Structure

Physi-Chem Properties

Molecular Weight:  332.18
Volume:  392.307
LogP:  5.102
LogD:  2.749
LogS:  -5.403
# Rotatable Bonds:  8
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.53
Synthetic Accessibility Score:  4.496
Fsp3:  0.391
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:  -4.376
MDCK Permeability:  0.00024182199558708817
Pgp-inhibitor:  0.004
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.969
20% Bioavailability (F20%):  0.988
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  104.07987976074219%
Volume Distribution (VD):  1.76
Pgp-substrate:  1.6099092960357666%

ADMET: Metabolism

CYP1A2-inhibitor:  0.889
CYP1A2-substrate:  0.101
CYP2C19-inhibitor:  0.773
CYP2C19-substrate:  0.19
CYP2C9-inhibitor:  0.638
CYP2C9-substrate:  0.742
CYP2D6-inhibitor:  0.798
CYP2D6-substrate:  0.059
CYP3A4-inhibitor:  0.83
CYP3A4-substrate:  0.146

ADMET: Excretion

Clearance (CL):  8.517
Half-life (T1/2):  0.163

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.794
Drug-inuced Liver Injury (DILI):  0.99
AMES Toxicity:  0.658
Rat Oral Acute Toxicity:  0.975
Maximum Recommended Daily Dose:  0.994
Skin Sensitization:  0.972
Carcinogencity:  0.172
Eye Corrosion:  0.944
Eye Irritation:  0.992
Respiratory Toxicity:  0.762

Download Data

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

  Natural Product: NPC157096

Natural Product ID:  NPC157096
Common Name*:   Siphonodiol
IUPAC Name:   (2R,14Z,20Z)-tricosa-14,20-dien-3,5,10,12,22-pentayne-1,2-diol
Synonyms:   Siphonodiol
Standard InCHIKey:  QNUJNVFQFSGZFW-BZEHIAJVSA-N
Standard InCHI:  InChI=1S/C23H24O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-23(25)22-24/h1,3-4,9-10,23-25H,5-8,15-17,22H2/b4-3-,10-9-/t23-/m1/s1
SMILES:  C#C/C=CCCCC/C=CC#CC#CCCCC#CC#C[C@H](CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464329
PubChem CID:   11151732
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
NPO29092 Machilus japonica Species Lauraceae Eukaryota leaves n.a. n.a. PMID[19719245]
NPO13962 Corydalis turtschaninovii Species Papaveraceae Eukaryota n.a. rhizome n.a. PMID[25277281]
NPO13962 Corydalis turtschaninovii Species Papaveraceae Eukaryota n.a. tuber n.a. PMID[25670016]
NPO29092 Machilus japonica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29316 Thalictrum baicalense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29316 Thalictrum baicalense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21845 Calvatia fenzlii Species Lycoperdaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29092 Machilus japonica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3251 Jacobaea maritima Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21845 Calvatia fenzlii Species Lycoperdaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13962 Corydalis turtschaninovii Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29425 Teucrium africanum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3251 Jacobaea maritima Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21845 Calvatia fenzlii Species Lycoperdaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16292 Trichosanthes anguina Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29316 Thalictrum baicalense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15777 Didymella pinodes Species Didymellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29304 Pseudosindora palustris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29092 Machilus japonica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13962 Corydalis turtschaninovii Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29501 Pinus oocarpa Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18060 Plexaura flava Species Plexauridae 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
NPT2540 Organism Balanus amphitrite Balanus amphitrite ED50 = 0.25 ug ml-1 PMID[536120]
NPT3550 Organism Halocynthia roretzi Halocynthia roretzi ED50 = 4.5 ug ml-1 PMID[536120]
NPT610 Others Molecular identity unknown MIC = 13000.0 nM PMID[536121]
NPT610 Others Molecular identity unknown MIC > 200000.0 nM PMID[536121]

