Structure

Physi-Chem Properties

Molecular Weight:  320.04
Volume:  301.065
LogP:  3.301
LogD:  2.285
LogS:  -4.06
# Rotatable Bonds:  5
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.603
Synthetic Accessibility Score:  4.448
Fsp3:  0.375
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -3.991
MDCK Permeability:  0.0001550528540974483
Pgp-inhibitor:  0.002
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.653
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.008
Plasma Protein Binding (PPB):  101.77124786376953%
Volume Distribution (VD):  1.205
Pgp-substrate:  2.23268461227417%

ADMET: Metabolism

CYP1A2-inhibitor:  0.784
CYP1A2-substrate:  0.185
CYP2C19-inhibitor:  0.936
CYP2C19-substrate:  0.718
CYP2C9-inhibitor:  0.928
CYP2C9-substrate:  0.995
CYP2D6-inhibitor:  0.916
CYP2D6-substrate:  0.899
CYP3A4-inhibitor:  0.922
CYP3A4-substrate:  0.224

ADMET: Excretion

Clearance (CL):  2.33
Half-life (T1/2):  0.284

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.958
Drug-inuced Liver Injury (DILI):  0.989
AMES Toxicity:  0.875
Rat Oral Acute Toxicity:  0.944
Maximum Recommended Daily Dose:  0.941
Skin Sensitization:  0.951
Carcinogencity:  0.46
Eye Corrosion:  0.873
Eye Irritation:  0.982
Respiratory Toxicity:  0.912

Download Data

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

  Natural Product: NPC473768

Natural Product ID:  NPC473768
Common Name*:   Diplyne E
IUPAC Name:   (11E,15E)-16-bromohexadeca-11,15-dien-3,5,13-triyne-1,2-diol
Synonyms:   Diplyne E
Standard InCHIKey:  DJSFMRMJRHIIBW-LZUOLKHISA-N
Standard InCHI:  InChI=1S/C16H17BrO2/c17-14-12-10-8-6-4-2-1-3-5-7-9-11-13-16(19)15-18/h4,6,12,14,16,18-19H,1-3,5,15H2/b6-4+,14-12+
SMILES:  Br/C=C/C#C/C=C/CCCCC#CC#CC(CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL451305
PubChem CID:   11141768
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0002286] Polyols
            • [CHEMONTID:0002467] 1,2-diols

*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
NPO32781 diplastrella sp. Species Spirastrellidae Eukaryota n.a. Philippines n.a. PMID[12762803]

☑ 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
NPT12 Individual Protein Human immunodeficiency virus type 1 integrase Human immunodeficiency virus 1 IC50 > 50.0 ug.mL-1 PMID[512027]

