Structure

Physi-Chem Properties

Molecular Weight:  304.18
Volume:  368.857
LogP:  5.449
LogD:  3.32
LogS:  -5.875
# Rotatable Bonds:  8
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.53
Synthetic Accessibility Score:  3.923
Fsp3:  0.364
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:  -4.122
MDCK Permeability:  7.870819536037743e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.898
20% Bioavailability (F20%):  0.985
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  102.62691497802734%
Volume Distribution (VD):  1.942
Pgp-substrate:  1.4084323644638062%

ADMET: Metabolism

CYP1A2-inhibitor:  0.953
CYP1A2-substrate:  0.148
CYP2C19-inhibitor:  0.862
CYP2C19-substrate:  0.292
CYP2C9-inhibitor:  0.793
CYP2C9-substrate:  0.087
CYP2D6-inhibitor:  0.925
CYP2D6-substrate:  0.046
CYP3A4-inhibitor:  0.961
CYP3A4-substrate:  0.319

ADMET: Excretion

Clearance (CL):  9.811
Half-life (T1/2):  0.319

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.85
Drug-inuced Liver Injury (DILI):  0.986
AMES Toxicity:  0.466
Rat Oral Acute Toxicity:  0.381
Maximum Recommended Daily Dose:  0.848
Skin Sensitization:  0.973
Carcinogencity:  0.522
Eye Corrosion:  0.986
Eye Irritation:  0.997
Respiratory Toxicity:  0.58

Download Data

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

  Natural Product: NPC103236

Natural Product ID:  NPC103236
Common Name*:   Callyspongenol C
IUPAC Name:   (4Z,13Z,19Z)-docosa-4,13,19-trien-2,9,11,21-tetrayn-1-ol
Synonyms:   Callyspongenol C
Standard InCHIKey:  XCLAUSBLXUZFRL-FNASMSCBSA-N
Standard InCHI:  InChI=1S/C22H24O/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23/h1,3-4,9-10,18-19,23H,5-8,15-17,22H2/b4-3-,10-9-,19-18-
SMILES:  C#C/C=CCCCC/C=CC#CC#CCCC/C=CC#CCO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464753
PubChem CID:   10063645
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
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. red sea n.a. PMID[12762806]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[18027906]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[22469701]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. collected by hand at a depth of 10 m off the shore of Iriomote Island, Okinawa Prefecture, Japan 2009-JUN PMID[23855338]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[24948562]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[27015002]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. New Guinea n.a. PMID[8158156]

☑ 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
NPT168 Cell Line P388 Mus musculus IC50 = 2.2 ug.mL-1 PMID[564540]
NPT165 Cell Line HeLa Homo sapiens IC50 = 3.9 ug.mL-1 PMID[564540]

