662 Remote Similarity NPC469641
0.662 Remote Similarity NPC477867
0.6618 Remote Similarity NPC470956
0.6618 Remote Similarity NPC476629
0.6607 Remote Similarity NPC326957
0.6607 Remote Similarity NPC131981
0.6607 Remote Similarity NPC285814
0.6607 Remote Similarity NPC98246
0.6607 Remote Similarity NPC173996
0.6607 Remote Similarity NPC40249
0.6607 Remote Similarity NPC83187
0.6604 Remote Similarity NPC325452
0.6604 Remote Similarity NPC53541
0.6604 Remote Similarity NPC248763
0.6575 Remote Similarity NPC74685
0.6571 Remote Similarity NPC197701
0.6562 Remote Similarity NPC472021
0.6562 Remote Similarity NPC66145
0.6545 Remote Similarity NPC47363
0.6545 Remote Similarity NPC273545
0.6545 Remote Similarity NPC287231
0.6538 Remote Similarity NPC80234
0.6538 Remote Similarity NPC223249
0.6522 Remote Similarity NPC295788
0.6522 Remote Similarity NPC144511
0.6522 Remote Similarity NPC474962
0.6522 Remote Similarity NPC296522
0.6491 Remote Similarity NPC294440
0.6481 Remote Similarity NPC203531
0.6481 Remote Similarity NPC236579
0.6471 Remote Similarity NPC476626
0.6462 Remote Similarity NPC469923
0.6462 Remote Similarity NPC253204
0.6441 Remote Similarity NPC274261
0.6441 Remote Similarity NPC291724
0.6438 Remote Similarity NPC471046
0.6429 Remote Similarity NPC18543
0.6429 Remote Similarity NPC477929
0.6429 Remote Similarity NPC108131
0.6418 Remote Similarity NPC306805
0.6418 Remote Similarity NPC476330
0.6418 Remote Similarity NPC215987
0.6415 Remote Similarity NPC165533
0.6415 Remote Similarity NPC45270
0.6415 Remote Similarity NPC59570
0.6415 Remote Similarity NPC215118
0.6415 Remote Similarity NPC135077
0.6415 Remote Similarity NPC12156
0.641 Remote Similarity NPC238197
0.6406 Remote Similarity NPC230070
0.6406 Remote Similarity NPC9880
0.6406 Remote Similarity NPC87828
0.6406 Remote Similarity NPC469924
0.6406 Remote Similarity NPC475821
0.6406 Remote Similarity NPC470363
0.64 Remote Similarity NPC472310
0.64 Remote Similarity NPC469620
0.64 Remote Similarity NPC469690
0.64 Remote Similarity NPC156630
0.6389 Remote Similarity NPC133922
0.6379 Remote Similarity NPC258672
0.6379 Remote Similarity NPC247786
0.6379 Remote Similarity NPC293343
0.6377 Remote Similarity NPC82315
0.6364 Remote Similarity NPC74845
0.6364 Remote Similarity NPC235788
0.6364 Remote Similarity NPC30583
0.6351 Remote Similarity NPC83108
0.6351 Remote Similarity NPC471151
0.6351 Remote Similarity NPC208223
0.6351 Remote Similarity NPC214030
0.6351 Remote Similarity NPC70996
0.6351 Remote Similarity NPC477918
0.6346 Remote Similarity NPC316546
0.6338 Remote Similarity NPC469940
0.6338 Remote Similarity NPC311102
0.6324 Remote Similarity NPC241949
0.6324 Remote Similarity NPC42060
0.6324 Remote Similarity NPC477931
0.6324 Remote Similarity NPC84562
0.6324 Remote Similarity NPC268736
0.6316 Remote Similarity NPC51507
0.6316 Remote Similarity NPC1882
0.6316 Remote Similarity NPC293418
0.6316 Remote Similarity NPC73052
0.6316 Remote Similarity NPC290508
0.6308 Remote Similarity NPC469921
0.6286 Remote Similarity NPC199557
0.6286 Remote Similarity NPC196197
0.6286 Remote Similarity NPC319671
0.6286 Remote Similarity NPC476734
0.6286 Remote Similarity NPC469941
0.6286 Remote Similarity NPC252032
0.6286 Remote Similarity NPC64466
0.6282 Remote Similarity NPC472847
0.6282 Remote Similarity NPC271784
0.6282 Remote Similarity NPC469561
0.6269 Remote Similarity NPC128608
0.6269 Remote Similarity NPC314103
0.6267 Remote Similarity NPC185465
0.6267 Remote Similarity NPC63020
0.625 Remote Similarity NPC474100
0.625 Remote Similarity NPC473775
0.625 Remote Similarity NPC51249
0.625 Remote Similarity NPC475232
0.625 Remote Similarity NPC473699
0.625 Remote Similarity NPC177826
0.625 Remote Similarity NPC321017
0.625 Remote Similarity NPC475260
0.625 Remote Similarity NPC474755
0.6232 Remote Similarity NPC469868
0.6232 Remote Similarity NPC286842
0.6232 Remote Similarity NPC130459
0.6232 Remote Similarity NPC474221
0.6232 Remote Similarity NPC478180
0.6232 Remote Similarity NPC41542
0.6226 Remote Similarity NPC261080
0.6226 Remote Similarity NPC14227
0.6226 Remote Similarity NPC279026
0.6226 Remote Similarity NPC141634
0.6226 Remote Similarity NPC3531