☑ 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 NPC473768 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
0.8958 High Similarity NPC475153
0.8936 High Similarity NPC157096
0.8261 Intermediate Similarity NPC473625
0.8235 Intermediate Similarity NPC93639
0.8125 Intermediate Similarity NPC474413
0.8125 Intermediate Similarity NPC473539
0.7925 Intermediate Similarity NPC475723
0.7843 Intermediate Similarity NPC153538
0.7843 Intermediate Similarity NPC302310
0.78 Intermediate Similarity NPC124183
0.78 Intermediate Similarity NPC35141
0.7755 Intermediate Similarity NPC101616
0.7692 Intermediate Similarity NPC72699
0.766 Intermediate Similarity NPC27444
0.766 Intermediate Similarity NPC329762
0.766 Intermediate Similarity NPC103236
0.7547 Intermediate Similarity NPC29234
0.7547 Intermediate Similarity NPC151782
0.75 Intermediate Similarity NPC248884
0.75 Intermediate Similarity NPC85079
0.75 Intermediate Similarity NPC471276
0.75 Intermediate Similarity NPC31194
0.75 Intermediate Similarity NPC125122
0.75 Intermediate Similarity NPC471275
0.75 Intermediate Similarity NPC471280
0.7451 Intermediate Similarity NPC55063
0.7451 Intermediate Similarity NPC19834
0.74 Intermediate Similarity NPC108195
0.7358 Intermediate Similarity NPC291437
0.7358 Intermediate Similarity NPC328784
0.7358 Intermediate Similarity NPC199286
0.7358 Intermediate Similarity NPC477727
0.7358 Intermediate Similarity NPC471281
0.7347 Intermediate Similarity NPC149668
0.7273 Intermediate Similarity NPC26102
0.7273 Intermediate Similarity NPC477724
0.7273 Intermediate Similarity NPC187361
0.7255 Intermediate Similarity NPC276825
0.7222 Intermediate Similarity NPC55383
0.7222 Intermediate Similarity NPC165447
0.7222 Intermediate Similarity NPC294278
0.7222 Intermediate Similarity NPC471959
0.7222 Intermediate Similarity NPC256656
0.7222 Intermediate Similarity NPC89824
0.7222 Intermediate Similarity NPC59408
0.7222 Intermediate Similarity NPC71053
0.7222 Intermediate Similarity NPC329608
0.7222 Intermediate Similarity NPC477723
0.7222 Intermediate Similarity NPC475477
0.7222 Intermediate Similarity NPC170776
0.7222 Intermediate Similarity NPC9273
0.7222 Intermediate Similarity NPC197272
0.7222 Intermediate Similarity NPC76198
0.7222 Intermediate Similarity NPC224148
0.717 Intermediate Similarity NPC474445
0.7143 Intermediate Similarity NPC256209
0.7143 Intermediate Similarity NPC110732
0.7143 Intermediate Similarity NPC49059
0.7143 Intermediate Similarity NPC473532
0.7091 Intermediate Similarity NPC142092
0.7069 Intermediate Similarity NPC121034
0.7037 Intermediate Similarity NPC474642
0.7037 Intermediate Similarity NPC473913
0.7037 Intermediate Similarity NPC249670
0.7018 Intermediate Similarity NPC477725
0.7018 Intermediate Similarity NPC475353
0.7018 Intermediate Similarity NPC473896
0.7018 Intermediate Similarity NPC473735
0.7018 Intermediate Similarity NPC477726
0.7018 Intermediate Similarity NPC473910
0.7018 Intermediate Similarity NPC473725
0.7018 Intermediate Similarity NPC473721
0.7 Intermediate Similarity NPC31121
0.7 Intermediate Similarity NPC304151
0.6964 Remote Similarity NPC284224
0.6964 Remote Similarity NPC10081
0.6964 Remote Similarity NPC225066
0.6923 Remote Similarity NPC269074
0.6909 Remote Similarity NPC129263
0.6897 Remote Similarity NPC470966
0.6897 Remote Similarity NPC470967
0.6897 Remote Similarity NPC473847
0.6897 Remote Similarity NPC475384
0.6897 Remote Similarity NPC470969
0.6897 Remote Similarity NPC471960
0.6897 Remote Similarity NPC161838
0.6897 Remote Similarity NPC477661
0.6897 Remote Similarity NPC470968
0.6842 Remote Similarity NPC48058
0.6833 Remote Similarity NPC473866
0.6809 Remote Similarity NPC213767
0.6792 Remote Similarity NPC180575
0.6786 Remote Similarity NPC303765
0.6786 Remote Similarity NPC129458
0.678 Remote Similarity NPC470970
0.6727 Remote Similarity NPC475071
0.6724 Remote Similarity NPC474513
0.6724 Remote Similarity NPC471239
0.6724 Remote Similarity NPC146551
