Structure

Physi-Chem Properties

Molecular Weight:  270.16
Volume:  316.373
LogP:  5.401
LogD:  2.522
LogS:  -5.281
# Rotatable Bonds:  9
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.393
Synthetic Accessibility Score:  3.092
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.994
MDCK Permeability:  7.086463301675394e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.035
20% Bioavailability (F20%):  0.647
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  102.87264251708984%
Volume Distribution (VD):  0.523
Pgp-substrate:  0.9141954779624939%

ADMET: Metabolism

CYP1A2-inhibitor:  0.404
CYP1A2-substrate:  0.167
CYP2C19-inhibitor:  0.832
CYP2C19-substrate:  0.233
CYP2C9-inhibitor:  0.835
CYP2C9-substrate:  0.996
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.649
CYP3A4-inhibitor:  0.581
CYP3A4-substrate:  0.03

ADMET: Excretion

Clearance (CL):  2.549
Half-life (T1/2):  0.605

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.103
Drug-inuced Liver Injury (DILI):  0.966
AMES Toxicity:  0.49
Rat Oral Acute Toxicity:  0.065
Maximum Recommended Daily Dose:  0.055
Skin Sensitization:  0.97
Carcinogencity:  0.617
Eye Corrosion:  0.987
Eye Irritation:  0.979
Respiratory Toxicity:  0.719

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

  Natural Product: NPC18357

Natural Product ID:  NPC18357
Common Name*:   Oropheic Acid
IUPAC Name:   octadec-17-en-9,11,13-triynoic acid
Synonyms:   oropheic acid
Standard InCHIKey:  YESBZXSFUYCBEH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C18H22O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2H,1,3-4,11-17H2,(H,19,20)
SMILES:  C=CCCC#CC#CC#CCCCCCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL451921
PubChem CID:   10730773
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0002949] Long-chain 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
NPO431 Mitrephora celebica Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11678665]
NPO10501 Mitrephora glabra Species Annonaceae Eukaryota stem bark n.a. n.a. PMID[19874044]
NPO10501 Mitrephora glabra Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO431 Mitrephora celebica Species Annonaceae 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
NPT91 Cell Line KB Homo sapiens IC50 = 10000.0 nM PMID[533999]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 10000.0 nM PMID[533999]
NPT397 Cell Line NCI-H460 Homo sapiens IC50 = 10000.0 nM PMID[533999]
NPT395 Cell Line SF-268 Homo sapiens IC50 = 10000.0 nM PMID[533999]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 12.5 ug.mL-1 PMID[533998]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 12.5 ug.mL-1 PMID[533998]
NPT729 Organism Micrococcus luteus Micrococcus luteus MIC = 94.0 ug.mL-1 PMID[533999]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 94.0 ug.mL-1 PMID[533999]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC = 47.0 ug.mL-1 PMID[533999]
NPT21 Organism Aspergillus niger Aspergillus niger MIC = 188.0 ug.mL-1 PMID[533999]

