Structure

Physi-Chem Properties

Molecular Weight:  322.06
Volume:  303.701
LogP:  3.844
LogD:  2.434
LogS:  -4.014
# Rotatable Bonds:  6
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.583
Synthetic Accessibility Score:  4.17
Fsp3:  0.5
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:  7.381376781268045e-05
Pgp-inhibitor:  0.008
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.672
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.017
Plasma Protein Binding (PPB):  101.4743881225586%
Volume Distribution (VD):  1.587
Pgp-substrate:  1.8859455585479736%

ADMET: Metabolism

CYP1A2-inhibitor:  0.84
CYP1A2-substrate:  0.192
CYP2C19-inhibitor:  0.902
CYP2C19-substrate:  0.608
CYP2C9-inhibitor:  0.89
CYP2C9-substrate:  0.992
CYP2D6-inhibitor:  0.834
CYP2D6-substrate:  0.861
CYP3A4-inhibitor:  0.864
CYP3A4-substrate:  0.179

ADMET: Excretion

Clearance (CL):  3.483
Half-life (T1/2):  0.229

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.853
Drug-inuced Liver Injury (DILI):  0.983
AMES Toxicity:  0.877
Rat Oral Acute Toxicity:  0.95
Maximum Recommended Daily Dose:  0.953
Skin Sensitization:  0.951
Carcinogencity:  0.47
Eye Corrosion:  0.781
Eye Irritation:  0.98
Respiratory Toxicity:  0.945

Download Data

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

  Natural Product: NPC473539

Natural Product ID:  NPC473539
Common Name*:   Diplyne A
IUPAC Name:   (E)-16-bromohexadec-15-en-3,5,13-triyne-1,2-diol
Synonyms:  
Standard InCHIKey:  VNGBJHIEIWROOZ-WYMLVPIESA-N
Standard InCHI:  InChI=1S/C16H19BrO2/c17-14-12-10-8-6-4-2-1-3-5-7-9-11-13-16(19)15-18/h12,14,16,18-19H,1-6,15H2/b14-12+
SMILES:  Br/C=C/C#CCCCCCCC#CC#CC(CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL444968
PubChem CID:   10471419
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[536060]

