Structure

Physi-Chem Properties

Molecular Weight:  272.16
Volume:  340.135
LogP:  5.973
LogD:  3.383
LogS:  -6.465
# Rotatable Bonds:  7
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.483
Synthetic Accessibility Score:  3.977
Fsp3:  0.333
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:  -3.964
MDCK Permeability:  0.00011325182276777923
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.924
20% Bioavailability (F20%):  0.979
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.0
Plasma Protein Binding (PPB):  102.66588592529297%
Volume Distribution (VD):  2.537
Pgp-substrate:  1.2858539819717407%

ADMET: Metabolism

CYP1A2-inhibitor:  0.931
CYP1A2-substrate:  0.182
CYP2C19-inhibitor:  0.789
CYP2C19-substrate:  0.253
CYP2C9-inhibitor:  0.617
CYP2C9-substrate:  0.654
CYP2D6-inhibitor:  0.514
CYP2D6-substrate:  0.135
CYP3A4-inhibitor:  0.856
CYP3A4-substrate:  0.176

ADMET: Excretion

Clearance (CL):  8.946
Half-life (T1/2):  0.071

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.644
Drug-inuced Liver Injury (DILI):  0.989
AMES Toxicity:  0.37
Rat Oral Acute Toxicity:  0.338
Maximum Recommended Daily Dose:  0.67
Skin Sensitization:  0.975
Carcinogencity:  0.396
Eye Corrosion:  0.99
Eye Irritation:  0.995
Respiratory Toxicity:  0.589

Download Data

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

  Natural Product: NPC196831

Natural Product ID:  NPC196831
Common Name*:   Callypentayne
IUPAC Name:   (12Z,18Z)-henicosa-12,18-dien-1,3,8,10,20-pentayne
Synonyms:   callypentayne
Standard InCHIKey:  BZASOWOKZUQCSW-PICUFFSDSA-N
Standard InCHI:  InChI=1S/C21H20/c1-3-5-7-9-11-13-15-17-19-21-20-18-16-14-12-10-8-6-4-2/h1-2,5,7,17,19H,9-15H2/b7-5-,19-17-
SMILES:  C#C/C=CCCCC/C=CC#CC#CCCCC#CC#C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL448827
PubChem CID:   10778600
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004475] Unsaturated hydrocarbons
        • [CHEMONTID:0001566] Enynes

*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
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]
NPO21845 Calvatia fenzlii Species Lycoperdaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13962 Corydalis turtschaninovii Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21845 Calvatia fenzlii Species Lycoperdaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
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]
NPO13962 Corydalis turtschaninovii Species Papaveraceae 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[451679]

