Structure

Physi-Chem Properties

Molecular Weight:  292.28
Volume:  355.357
LogP:  7.277
LogD:  4.516
LogS:  -5.522
# Rotatable Bonds:  15
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.222
Synthetic Accessibility Score:  2.887
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:  -4.868
MDCK Permeability:  1.5188677934929729e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.114
20% Bioavailability (F20%):  0.996
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.167
Plasma Protein Binding (PPB):  97.45365142822266%
Volume Distribution (VD):  2.507
Pgp-substrate:  1.3452507257461548%

ADMET: Metabolism

CYP1A2-inhibitor:  0.537
CYP1A2-substrate:  0.193
CYP2C19-inhibitor:  0.638
CYP2C19-substrate:  0.131
CYP2C9-inhibitor:  0.434
CYP2C9-substrate:  0.979
CYP2D6-inhibitor:  0.527
CYP2D6-substrate:  0.073
CYP3A4-inhibitor:  0.417
CYP3A4-substrate:  0.059

ADMET: Excretion

Clearance (CL):  3.76
Half-life (T1/2):  0.139

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.336
Drug-inuced Liver Injury (DILI):  0.091
AMES Toxicity:  0.092
Rat Oral Acute Toxicity:  0.84
Maximum Recommended Daily Dose:  0.998
Skin Sensitization:  0.959
Carcinogencity:  0.267
Eye Corrosion:  0.983
Eye Irritation:  0.957
Respiratory Toxicity:  0.975

Download Data

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

  Natural Product: NPC249670

Natural Product ID:  NPC249670
Common Name*:   (S,E)-Icos-4-En-1-Yn-3-Ol
IUPAC Name:   (E,3S)-icos-4-en-1-yn-3-ol
Synonyms:  
Standard InCHIKey:  MQUXQBHHZDPZOB-LNEUUDGLSA-N
Standard InCHI:  InChI=1S/C20H36O/c1-3-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20(21)4-2/h2,18-21H,3,5-17H2,1H3/b19-18+/t20-/m1/s1
SMILES:  CCCCCCCCCCCCCCC/C=C/[C@@H](C#C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL443123
PubChem CID:   5469791
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
NPO15047 Cribrochalina vasculum Species Niphatidae Eukaryota n.a. Caribbean n.a. PMID[1431945]
NPO15047 Cribrochalina vasculum Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[8691203]
NPO15047 Cribrochalina vasculum Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[8984159]
NPO15047 Cribrochalina vasculum Species Niphatidae 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
NPT458 Cell Line IGROV-1 Homo sapiens Activity = 36.5 day PMID[489402]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 90.0 nM PMID[489403]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 60.0 nM PMID[489403]