☑ 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 NPC473539 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
1.0 High Similarity NPC474413
0.9268 High Similarity NPC473625
0.9111 High Similarity NPC475153
0.8696 High Similarity NPC474445
0.8125 Intermediate Similarity NPC473768
0.8 Intermediate Similarity NPC475723
0.766 Intermediate Similarity NPC201948
0.7143 Intermediate Similarity NPC157096
0.7115 Intermediate Similarity NPC295765
0.6981 Remote Similarity NPC475560
0.6923 Remote Similarity NPC93639
0.6739 Remote Similarity NPC57011
0.6731 Remote Similarity NPC72699
0.6667 Remote Similarity NPC31121
0.6667 Remote Similarity NPC216416
0.6604 Remote Similarity NPC151782
0.6538 Remote Similarity NPC471280
0.6538 Remote Similarity NPC302310
0.6538 Remote Similarity NPC125122
0.6538 Remote Similarity NPC471275
0.6538 Remote Similarity NPC471276
0.6538 Remote Similarity NPC31194
0.6538 Remote Similarity NPC153538
0.6538 Remote Similarity NPC248884
0.6538 Remote Similarity NPC85079
0.6491 Remote Similarity NPC474577
0.6481 Remote Similarity NPC473705
0.6471 Remote Similarity NPC55063
0.6471 Remote Similarity NPC35141
0.6471 Remote Similarity NPC19834
0.6471 Remote Similarity NPC124183
0.6444 Remote Similarity NPC213767
0.6415 Remote Similarity NPC471281
0.6415 Remote Similarity NPC477727
0.6415 Remote Similarity NPC199286
0.64 Remote Similarity NPC62014
0.64 Remote Similarity NPC101616
0.64 Remote Similarity NPC108195
0.6383 Remote Similarity NPC471282
0.6364 Remote Similarity NPC187361
0.6364 Remote Similarity NPC477724
0.6364 Remote Similarity NPC26102
0.6327 Remote Similarity NPC149668
0.6304 Remote Similarity NPC174396
0.6296 Remote Similarity NPC329608
0.6296 Remote Similarity NPC170776
0.6296 Remote Similarity NPC165447
0.6296 Remote Similarity NPC29234
0.6296 Remote Similarity NPC76198
0.6296 Remote Similarity NPC9273
0.6296 Remote Similarity NPC89824
0.6296 Remote Similarity NPC477723
0.6296 Remote Similarity NPC475477
0.6296 Remote Similarity NPC294278
0.6296 Remote Similarity NPC197272
0.6296 Remote Similarity NPC471959
0.6296 Remote Similarity NPC256656
0.6296 Remote Similarity NPC224148
0.6296 Remote Similarity NPC55383
0.625 Remote Similarity NPC256209
0.625 Remote Similarity NPC473532
0.625 Remote Similarity NPC49059
0.6154 Remote Similarity NPC8597
0.614 Remote Similarity NPC473735
0.614 Remote Similarity NPC475353
0.614 Remote Similarity NPC473721
0.614 Remote Similarity NPC477725
0.614 Remote Similarity NPC473725
0.614 Remote Similarity NPC473910
0.614 Remote Similarity NPC477726
0.614 Remote Similarity NPC473896
0.6111 Remote Similarity NPC473487
0.6111 Remote Similarity NPC474642
0.6111 Remote Similarity NPC249670
0.6111 Remote Similarity NPC473913
0.6042 Remote Similarity NPC306850
0.6034 Remote Similarity NPC470969
0.6034 Remote Similarity NPC475384
0.6034 Remote Similarity NPC471960
0.6034 Remote Similarity NPC470968
0.6034 Remote Similarity NPC473847
0.6034 Remote Similarity NPC161838
0.6034 Remote Similarity NPC477661
0.6034 Remote Similarity NPC470966
0.6034 Remote Similarity NPC470967
0.6 Remote Similarity NPC71053
0.6 Remote Similarity NPC59408
0.6 Remote Similarity NPC129263
0.6 Remote Similarity NPC473866
0.5965 Remote Similarity NPC48058
0.5965 Remote Similarity NPC110732
0.5962 Remote Similarity NPC269074
0.5962 Remote Similarity NPC276825
0.5952 Remote Similarity NPC223195
0.5932 Remote Similarity NPC470970
0.5932 Remote Similarity NPC121034
0.5918 Remote Similarity NPC329762
0.5918 Remote Similarity NPC27444
0.5918 Remote Similarity NPC103236
0.5893 Remote Similarity NPC236872
0.5893 Remote Similarity NPC142092
0.5862 Remote Similarity NPC474513
0.5862 Remote Similarity NPC471239
0.5862 Remote Similarity NPC45626
0.5862 Remote Similarity NPC470963
0.5862 Remote Similarity NPC146551
0.5818 Remote Similarity NPC475071
0.5818 Remote Similarity NPC328784
0.5818 Remote Similarity NPC291437
0.58 Remote Similarity NPC474361
0.5789 Remote Similarity NPC284224
0.5789 Remote Similarity NPC34577
0.5763 Remote Similarity NPC311648
0.5763 Remote Similarity NPC470964
0.5745 Remote Similarity NPC474914
0.5745 Remote Similarity NPC474392
0.5714 Remote Similarity NPC100096
0.5686 Remote Similarity NPC46248
0.5686 Remote Similarity NPC249801
0.5667 Remote Similarity NPC193975
0.5667 Remote Similarity NPC594
0.5667 Remote Similarity NPC48968

  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 NPC473539 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
0.5833 Remote Similarity NPD8976 Approved
0.5833 Remote Similarity NPD8977 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