☑ 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 NPC103236 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 NPC27444
1.0 High Similarity NPC329762
0.9487 High Similarity NPC149668
0.8605 High Similarity NPC157096
0.8571 High Similarity NPC108195
0.8571 High Similarity NPC101616
0.8537 High Similarity NPC304151
0.8421 Intermediate Similarity NPC213767
0.8372 Intermediate Similarity NPC269074
0.8372 Intermediate Similarity NPC276825
0.8222 Intermediate Similarity NPC125122
0.8222 Intermediate Similarity NPC471275
0.8222 Intermediate Similarity NPC471276
0.8222 Intermediate Similarity NPC471280
0.8205 Intermediate Similarity NPC216416
0.8182 Intermediate Similarity NPC19834
0.8182 Intermediate Similarity NPC124183
0.8182 Intermediate Similarity NPC35141
0.8182 Intermediate Similarity NPC180575
0.8182 Intermediate Similarity NPC55063
0.8043 Intermediate Similarity NPC473913
0.8043 Intermediate Similarity NPC199286
0.8043 Intermediate Similarity NPC474642
0.8043 Intermediate Similarity NPC471281
0.8043 Intermediate Similarity NPC477727
0.8043 Intermediate Similarity NPC249670
0.7872 Intermediate Similarity NPC197272
0.7872 Intermediate Similarity NPC76198
0.7872 Intermediate Similarity NPC471959
0.7872 Intermediate Similarity NPC170776
0.7872 Intermediate Similarity NPC256656
0.7872 Intermediate Similarity NPC475477
0.7872 Intermediate Similarity NPC294278
0.7872 Intermediate Similarity NPC165447
0.7872 Intermediate Similarity NPC89824
0.7872 Intermediate Similarity NPC477723
0.7872 Intermediate Similarity NPC329608
0.7872 Intermediate Similarity NPC224148
0.7872 Intermediate Similarity NPC55383
0.7872 Intermediate Similarity NPC9273
0.7838 Intermediate Similarity NPC196831
0.7826 Intermediate Similarity NPC85079
0.7826 Intermediate Similarity NPC302310
0.7826 Intermediate Similarity NPC153538
0.7826 Intermediate Similarity NPC31194
0.7826 Intermediate Similarity NPC248884
0.7805 Intermediate Similarity NPC15934
0.7674 Intermediate Similarity NPC206906
0.766 Intermediate Similarity NPC473768
0.766 Intermediate Similarity NPC72699
0.7561 Intermediate Similarity NPC34873
0.7561 Intermediate Similarity NPC40434
0.7551 Intermediate Similarity NPC26102
0.7551 Intermediate Similarity NPC187361
0.7551 Intermediate Similarity NPC477724
0.75 Intermediate Similarity NPC93639
0.75 Intermediate Similarity NPC129263
0.75 Intermediate Similarity NPC151782
0.7436 Intermediate Similarity NPC62779
0.74 Intermediate Similarity NPC48058
0.74 Intermediate Similarity NPC473532
0.7347 Intermediate Similarity NPC142092
0.7292 Intermediate Similarity NPC328784
0.7292 Intermediate Similarity NPC291437
0.7273 Intermediate Similarity NPC31121
0.7255 Intermediate Similarity NPC475353
0.7255 Intermediate Similarity NPC474644
0.7255 Intermediate Similarity NPC470963
0.7255 Intermediate Similarity NPC473896
0.7255 Intermediate Similarity NPC146551
0.7255 Intermediate Similarity NPC473725
0.7255 Intermediate Similarity NPC474513
0.7255 Intermediate Similarity NPC477726
0.7255 Intermediate Similarity NPC473735
0.7255 Intermediate Similarity NPC473721
0.7255 Intermediate Similarity NPC473910
0.7255 Intermediate Similarity NPC152668
0.7255 Intermediate Similarity NPC477725
0.7255 Intermediate Similarity NPC471239
0.72 Intermediate Similarity NPC34577
0.72 Intermediate Similarity NPC284224
0.7174 Intermediate Similarity NPC76976
0.7143 Intermediate Similarity NPC59408
0.7143 Intermediate Similarity NPC71053
0.7115 Intermediate Similarity NPC471960
0.7115 Intermediate Similarity NPC473865
0.7115 Intermediate Similarity NPC470966
0.7115 Intermediate Similarity NPC475384
0.7115 Intermediate Similarity NPC470969
0.7115 Intermediate Similarity NPC470968
0.7115 Intermediate Similarity NPC470964
0.7115 Intermediate Similarity NPC311648
0.7115 Intermediate Similarity NPC477661
0.7115 Intermediate Similarity NPC473847
0.7115 Intermediate Similarity NPC470967
0.7115 Intermediate Similarity NPC161838
0.7115 Intermediate Similarity NPC474643
0.7111 Intermediate Similarity NPC252978
0.7059 Intermediate Similarity NPC49059