☑ 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 NPC157096 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
0.8936 High Similarity NPC473768
0.875 High Similarity NPC93639
0.8605 High Similarity NPC27444
0.8605 High Similarity NPC103236
0.8605 High Similarity NPC329762
0.8333 Intermediate Similarity NPC471275
0.8333 Intermediate Similarity NPC302310
0.8333 Intermediate Similarity NPC153538
0.8333 Intermediate Similarity NPC471276
0.8333 Intermediate Similarity NPC471280
0.8333 Intermediate Similarity NPC125122
0.8298 Intermediate Similarity NPC124183
0.8298 Intermediate Similarity NPC35141
0.8261 Intermediate Similarity NPC101616
0.8222 Intermediate Similarity NPC149668
0.8163 Intermediate Similarity NPC471281
0.8163 Intermediate Similarity NPC72699
0.8163 Intermediate Similarity NPC477727
0.8163 Intermediate Similarity NPC199286
0.8039 Intermediate Similarity NPC26102
0.8039 Intermediate Similarity NPC477724
0.8039 Intermediate Similarity NPC187361
0.8 Intermediate Similarity NPC76198
0.8 Intermediate Similarity NPC224148
0.8 Intermediate Similarity NPC197272
0.8 Intermediate Similarity NPC170776
0.8 Intermediate Similarity NPC294278
0.8 Intermediate Similarity NPC256656
0.8 Intermediate Similarity NPC329608
0.8 Intermediate Similarity NPC151782
0.8 Intermediate Similarity NPC165447
0.8 Intermediate Similarity NPC9273
0.8 Intermediate Similarity NPC89824
0.8 Intermediate Similarity NPC475477
0.8 Intermediate Similarity NPC29234
0.8 Intermediate Similarity NPC55383
0.8 Intermediate Similarity NPC477723
0.8 Intermediate Similarity NPC471959
0.7959 Intermediate Similarity NPC31194
0.7959 Intermediate Similarity NPC475153
0.7959 Intermediate Similarity NPC248884
0.7959 Intermediate Similarity NPC85079
0.7917 Intermediate Similarity NPC55063
0.7917 Intermediate Similarity NPC19834
0.7885 Intermediate Similarity NPC473532
0.7872 Intermediate Similarity NPC108195
0.78 Intermediate Similarity NPC291437
0.78 Intermediate Similarity NPC473913
0.78 Intermediate Similarity NPC328784
0.78 Intermediate Similarity NPC249670
0.78 Intermediate Similarity NPC474642
0.7736 Intermediate Similarity NPC477726
0.7736 Intermediate Similarity NPC475353
0.7736 Intermediate Similarity NPC473725
0.7736 Intermediate Similarity NPC473896
0.7736 Intermediate Similarity NPC473735
0.7736 Intermediate Similarity NPC477725
0.7736 Intermediate Similarity NPC473721
0.7736 Intermediate Similarity NPC473910
0.7708 Intermediate Similarity NPC276825
0.7647 Intermediate Similarity NPC59408
0.7647 Intermediate Similarity NPC71053
0.7593 Intermediate Similarity NPC475384
0.7593 Intermediate Similarity NPC470968
0.7593 Intermediate Similarity NPC477661
0.7593 Intermediate Similarity NPC470969
0.7593 Intermediate Similarity NPC473847
0.7593 Intermediate Similarity NPC471960
0.7593 Intermediate Similarity NPC470966
0.7593 Intermediate Similarity NPC470967
0.7593 Intermediate Similarity NPC161838
0.7547 Intermediate Similarity NPC48058
0.7547 Intermediate Similarity NPC110732
0.7547 Intermediate Similarity NPC256209
0.7547 Intermediate Similarity NPC49059
0.75 Intermediate Similarity NPC142092
0.7455 Intermediate Similarity NPC121034
0.7455 Intermediate Similarity NPC470970
0.7447 Intermediate Similarity NPC304151
0.7447 Intermediate Similarity NPC31121
0.7407 Intermediate Similarity NPC146551
0.7407 Intermediate Similarity NPC470963
0.7407 Intermediate Similarity NPC152668
0.7407 Intermediate Similarity NPC471239
0.7407 Intermediate Similarity NPC474513
0.7358 Intermediate Similarity NPC284224
0.7347 Intermediate Similarity NPC269074
0.7308 Intermediate Similarity NPC129263
0.7273 Intermediate Similarity NPC213767
0.7273 Intermediate Similarity NPC311648
0.7273 Intermediate Similarity NPC470964
0.7234 Intermediate Similarity NPC473625
0.72 Intermediate Similarity NPC180575
0.7193 Intermediate Similarity NPC473866
0.7143 Intermediate Similarity NPC473539
0.7143 Intermediate Similarity NPC48968
0.7143 Intermediate Similarity NPC474413
0.7143 Intermediate Similarity NPC594
0.7111 Intermediate Similarity NPC216416
0.7091 Intermediate Similarity NPC474644
0.7037 Intermediate Similarity NPC475723
