Structure

Physi-Chem Properties

Molecular Weight:  306.26
Volume:  361.511
LogP:  4.911
LogD:  3.638
LogS:  -3.96
# Rotatable Bonds:  15
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.347
Synthetic Accessibility Score:  3.216
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.88
MDCK Permeability:  1.776398130459711e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.229
20% Bioavailability (F20%):  0.052
30% Bioavailability (F30%):  0.885

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.548
Plasma Protein Binding (PPB):  96.87181854248047%
Volume Distribution (VD):  0.869
Pgp-substrate:  0.7235391139984131%

ADMET: Metabolism

CYP1A2-inhibitor:  0.63
CYP1A2-substrate:  0.186
CYP2C19-inhibitor:  0.814
CYP2C19-substrate:  0.268
CYP2C9-inhibitor:  0.555
CYP2C9-substrate:  0.976
CYP2D6-inhibitor:  0.497
CYP2D6-substrate:  0.053
CYP3A4-inhibitor:  0.348
CYP3A4-substrate:  0.098

ADMET: Excretion

Clearance (CL):  5.139
Half-life (T1/2):  0.22

ADMET: Toxicity

hERG Blockers:  0.105
Human Hepatotoxicity (H-HT):  0.106
Drug-inuced Liver Injury (DILI):  0.389
AMES Toxicity:  0.04
Rat Oral Acute Toxicity:  0.959
Maximum Recommended Daily Dose:  0.996
Skin Sensitization:  0.959
Carcinogencity:  0.133
Eye Corrosion:  0.61
Eye Irritation:  0.968
Respiratory Toxicity:  0.96

Download Data

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

  Natural Product: NPC471282

Natural Product ID:  NPC471282
Common Name*:   Icosa-1,19-Diyne-3,18-Diol
IUPAC Name:   icosa-1,19-diyne-3,18-diol
Synonyms:  
Standard InCHIKey:  XDTMHGOGPDXGIJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C20H34O2/c1-3-19(21)17-15-13-11-9-7-5-6-8-10-12-14-16-18-20(22)4-2/h1-2,19-22H,5-18H2
SMILES:  OC(C#C)CCCCCCCCCCCCCCC(C#C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2408397
PubChem CID:   71745715
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002951] Long-chain 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 170.0 nM PMID[519009]