0.6226 Remote Similarity NPC301696
0.6226 Remote Similarity NPC113928
0.6226 Remote Similarity NPC301585
0.6226 Remote Similarity NPC81263
0.6226 Remote Similarity NPC201844
0.6226 Remote Similarity NPC154186
0.6216 Remote Similarity NPC279537
0.6212 Remote Similarity NPC83088
0.6207 Remote Similarity NPC106872
0.6203 Remote Similarity NPC320801
0.62 Remote Similarity NPC248190
0.6197 Remote Similarity NPC477850
0.6197 Remote Similarity NPC472955
0.6184 Remote Similarity NPC320144
0.6184 Remote Similarity NPC28319
0.6182 Remote Similarity NPC176500
0.6176 Remote Similarity NPC469926
0.6167 Remote Similarity NPC274182
0.6164 Remote Similarity NPC167702
0.6164 Remote Similarity NPC143979

  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 NPC319589 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
0.75 Intermediate Similarity NPD3198 Approved
0.7358 Intermediate Similarity NPD634 Phase 3
0.7115 Intermediate Similarity NPD387 Clinical (unspecified phase)
0.6949 Remote Similarity NPD615 Clinical (unspecified phase)
0.6812 Remote Similarity NPD6081 Approved
0.6812 Remote Similarity NPD5777 Approved
0.68 Remote Similarity NPD9449 Clinical (unspecified phase)
0.661 Remote Similarity NPD3186 Phase 1
0.6607 Remote Similarity NPD345 Approved
0.6607 Remote Similarity NPD343 Approved
0.6607 Remote Similarity NPD344 Approved
0.6567 Remote Similarity NPD4224 Phase 2
0.6545 Remote Similarity NPD2699 Approved
0.6528 Remote Similarity NPD3702 Approved
0.6515 Remote Similarity NPD7909 Approved
0.6418 Remote Similarity NPD3171 Clinical (unspecified phase)
0.64 Remote Similarity NPD9447 Approved
0.6393 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6346 Remote Similarity NPD3206 Approved
0.6267 Remote Similarity NPD4802 Phase 2
0.6267 Remote Similarity NPD4238 Approved
0.6226 Remote Similarity NPD633 Phase 3
0.6226 Remote Similarity NPD9450 Approved
0.6226 Remote Similarity NPD77 Approved
0.6226 Remote Similarity NPD9448 Phase 2
0.6164 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6154 Remote Similarity NPD6435 Approved
0.6104 Remote Similarity NPD5368 Approved
0.6087 Remote Similarity NPD375 Phase 2
0.6056 Remote Similarity NPD3700 Clinical (unspecified phase)
0.6056 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6056 Remote Similarity NPD3698 Phase 2
0.6026 Remote Similarity NPD5369 Approved
0.6 Remote Similarity NPD6117 Approved
0.6 Remote Similarity NPD2270 Approved
0.5972 Remote Similarity NPD4245 Approved
0.5972 Remote Similarity NPD4789 Approved
0.5972 Remote Similarity NPD4244 Approved
0.5942 Remote Similarity NPD9496 Clinical (unspecified phase)
0.5932 Remote Similarity NPD6125 Clinical (unspecified phase)
0.5926 Remote Similarity NPD9655 Approved
0.5921 Remote Similarity NPD6116 Phase 1
0.5915 Remote Similarity NPD5360 Phase 3
0.5915 Remote Similarity NPD229 Approved
0.5915 Remote Similarity NPD5361 Clinical (unspecified phase)
0.589 Remote Similarity NPD4808 Clinical (unspecified phase)
0.589 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5873 Remote Similarity NPD9298 Approved
0.5867 Remote Similarity NPD3703 Phase 2
0.5854 Remote Similarity NPD5786 Approved
0.5844 Remote Similarity NPD6115 Approved
0.5844 Remote Similarity NPD6697 Approved
0.5844 Remote Similarity NPD6114 Approved
0.5844 Remote Similarity NPD6118 Approved
0.5844 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5833 Remote Similarity NPD3725 Approved
0.5833 Remote Similarity NPD3726 Approved
0.575 Remote Similarity NPD4269 Approved
0.575 Remote Similarity NPD4270 Approved
0.569 Remote Similarity NPD3199 Clinical (unspecified phase)
0.5679 Remote Similarity NPD5362 Discontinued
0.5676 Remote Similarity NPD4758 Discontinued
0.5667 Remote Similarity NPD2266 Phase 2
0.5663 Remote Similarity NPD5330 Approved
0.5663 Remote Similarity NPD6684 Approved
0.5663 Remote Similarity NPD7521 Approved
0.5663 Remote Similarity NPD7334 Approved
0.5663 Remote Similarity NPD6409 Approved
0.5663 Remote Similarity NPD7146 Approved
0.5645 Remote Similarity NPD9638 Phase 2
0.5625 Remote Similarity NPD3728 Approved
0.5625 Remote Similarity NPD3730 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