0.7037 Intermediate Similarity NPC34577
0.6964 Remote Similarity NPC474643
0.6964 Remote Similarity NPC473865
0.6957 Remote Similarity NPC34873
0.6957 Remote Similarity NPC40434
0.6949 Remote Similarity NPC475984
0.6909 Remote Similarity NPC300121
0.6897 Remote Similarity NPC473652
0.6852 Remote Similarity NPC473705
0.6842 Remote Similarity NPC265551
0.6842 Remote Similarity NPC212730
0.6842 Remote Similarity NPC193975
0.6842 Remote Similarity NPC323436
0.6842 Remote Similarity NPC472445
0.6833 Remote Similarity NPC470965
0.6809 Remote Similarity NPC306850
0.6809 Remote Similarity NPC15934
0.6792 Remote Similarity NPC473487
0.6792 Remote Similarity NPC20934
0.6792 Remote Similarity NPC288381
0.6786 Remote Similarity NPC281590
0.6786 Remote Similarity NPC227135
0.678 Remote Similarity NPC471278
0.6744 Remote Similarity NPC196831
0.6739 Remote Similarity NPC174396
0.6735 Remote Similarity NPC206906
0.6727 Remote Similarity NPC61177
0.6667 Remote Similarity NPC76976
0.6667 Remote Similarity NPC474495
0.6667 Remote Similarity NPC200772
0.6667 Remote Similarity NPC474362
0.6667 Remote Similarity NPC473672
0.6667 Remote Similarity NPC474202
0.6667 Remote Similarity NPC201948
0.6667 Remote Similarity NPC168407
0.661 Remote Similarity NPC222852
0.66 Remote Similarity NPC116934
0.66 Remote Similarity NPC252978
0.6557 Remote Similarity NPC29697
0.6552 Remote Similarity NPC474577
0.6552 Remote Similarity NPC52012
0.6552 Remote Similarity NPC44542
0.6545 Remote Similarity NPC35756
0.65 Remote Similarity NPC321919
0.65 Remote Similarity NPC81896
0.6481 Remote Similarity NPC225974
0.6481 Remote Similarity NPC474460
0.6444 Remote Similarity NPC62779
0.6429 Remote Similarity NPC217188
0.6429 Remote Similarity NPC474496
0.6415 Remote Similarity NPC471958
0.64 Remote Similarity NPC249801
0.64 Remote Similarity NPC46248
0.6393 Remote Similarity NPC321838
0.6393 Remote Similarity NPC271282
0.6393 Remote Similarity NPC325929
0.6393 Remote Similarity NPC66460
0.6393 Remote Similarity NPC477829
0.6346 Remote Similarity NPC160628
0.6346 Remote Similarity NPC140501
0.6333 Remote Similarity NPC329424
0.6333 Remote Similarity NPC278202
0.6333 Remote Similarity NPC322186
0.6296 Remote Similarity NPC267110
0.6296 Remote Similarity NPC474445
0.6271 Remote Similarity NPC471279
0.6271 Remote Similarity NPC471277
0.625 Remote Similarity NPC129458
0.625 Remote Similarity NPC295765
0.625 Remote Similarity NPC236872
0.623 Remote Similarity NPC477430
0.6222 Remote Similarity NPC63121
0.6222 Remote Similarity NPC197356
0.6207 Remote Similarity NPC317899
0.62 Remote Similarity NPC269823
0.619 Remote Similarity NPC470320
0.619 Remote Similarity NPC476658
0.619 Remote Similarity NPC226592
0.617 Remote Similarity NPC79544
0.6167 Remote Similarity NPC181872
0.6167 Remote Similarity NPC469373
0.6154 Remote Similarity NPC267514
0.6154 Remote Similarity NPC473752
0.6154 Remote Similarity NPC138935
0.6154 Remote Similarity NPC145755
0.614 Remote Similarity NPC10081
0.614 Remote Similarity NPC225066
0.614 Remote Similarity NPC475560
0.6129 Remote Similarity NPC64971
0.6122 Remote Similarity NPC103213
0.6122 Remote Similarity NPC182840
0.6122 Remote Similarity NPC255042
0.6122 Remote Similarity NPC29091
0.6102 Remote Similarity NPC472808
0.6102 Remote Similarity NPC327388
0.6102 Remote Similarity NPC324224
0.6094 Remote Similarity NPC176215
0.6094 Remote Similarity NPC476654
0.6094 Remote Similarity NPC296436

  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 NPC157096 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
0.6346 Remote Similarity NPD4265 Approved
0.619 Remote Similarity NPD3197 Phase 1
0.6167 Remote Similarity NPD585 Clinical (unspecified phase)
0.6167 Remote Similarity NPD6109 Phase 1
0.6038 Remote Similarity NPD39 Approved
0.5968 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5781 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5741 Remote Similarity NPD4222 Approved
0.5714 Remote Similarity NPD3173 Approved
0.5667 Remote Similarity NPD4627 Clinical (unspecified phase)
0.566 Remote Similarity NPD5326 Phase 3

  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