☑ 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 NPC471282 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
0.8649 High Similarity NPC474392
0.8649 High Similarity NPC474914
0.8378 Intermediate Similarity NPC97967
0.8333 Intermediate Similarity NPC215358
0.8333 Intermediate Similarity NPC12231
0.8333 Intermediate Similarity NPC152759
0.814 Intermediate Similarity NPC473914
0.8056 Intermediate Similarity NPC267243
0.7907 Intermediate Similarity NPC62014
0.7838 Intermediate Similarity NPC272998
0.7838 Intermediate Similarity NPC66124
0.7838 Intermediate Similarity NPC139131
0.7838 Intermediate Similarity NPC1748
0.7838 Intermediate Similarity NPC291158
0.7838 Intermediate Similarity NPC181516
0.7838 Intermediate Similarity NPC319034
0.7838 Intermediate Similarity NPC193062
0.7838 Intermediate Similarity NPC185538
0.7838 Intermediate Similarity NPC72324
0.7838 Intermediate Similarity NPC205141
0.7568 Intermediate Similarity NPC126915
0.7568 Intermediate Similarity NPC122962
0.7556 Intermediate Similarity NPC8597
0.75 Intermediate Similarity NPC74352
0.7347 Intermediate Similarity NPC26102
0.7347 Intermediate Similarity NPC477724
0.7347 Intermediate Similarity NPC187361
0.7297 Intermediate Similarity NPC24506
0.7297 Intermediate Similarity NPC147096
0.7297 Intermediate Similarity NPC185041
0.7297 Intermediate Similarity NPC112242
0.7297 Intermediate Similarity NPC225783
0.7297 Intermediate Similarity NPC236797
0.7297 Intermediate Similarity NPC163556
0.7234 Intermediate Similarity NPC304162
0.72 Intermediate Similarity NPC289979
0.7111 Intermediate Similarity NPC469781
0.7059 Intermediate Similarity NPC477726
0.7059 Intermediate Similarity NPC477725
0.7027 Intermediate Similarity NPC110884
0.6939 Remote Similarity NPC100096
0.6923 Remote Similarity NPC470969
0.6923 Remote Similarity NPC161838
0.6923 Remote Similarity NPC477661
0.6923 Remote Similarity NPC471960
0.6923 Remote Similarity NPC473847
0.6923 Remote Similarity NPC470966
0.6923 Remote Similarity NPC470967
0.6923 Remote Similarity NPC470968
0.6923 Remote Similarity NPC475384
0.6905 Remote Similarity NPC197039
0.6818 Remote Similarity NPC474361
0.6809 Remote Similarity NPC324004
0.6809 Remote Similarity NPC328497
0.6792 Remote Similarity NPC470970
0.6757 Remote Similarity NPC159845
0.6757 Remote Similarity NPC279895
0.6757 Remote Similarity NPC223195
0.675 Remote Similarity NPC139569
0.6744 Remote Similarity NPC221022
0.6731 Remote Similarity NPC473910
0.6731 Remote Similarity NPC473725
0.6731 Remote Similarity NPC473721
0.6731 Remote Similarity NPC473896
0.6731 Remote Similarity NPC473735
0.6731 Remote Similarity NPC475353
0.6667 Remote Similarity NPC106872
0.6591 Remote Similarity NPC160261
0.6591 Remote Similarity NPC152008
0.6591 Remote Similarity NPC469759
0.6538 Remote Similarity NPC473532
0.6538 Remote Similarity NPC49059
0.6538 Remote Similarity NPC256209
0.64 Remote Similarity NPC90904
0.6389 Remote Similarity NPC213764
0.6383 Remote Similarity NPC240994
0.6383 Remote Similarity NPC8219
0.6383 Remote Similarity NPC474413
0.6383 Remote Similarity NPC473539
0.6341 Remote Similarity NPC474120
0.6341 Remote Similarity NPC474089
0.6316 Remote Similarity NPC475984
0.6316 Remote Similarity NPC325345
0.6304 Remote Similarity NPC301528
0.6304 Remote Similarity NPC71317
0.6304 Remote Similarity NPC129972
0.6279 Remote Similarity NPC177022
0.6275 Remote Similarity NPC129263
0.625 Remote Similarity NPC30195
0.625 Remote Similarity NPC12438
0.6216 Remote Similarity NPC560
0.6207 Remote Similarity NPC470965
0.6182 Remote Similarity NPC474577
0.617 Remote Similarity NPC19305
0.617 Remote Similarity NPC76051
0.617 Remote Similarity NPC255837
0.6154 Remote Similarity NPC474322
0.6154 Remote Similarity NPC123814
0.6122 Remote Similarity NPC319709
0.6122 Remote Similarity NPC289484
0.6087 Remote Similarity NPC103286
0.6087 Remote Similarity NPC163746
0.6078 Remote Similarity NPC477727
0.6078 Remote Similarity NPC199286
0.6078 Remote Similarity NPC471281
0.6038 Remote Similarity NPC34577
0.6038 Remote Similarity NPC270041
0.6 Remote Similarity NPC200618
0.6 Remote Similarity NPC131770
0.5962 Remote Similarity NPC89824
0.5962 Remote Similarity NPC294278
0.5962 Remote Similarity NPC55383
0.5962 Remote Similarity NPC170776
0.5962 Remote Similarity NPC224148
0.5962 Remote Similarity NPC329608
0.5962 Remote Similarity NPC475477
0.5962 Remote Similarity NPC256656
0.5962 Remote Similarity NPC477723
0.5962 Remote Similarity NPC471959
0.5962 Remote Similarity NPC165447
0.5962 Remote Similarity NPC197272
0.5962 Remote Similarity NPC151782
0.5962 Remote Similarity NPC76198
0.5962 Remote Similarity NPC9273
0.5952 Remote Similarity NPC283682
0.5946 Remote Similarity NPC275462
0.5946 Remote Similarity NPC232554
0.5926 Remote Similarity NPC320588
0.5926 Remote Similarity NPC23155
0.5926 Remote Similarity NPC110732
0.5926 Remote Similarity NPC53463
0.5926 Remote Similarity NPC469937
0.5918 Remote Similarity NPC76976
0.5918 Remote Similarity NPC201948
0.5909 Remote Similarity NPC128996
0.5882 Remote Similarity NPC471276
0.5882 Remote Similarity NPC125122
0.5882 Remote Similarity NPC302310
0.5882 Remote Similarity NPC475153
0.5882 Remote Similarity NPC471275
0.5882 Remote Similarity NPC471280
0.5854 Remote Similarity NPC272426
0.5849 Remote Similarity NPC473705
0.5833 Remote Similarity NPC144891
0.5833 Remote Similarity NPC74845
0.5814 Remote Similarity NPC192065
0.5814 Remote Similarity NPC66052
0.5814 Remote Similarity NPC325034
0.5814 Remote Similarity NPC86412
0.5814 Remote Similarity NPC293908
0.58 Remote Similarity NPC287550
0.58 Remote Similarity NPC198540
0.58 Remote Similarity NPC223468
0.58 Remote Similarity NPC84030
0.58 Remote Similarity NPC147343
0.58 Remote Similarity NPC176309
0.58 Remote Similarity NPC157096
0.5789 Remote Similarity NPC252154
0.5769 Remote Similarity NPC249670
0.5769 Remote Similarity NPC474642
0.5769 Remote Similarity NPC72699
0.5769 Remote Similarity NPC473913
0.5745 Remote Similarity NPC473625
0.5745 Remote Similarity NPC216630
0.5745 Remote Similarity NPC196924
0.5745 Remote Similarity NPC149184
0.5745 Remote Similarity NPC307783
0.5745 Remote Similarity NPC209970
0.5745 Remote Similarity NPC171736
0.5741 Remote Similarity NPC474496
0.5714 Remote Similarity NPC287231
0.5714 Remote Similarity NPC148424
0.5714 Remote Similarity NPC8979
0.5714 Remote Similarity NPC47363
0.5714 Remote Similarity NPC108195
0.5686 Remote Similarity NPC96966
0.5686 Remote Similarity NPC29222
0.5686 Remote Similarity NPC121062
0.5686 Remote Similarity NPC314087
0.5676 Remote Similarity NPC199270
0.5676 Remote Similarity NPC245688
0.5667 Remote Similarity NPC29697
0.566 Remote Similarity NPC470411
0.566 Remote Similarity NPC474495
0.566 Remote Similarity NPC473672
0.566 Remote Similarity NPC307022
0.5652 Remote Similarity NPC28394
0.5652 Remote Similarity NPC31557
0.5636 Remote Similarity NPC48058
0.5625 Remote Similarity NPC67462
0.5625 Remote Similarity NPC249801
0.5625 Remote Similarity NPC46248
0.5625 Remote Similarity NPC149668
0.5614 Remote Similarity NPC322148