☑ 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 NPC18357 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
0.9412 High Similarity NPC54766
0.9388 High Similarity NPC470410
0.9388 High Similarity NPC470412
0.9231 High Similarity NPC187777
0.9231 High Similarity NPC179764
0.9167 High Similarity NPC180534
0.9038 High Similarity NPC274290
0.9038 High Similarity NPC473863
0.8824 High Similarity NPC161366
0.8704 High Similarity NPC225929
0.8654 High Similarity NPC294548
0.8654 High Similarity NPC1813
0.8654 High Similarity NPC36061
0.8654 High Similarity NPC139029
0.8545 High Similarity NPC267817
0.8491 Intermediate Similarity NPC25417
0.8491 Intermediate Similarity NPC281972
0.8491 Intermediate Similarity NPC85813
0.8491 Intermediate Similarity NPC6095
0.8491 Intermediate Similarity NPC87564
0.8491 Intermediate Similarity NPC261831
0.8491 Intermediate Similarity NPC88966
0.8491 Intermediate Similarity NPC154245
0.8491 Intermediate Similarity NPC290563
0.8491 Intermediate Similarity NPC424
0.8491 Intermediate Similarity NPC32467
0.8462 Intermediate Similarity NPC281245
0.8302 Intermediate Similarity NPC70387
0.8302 Intermediate Similarity NPC321062
0.8269 Intermediate Similarity NPC284212
0.8269 Intermediate Similarity NPC28205
0.8246 Intermediate Similarity NPC235242
0.8182 Intermediate Similarity NPC477201
0.8182 Intermediate Similarity NPC18951
0.8113 Intermediate Similarity NPC92114
0.8077 Intermediate Similarity NPC224227
0.8039 Intermediate Similarity NPC207292
0.8039 Intermediate Similarity NPC216130
0.8 Intermediate Similarity NPC45626
0.7959 Intermediate Similarity NPC255837
0.7959 Intermediate Similarity NPC19305
0.7925 Intermediate Similarity NPC262968
0.7885 Intermediate Similarity NPC5413
0.7885 Intermediate Similarity NPC149821
0.7833 Intermediate Similarity NPC470320
0.7833 Intermediate Similarity NPC226592
0.78 Intermediate Similarity NPC8219
0.7778 Intermediate Similarity NPC129458
0.7759 Intermediate Similarity NPC274927
0.7759 Intermediate Similarity NPC106851
0.7736 Intermediate Similarity NPC59051
0.7636 Intermediate Similarity NPC139545
0.7636 Intermediate Similarity NPC10081
0.7636 Intermediate Similarity NPC225066
0.7636 Intermediate Similarity NPC71761
0.7636 Intermediate Similarity NPC39633
0.7636 Intermediate Similarity NPC309606
0.7627 Intermediate Similarity NPC122521
0.7627 Intermediate Similarity NPC251042
0.7627 Intermediate Similarity NPC174447
0.7627 Intermediate Similarity NPC243532
0.7593 Intermediate Similarity NPC470411
0.7586 Intermediate Similarity NPC34416
0.7586 Intermediate Similarity NPC329819
0.7551 Intermediate Similarity NPC163746
0.7551 Intermediate Similarity NPC103286
0.75 Intermediate Similarity NPC201939
0.75 Intermediate Similarity NPC174560
0.75 Intermediate Similarity NPC477829
0.75 Intermediate Similarity NPC40082
0.75 Intermediate Similarity NPC42304
0.75 Intermediate Similarity NPC125312
0.7455 Intermediate Similarity NPC303765
0.74 Intermediate Similarity NPC301528
0.74 Intermediate Similarity NPC129972
0.74 Intermediate Similarity NPC71317
0.7368 Intermediate Similarity NPC228473
0.7368 Intermediate Similarity NPC223677
0.7368 Intermediate Similarity NPC10316
0.7368 Intermediate Similarity NPC28779
0.7368 Intermediate Similarity NPC128061
0.7368 Intermediate Similarity NPC200845
0.7358 Intermediate Similarity NPC91495
0.7308 Intermediate Similarity NPC117572
0.7258 Intermediate Similarity NPC328089
0.7258 Intermediate Similarity NPC68343
0.7222 Intermediate Similarity NPC304162
0.72 Intermediate Similarity NPC209970
0.72 Intermediate Similarity NPC149184
0.72 Intermediate Similarity NPC171736
0.72 Intermediate Similarity NPC307783
0.72 Intermediate Similarity NPC196924
0.72 Intermediate Similarity NPC216630
0.7193 Intermediate Similarity NPC87394
0.7143 Intermediate Similarity NPC118968
0.7143 Intermediate Similarity NPC154186
0.7143 Intermediate Similarity NPC301696
0.7143 Intermediate Similarity NPC294085
0.7143 Intermediate Similarity NPC255863
0.7143 Intermediate Similarity NPC14227
0.7143 Intermediate Similarity NPC113928
0.7143 Intermediate Similarity NPC279026
0.7143 Intermediate Similarity NPC214610
0.7143 Intermediate Similarity NPC245947
0.7143 Intermediate Similarity NPC318420
0.7143 Intermediate Similarity NPC261080
0.7143 Intermediate Similarity NPC301585
0.7143 Intermediate Similarity NPC183424
0.7143 Intermediate Similarity NPC201844
0.7143 Intermediate Similarity NPC326268
0.7143 Intermediate Similarity NPC136164
0.7069 Intermediate Similarity NPC474672
0.7069 Intermediate Similarity NPC477984
0.7069 Intermediate Similarity NPC52264
0.7059 Intermediate Similarity NPC67462
0.7 Intermediate Similarity NPC469373
0.6964 Remote Similarity NPC100096
0.6964 Remote Similarity NPC48162
0.6957 Remote Similarity NPC81052
0.6949 Remote Similarity NPC325977
0.6939 Remote Similarity NPC73245
0.6939 Remote Similarity NPC268826
0.6935 Remote Similarity NPC328776
0.6935 Remote Similarity NPC475984
0.6935 Remote Similarity NPC321838
0.6935 Remote Similarity NPC320305
0.6923 Remote Similarity NPC271921
0.6923 Remote Similarity NPC330426
0.6923 Remote Similarity NPC99619
0.6923 Remote Similarity NPC148192
0.6923 Remote Similarity NPC22101
0.6923 Remote Similarity NPC127091
0.6923 Remote Similarity NPC74845
0.6923 Remote Similarity NPC26500
0.6923 Remote Similarity NPC104537
0.6897 Remote Similarity NPC137538
0.6842 Remote Similarity NPC473705
0.6842 Remote Similarity NPC310746
0.6825 Remote Similarity NPC470965
0.6825 Remote Similarity NPC29697
0.6818 Remote Similarity NPC476614
0.6818 Remote Similarity NPC473559
0.6818 Remote Similarity NPC324981
0.6818 Remote Similarity NPC48218
0.6818 Remote Similarity NPC141481
0.6774 Remote Similarity NPC45097
0.6774 Remote Similarity NPC143857
0.6774 Remote Similarity NPC229252
0.6735 Remote Similarity NPC158179
0.6719 Remote Similarity NPC234767
0.6716 Remote Similarity NPC317583
0.6716 Remote Similarity NPC143396
0.6667 Remote Similarity NPC129263
0.6667 Remote Similarity NPC66460
0.6667 Remote Similarity NPC473829
0.6667 Remote Similarity NPC469495
0.6667 Remote Similarity NPC12438
0.6667 Remote Similarity NPC475443
0.6667 Remote Similarity NPC271282
0.6667 Remote Similarity NPC325929
0.6667 Remote Similarity NPC30195
0.6667 Remote Similarity NPC60120
0.6618 Remote Similarity NPC42526
0.6618 Remote Similarity NPC476660
0.6613 Remote Similarity NPC329550
0.661 Remote Similarity NPC322461
0.6607 Remote Similarity NPC250919
0.6607 Remote Similarity NPC207815
0.6604 Remote Similarity NPC270796
0.6575 Remote Similarity NPC209995
0.6567 Remote Similarity NPC477980
0.6567 Remote Similarity NPC53302
0.6562 Remote Similarity NPC477707
0.6562 Remote Similarity NPC54925
0.6552 Remote Similarity NPC236872
0.6545 Remote Similarity NPC21844
0.6545 Remote Similarity NPC324004
0.6545 Remote Similarity NPC328497
0.6531 Remote Similarity NPC134782
0.6531 Remote Similarity NPC155263
0.6515 Remote Similarity NPC308294
0.6515 Remote Similarity NPC142423
0.6508 Remote Similarity NPC328311
0.6508 Remote Similarity NPC327112
0.6491 Remote Similarity NPC474391
0.6491 Remote Similarity NPC473487
0.6486 Remote Similarity NPC200446
0.6481 Remote Similarity NPC55023
0.6471 Remote Similarity NPC473772
0.6462 Remote Similarity NPC470325
0.6462 Remote Similarity NPC53642
0.6441 Remote Similarity NPC26102
0.6441 Remote Similarity NPC187361
0.6441 Remote Similarity NPC284224
0.6441 Remote Similarity NPC477724
0.6441 Remote Similarity NPC34577
0.6429 Remote Similarity NPC106872
0.6429 Remote Similarity NPC324793
0.6429 Remote Similarity NPC477878
0.6393 Remote Similarity NPC327388