☑ 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 NPC196831 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
0.9355 High Similarity NPC62779
0.8485 Intermediate Similarity NPC182392
0.8065 Intermediate Similarity NPC34671
0.7838 Intermediate Similarity NPC329762
0.7838 Intermediate Similarity NPC103236
0.7838 Intermediate Similarity NPC27444
0.7742 Intermediate Similarity NPC138325
0.7576 Intermediate Similarity NPC151719
0.7436 Intermediate Similarity NPC149668
0.7059 Intermediate Similarity NPC471327
0.697 Remote Similarity NPC115959
0.697 Remote Similarity NPC123965
0.697 Remote Similarity NPC138113
0.6774 Remote Similarity NPC38513
0.6774 Remote Similarity NPC88325
0.6765 Remote Similarity NPC60288
0.6744 Remote Similarity NPC157096
0.6667 Remote Similarity NPC267514
0.6667 Remote Similarity NPC99088
0.6667 Remote Similarity NPC305759
0.6667 Remote Similarity NPC108195
0.6667 Remote Similarity NPC145755
0.6667 Remote Similarity NPC173592
0.6667 Remote Similarity NPC76765
0.6667 Remote Similarity NPC179103
0.6667 Remote Similarity NPC101616
0.6591 Remote Similarity NPC471958
0.6585 Remote Similarity NPC304151
0.6571 Remote Similarity NPC3649
0.6571 Remote Similarity NPC66577
0.6571 Remote Similarity NPC100879
0.6571 Remote Similarity NPC206088
0.6562 Remote Similarity NPC287191
0.6562 Remote Similarity NPC31891
0.6562 Remote Similarity NPC266539
0.6562 Remote Similarity NPC266144
0.6512 Remote Similarity NPC276825
0.6512 Remote Similarity NPC269074
0.6444 Remote Similarity NPC125122
0.6444 Remote Similarity NPC471280
0.6444 Remote Similarity NPC471275
0.6444 Remote Similarity NPC471276
0.6364 Remote Similarity NPC35141
0.6364 Remote Similarity NPC55063
0.6364 Remote Similarity NPC19834
0.6364 Remote Similarity NPC124183
0.6364 Remote Similarity NPC180575
0.6316 Remote Similarity NPC282119
0.6316 Remote Similarity NPC92224
0.6316 Remote Similarity NPC213767
0.6304 Remote Similarity NPC473913
0.6304 Remote Similarity NPC477727
0.6304 Remote Similarity NPC471281
0.6304 Remote Similarity NPC199286
0.6304 Remote Similarity NPC249670
0.6304 Remote Similarity NPC474642
0.6176 Remote Similarity NPC262789
0.6176 Remote Similarity NPC64176
0.6176 Remote Similarity NPC288991
0.617 Remote Similarity NPC256656
0.617 Remote Similarity NPC224148
0.617 Remote Similarity NPC165447
0.617 Remote Similarity NPC329608
0.617 Remote Similarity NPC76198
0.617 Remote Similarity NPC471959
0.617 Remote Similarity NPC89824
0.617 Remote Similarity NPC477723
0.617 Remote Similarity NPC294278
0.617 Remote Similarity NPC9273
0.617 Remote Similarity NPC170776
0.617 Remote Similarity NPC475477
0.617 Remote Similarity NPC55383
0.617 Remote Similarity NPC197272
0.6154 Remote Similarity NPC216416
0.6136 Remote Similarity NPC474202
0.6136 Remote Similarity NPC474362
0.6087 Remote Similarity NPC248884
0.6087 Remote Similarity NPC153538
0.6087 Remote Similarity NPC31194
0.6087 Remote Similarity NPC302310
0.6087 Remote Similarity NPC85079
0.6 Remote Similarity NPC92863
0.6 Remote Similarity NPC178306
0.6 Remote Similarity NPC155880
0.6 Remote Similarity NPC266298
0.5957 Remote Similarity NPC72699
0.5957 Remote Similarity NPC473768
0.5952 Remote Similarity NPC270170
0.5952 Remote Similarity NPC7754
0.5946 Remote Similarity NPC213749
0.5918 Remote Similarity NPC477724
0.5918 Remote Similarity NPC26102
0.5918 Remote Similarity NPC187361
0.5862 Remote Similarity NPC33192
0.5854 Remote Similarity NPC15934
0.5854 Remote Similarity NPC217923
0.5833 Remote Similarity NPC129263
0.5833 Remote Similarity NPC16561
0.5833 Remote Similarity NPC151782
0.5833 Remote Similarity NPC93639
0.5814 Remote Similarity NPC206906
0.58 Remote Similarity NPC473532
0.58 Remote Similarity NPC48058
0.575 Remote Similarity NPC34764
0.575 Remote Similarity NPC190810
0.575 Remote Similarity NPC76145
0.5714 Remote Similarity NPC142092
0.5714 Remote Similarity NPC129458
0.5714 Remote Similarity NPC183670
0.5686 Remote Similarity NPC475353
0.5686 Remote Similarity NPC146551
0.5686 Remote Similarity NPC470963
0.5686 Remote Similarity NPC152668
0.5686 Remote Similarity NPC473725
0.5686 Remote Similarity NPC473721
0.5686 Remote Similarity NPC474513
0.5686 Remote Similarity NPC477726
0.5686 Remote Similarity NPC474644
0.5686 Remote Similarity NPC473896
0.5686 Remote Similarity NPC477725
0.5686 Remote Similarity NPC473910
0.5686 Remote Similarity NPC471239
0.5686 Remote Similarity NPC473735
0.5667 Remote Similarity NPC225855
0.5625 Remote Similarity NPC291437
0.5625 Remote Similarity NPC474391
0.5625 Remote Similarity NPC328784
0.561 Remote Similarity NPC48638
0.561 Remote Similarity NPC229262
0.561 Remote Similarity NPC139717
0.561 Remote Similarity NPC34873
0.561 Remote Similarity NPC297643
0.561 Remote Similarity NPC45727
0.561 Remote Similarity NPC239039
0.561 Remote Similarity NPC40434
0.561 Remote Similarity NPC180840
0.56 Remote Similarity NPC34577
0.56 Remote Similarity NPC225066
0.56 Remote Similarity NPC10081
0.56 Remote Similarity NPC284224

  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 NPC196831 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
0.575 Remote Similarity NPD319 Phase 1

  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