0.7059 Intermediate Similarity NPC110732
0.7059 Intermediate Similarity NPC256209
0.7045 Intermediate Similarity NPC269823
0.6981 Remote Similarity NPC48968
0.6981 Remote Similarity NPC470970
0.6981 Remote Similarity NPC594
0.6977 Remote Similarity NPC29091
0.6977 Remote Similarity NPC103213
0.6977 Remote Similarity NPC255042
0.6977 Remote Similarity NPC182840
0.6957 Remote Similarity NPC138935
0.6889 Remote Similarity NPC256766
0.6889 Remote Similarity NPC213538
0.6863 Remote Similarity NPC61177
0.6829 Remote Similarity NPC182392
0.6829 Remote Similarity NPC58957
0.6809 Remote Similarity NPC474362
0.6809 Remote Similarity NPC474202
0.68 Remote Similarity NPC29234
0.675 Remote Similarity NPC197356
0.675 Remote Similarity NPC63121
0.6739 Remote Similarity NPC116934
0.6735 Remote Similarity NPC475153
0.6731 Remote Similarity NPC300121
0.6727 Remote Similarity NPC473652
0.6667 Remote Similarity NPC193975
0.6667 Remote Similarity NPC265551
0.6667 Remote Similarity NPC212730
0.6607 Remote Similarity NPC471278
0.6596 Remote Similarity NPC267514
0.6596 Remote Similarity NPC145755
0.6585 Remote Similarity NPC250734
0.6545 Remote Similarity NPC469373
0.6531 Remote Similarity NPC471958
0.6491 Remote Similarity NPC168407
0.6491 Remote Similarity NPC475984
0.6458 Remote Similarity NPC160628
0.6458 Remote Similarity NPC210560
0.6458 Remote Similarity NPC24824
0.6458 Remote Similarity NPC165651
0.6458 Remote Similarity NPC140501
0.641 Remote Similarity NPC34671
0.6383 Remote Similarity NPC269862
0.6379 Remote Similarity NPC470965
0.6364 Remote Similarity NPC472445
0.6364 Remote Similarity NPC121034
0.6364 Remote Similarity NPC44542
0.6346 Remote Similarity NPC129458
0.6346 Remote Similarity NPC473705
0.6304 Remote Similarity NPC469713
0.6304 Remote Similarity NPC33489
0.6275 Remote Similarity NPC474460
0.6275 Remote Similarity NPC288381
0.6275 Remote Similarity NPC20934
0.6275 Remote Similarity NPC182102
0.6275 Remote Similarity NPC473487
0.6275 Remote Similarity NPC26960
0.6226 Remote Similarity NPC225066
0.6226 Remote Similarity NPC475723
0.6226 Remote Similarity NPC10081
0.6222 Remote Similarity NPC171978
0.6222 Remote Similarity NPC33761
0.6222 Remote Similarity NPC306850
0.6222 Remote Similarity NPC277382
0.6207 Remote Similarity NPC271282
0.6207 Remote Similarity NPC66460
0.6207 Remote Similarity NPC325929
0.617 Remote Similarity NPC287397
0.617 Remote Similarity NPC298710
0.617 Remote Similarity NPC208936
0.617 Remote Similarity NPC67920
0.617 Remote Similarity NPC46248
0.617 Remote Similarity NPC249801
0.6154 Remote Similarity NPC284212
0.6154 Remote Similarity NPC474495
0.6154 Remote Similarity NPC473672
0.6154 Remote Similarity NPC28205
0.6154 Remote Similarity NPC138325
0.614 Remote Similarity NPC222852
0.614 Remote Similarity NPC473866
0.6136 Remote Similarity NPC174396
0.6136 Remote Similarity NPC195109
0.6122 Remote Similarity NPC239754
0.6111 Remote Similarity NPC13011
0.6111 Remote Similarity NPC124382
0.6111 Remote Similarity NPC269615
0.6102 Remote Similarity NPC29697
0.6098 Remote Similarity NPC151719
0.6078 Remote Similarity NPC267110
0.6071 Remote Similarity NPC471279
0.6071 Remote Similarity NPC471277
0.6038 Remote Similarity NPC303765
0.6038 Remote Similarity NPC106531
0.6038 Remote Similarity NPC236872
0.6038 Remote Similarity NPC35756
0.6034 Remote Similarity NPC477430
0.6 Remote Similarity NPC242930
0.6 Remote Similarity NPC42304
0.6 Remote Similarity NPC92863
0.6 Remote Similarity NPC45626
0.6 Remote Similarity NPC54766

  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 NPC103236 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
0.6458 Remote Similarity NPD4265 Approved
0.6122 Remote Similarity NPD39 Approved
0.5893 Remote Similarity NPD4219 Approved
0.58 Remote Similarity NPD4222 Approved
0.5769 Remote Similarity NPD3173 Approved
0.5714 Remote Similarity NPD5326 Phase 3
0.5714 Remote Similarity NPD4627 Clinical (unspecified phase)
0.56 Remote Similarity NPD6096 Approved
0.56 Remote Similarity NPD6097 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