0.6724 Remote Similarity NPC152668
0.6724 Remote Similarity NPC45626
0.6724 Remote Similarity NPC470963
0.6721 Remote Similarity NPC477430
0.6667 Remote Similarity NPC216416
0.6667 Remote Similarity NPC34577
0.661 Remote Similarity NPC311648
0.661 Remote Similarity NPC470964
0.6552 Remote Similarity NPC300121
0.6531 Remote Similarity NPC34873
0.6531 Remote Similarity NPC40434
0.65 Remote Similarity NPC193975
0.65 Remote Similarity NPC323436
0.65 Remote Similarity NPC212730
0.65 Remote Similarity NPC594
0.65 Remote Similarity NPC265551
0.65 Remote Similarity NPC48968
0.65 Remote Similarity NPC472445
0.6491 Remote Similarity NPC473705
0.6441 Remote Similarity NPC474644
0.6441 Remote Similarity NPC281590
0.6441 Remote Similarity NPC227135
0.6429 Remote Similarity NPC288381
0.6429 Remote Similarity NPC20934
0.6429 Remote Similarity NPC473487
0.64 Remote Similarity NPC306850
0.64 Remote Similarity NPC15934
0.6393 Remote Similarity NPC267817
0.6379 Remote Similarity NPC61177
0.6349 Remote Similarity NPC475984
0.6346 Remote Similarity NPC206906
0.6333 Remote Similarity NPC473865
0.6333 Remote Similarity NPC474643
0.6327 Remote Similarity NPC174396
0.6316 Remote Similarity NPC474495
0.6316 Remote Similarity NPC200772
0.6316 Remote Similarity NPC473672
0.6296 Remote Similarity NPC201948
0.6296 Remote Similarity NPC76976
0.6296 Remote Similarity NPC474202
0.6296 Remote Similarity NPC474362
0.629 Remote Similarity NPC473652
0.629 Remote Similarity NPC222852
0.625 Remote Similarity NPC29697
0.625 Remote Similarity NPC470965
0.623 Remote Similarity NPC44542
0.623 Remote Similarity NPC474577
0.623 Remote Similarity NPC52012
0.6226 Remote Similarity NPC252978
0.6226 Remote Similarity NPC116934
0.6207 Remote Similarity NPC35756
0.619 Remote Similarity NPC81896
0.619 Remote Similarity NPC321919
0.619 Remote Similarity NPC471278
0.6167 Remote Similarity NPC474672
0.614 Remote Similarity NPC225974
0.614 Remote Similarity NPC474460
0.6102 Remote Similarity NPC217188
0.6102 Remote Similarity NPC474496
0.6094 Remote Similarity NPC321838
0.6094 Remote Similarity NPC271282
0.6094 Remote Similarity NPC66460
0.6094 Remote Similarity NPC168407
0.6094 Remote Similarity NPC325929
0.6078 Remote Similarity NPC57011
0.6038 Remote Similarity NPC249801
0.6038 Remote Similarity NPC46248
0.6032 Remote Similarity NPC322186
0.6032 Remote Similarity NPC278202
0.6032 Remote Similarity NPC329424
0.6 Remote Similarity NPC140501
0.6 Remote Similarity NPC160628
0.5965 Remote Similarity NPC267110
0.5957 Remote Similarity NPC196831
0.5932 Remote Similarity NPC295765
0.5932 Remote Similarity NPC236872
0.5909 Remote Similarity NPC271000
0.5909 Remote Similarity NPC470320
0.5909 Remote Similarity NPC226592
0.5909 Remote Similarity NPC476658
0.5902 Remote Similarity NPC317899
0.5873 Remote Similarity NPC469373
0.5873 Remote Similarity NPC181872
0.5849 Remote Similarity NPC269823
0.5846 Remote Similarity NPC64971
0.5846 Remote Similarity NPC477829
0.5833 Remote Similarity NPC475560
0.5833 Remote Similarity NPC197356
0.5833 Remote Similarity NPC63121
0.5821 Remote Similarity NPC296436
0.5821 Remote Similarity NPC176215
0.5821 Remote Similarity NPC476654
0.5821 Remote Similarity NPC476657
0.5821 Remote Similarity NPC476655
0.5818 Remote Similarity NPC267514
0.5818 Remote Similarity NPC145755
0.5818 Remote Similarity NPC138935
0.5806 Remote Similarity NPC324224
0.5806 Remote Similarity NPC472808
0.5806 Remote Similarity NPC327388
0.58 Remote Similarity NPC79544

  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 NPC473768 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
0.6 Remote Similarity NPD4265 Approved
0.5909 Remote Similarity NPD3197 Phase 1
0.5873 Remote Similarity NPD585 Clinical (unspecified phase)
0.5873 Remote Similarity NPD6109 Phase 1
0.5714 Remote Similarity NPD39 Approved
0.5692 Remote Similarity NPD4246 Clinical (unspecified phase)

  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