  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 NPC471282 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
0.7838 Intermediate Similarity NPD5383 Approved
0.7838 Intermediate Similarity NPD2272 Approved
0.6591 Remote Similarity NPD7536 Approved
0.6316 Remote Similarity NPD8988 Clinical (unspecified phase)
0.6154 Remote Similarity NPD3215 Phase 1
0.6122 Remote Similarity NPD3211 Approved
0.6078 Remote Similarity NPD3214 Discontinued
0.5926 Remote Similarity NPD3728 Approved
0.5926 Remote Similarity NPD3730 Approved
0.5926 Remote Similarity NPD3729 Clinical (unspecified phase)
0.5854 Remote Similarity NPD908 Approved
0.5854 Remote Similarity NPD1461 Approved
0.5854 Remote Similarity NPD907 Approved
0.5814 Remote Similarity NPD9052 Approved
0.5814 Remote Similarity NPD9051 Approved
0.5814 Remote Similarity NPD9053 Approved
0.58 Remote Similarity NPD384 Approved
0.58 Remote Similarity NPD385 Approved
0.5745 Remote Similarity NPD2270 Approved
0.5714 Remote Similarity NPD2699 Approved
0.5652 Remote Similarity NPD5799 Discontinued
0.5625 Remote Similarity NPD1462 Approved
0.56 Remote Similarity NPD1152 Phase 2

  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