  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 NPC18357 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
0.9167 High Similarity NPD622 Approved
0.8654 High Similarity NPD3172 Approved
0.8491 Intermediate Similarity NPD3196 Approved
0.8491 Intermediate Similarity NPD4266 Approved
0.8491 Intermediate Similarity NPD3194 Approved
0.8491 Intermediate Similarity NPD3195 Phase 2
0.7925 Intermediate Similarity NPD28 Approved
0.7925 Intermediate Similarity NPD29 Approved
0.7885 Intermediate Similarity NPD3173 Approved
0.7308 Intermediate Similarity NPD4222 Approved
0.7308 Intermediate Similarity NPD3174 Discontinued
0.7258 Intermediate Similarity NPD3197 Phase 1
0.72 Intermediate Similarity NPD2270 Approved
0.7143 Intermediate Similarity NPD633 Phase 3
0.7143 Intermediate Similarity NPD9448 Phase 2
0.7143 Intermediate Similarity NPD9655 Approved
0.6981 Remote Similarity NPD39 Approved
0.6792 Remote Similarity NPD3199 Clinical (unspecified phase)
0.6604 Remote Similarity NPD5326 Phase 3
0.66 Remote Similarity NPD3206 Approved
0.6508 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6364 Remote Similarity NPD634 Phase 3
0.614 Remote Similarity NPD5343 Approved
0.6071 Remote Similarity NPD9430 Approved
0.6071 Remote Similarity NPD9431 Approved
0.6061 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6029 Remote Similarity NPD7331 Phase 2
0.6 Remote Similarity NPD3186 Phase 1
0.6 Remote Similarity NPD3732 Approved
0.5942 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5893 Remote Similarity NPD2699 Approved
0.5867 Remote Similarity NPD4756 Discovery
0.5844 Remote Similarity NPD5368 Approved
0.5823 Remote Similarity NPD5331 Approved
0.5823 Remote Similarity NPD5332 Approved
0.5818 Remote Similarity NPD387 Clinical (unspecified phase)
0.5806 Remote Similarity NPD3728 Approved
0.5806 Remote Similarity NPD3730 Approved
0.5806 Remote Similarity NPD3729 Clinical (unspecified phase)
0.5789 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5769 Remote Similarity NPD5369 Approved
0.5741 Remote Similarity NPD9635 Discontinued
0.5714 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5696 Remote Similarity NPD6435 Approved
0.5696 Remote Similarity NPD4269 Approved
0.5696 Remote Similarity NPD4270 Approved
0.5692 Remote Similarity NPD6109 Phase 1
0.566 Remote Similarity NPD9513 Phase 1
0.5641 Remote Similarity NPD4252 Approved
0.5625 Remote Similarity NPD5362 Discontinued
0.5625 Remote Similarity NPD7154 Phase 3
0.5614 Remote Similarity NPD6097 Approved
0.5614 Remote Similarity NPD6096 Approved
0.56 Remote Similarity NPD8039 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