☑ 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 NPC249670 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 NPC473913
1.0 High Similarity NPC474642
0.9574 High Similarity NPC199286
0.9574 High Similarity NPC471281
0.9574 High Similarity NPC477727
0.9375 High Similarity NPC170776
0.9375 High Similarity NPC475477
0.9375 High Similarity NPC329608
0.9375 High Similarity NPC294278
0.9375 High Similarity NPC55383
0.9375 High Similarity NPC197272
0.9375 High Similarity NPC477723
0.9375 High Similarity NPC76198
0.9375 High Similarity NPC224148
0.9375 High Similarity NPC89824
0.9375 High Similarity NPC471959
0.9375 High Similarity NPC256656
0.9375 High Similarity NPC9273
0.9375 High Similarity NPC165447
0.9362 High Similarity NPC248884
0.9362 High Similarity NPC31194
0.9362 High Similarity NPC471275
0.9362 High Similarity NPC471276
0.9362 High Similarity NPC471280
0.9362 High Similarity NPC85079
0.9362 High Similarity NPC125122
0.9348 High Similarity NPC55063
0.9348 High Similarity NPC19834
0.9167 High Similarity NPC72699
0.913 High Similarity NPC269074
0.902 High Similarity NPC474644
0.898 High Similarity NPC151782
0.8958 High Similarity NPC153538
0.8936 High Similarity NPC124183
0.8936 High Similarity NPC35141
0.8913 High Similarity NPC101616
0.8846 High Similarity NPC473865
0.8846 High Similarity NPC474643
0.8824 High Similarity NPC48058
0.8824 High Similarity NPC473532
0.8654 High Similarity NPC473725
0.8654 High Similarity NPC470963
0.8654 High Similarity NPC477725
0.8654 High Similarity NPC474513
0.8654 High Similarity NPC473721
0.8654 High Similarity NPC477726
0.8654 High Similarity NPC473896
0.8654 High Similarity NPC473735
0.8654 High Similarity NPC146551
0.8654 High Similarity NPC475353
0.8654 High Similarity NPC473910
0.86 High Similarity NPC93639
0.8542 High Similarity NPC180575
0.8491 Intermediate Similarity NPC470968
0.8491 Intermediate Similarity NPC470967
0.8491 Intermediate Similarity NPC477661
0.8491 Intermediate Similarity NPC470969
0.8491 Intermediate Similarity NPC161838
0.8491 Intermediate Similarity NPC471960
0.8491 Intermediate Similarity NPC473847
0.8491 Intermediate Similarity NPC470966
0.8491 Intermediate Similarity NPC311648
0.8491 Intermediate Similarity NPC470964
0.8491 Intermediate Similarity NPC475384
0.8478 Intermediate Similarity NPC149668
0.8478 Intermediate Similarity NPC304151
0.8462 Intermediate Similarity NPC256209
0.8462 Intermediate Similarity NPC49059
0.8431 Intermediate Similarity NPC142092
0.8333 Intermediate Similarity NPC470970
0.8333 Intermediate Similarity NPC594
0.8333 Intermediate Similarity NPC48968
0.8302 Intermediate Similarity NPC471239
0.8302 Intermediate Similarity NPC152668
0.8235 Intermediate Similarity NPC59408
0.8235 Intermediate Similarity NPC71053
0.8214 Intermediate Similarity NPC471278
0.8125 Intermediate Similarity NPC108195
0.8113 Intermediate Similarity NPC110732
0.8043 Intermediate Similarity NPC103236
0.8043 Intermediate Similarity NPC27444
0.8043 Intermediate Similarity NPC329762
0.8039 Intermediate Similarity NPC328784
0.8039 Intermediate Similarity NPC291437
0.8036 Intermediate Similarity NPC473652
0.8 Intermediate Similarity NPC193975
0.7925 Intermediate Similarity NPC187361
0.7925 Intermediate Similarity NPC26102
0.7925 Intermediate Similarity NPC477724
0.7885 Intermediate Similarity NPC129263
0.7885 Intermediate Similarity NPC474495
0.7885 Intermediate Similarity NPC473672
0.7843 Intermediate Similarity NPC302310
0.7826 Intermediate Similarity NPC15934
0.78 Intermediate Similarity NPC157096
0.7759 Intermediate Similarity NPC475984
0.7759 Intermediate Similarity NPC168407
0.7708 Intermediate Similarity NPC206906
0.7679 Intermediate Similarity NPC265551
0.7679 Intermediate Similarity NPC212730
0.7627 Intermediate Similarity NPC470965
0.76 Intermediate Similarity NPC276825
0.7593 Intermediate Similarity NPC34577
0.7593 Intermediate Similarity NPC61177
0.75 Intermediate Similarity NPC269823
0.7458 Intermediate Similarity NPC271282
0.7458 Intermediate Similarity NPC325929
0.7458 Intermediate Similarity NPC66460
0.74 Intermediate Similarity NPC138935
0.7391 Intermediate Similarity NPC216416
0.7368 Intermediate Similarity NPC44542
0.7368 Intermediate Similarity NPC471279
0.7368 Intermediate Similarity NPC471277
0.7358 Intermediate Similarity NPC182102
0.7358 Intermediate Similarity NPC475071
0.7358 Intermediate Similarity NPC26960
0.7347 Intermediate Similarity NPC213538
0.7347 Intermediate Similarity NPC256766
0.7333 Intermediate Similarity NPC29697
0.7273 Intermediate Similarity NPC474496
0.7255 Intermediate Similarity NPC76976
0.72 Intermediate Similarity NPC116934
0.7174 Intermediate Similarity NPC213767
0.7143 Intermediate Similarity NPC473752
0.7083 Intermediate Similarity NPC182840
0.7083 Intermediate Similarity NPC103213
0.7083 Intermediate Similarity NPC255042
0.7083 Intermediate Similarity NPC29091
0.7069 Intermediate Similarity NPC472445
0.7037 Intermediate Similarity NPC473768
0.7037 Intermediate Similarity NPC474460
0.7018 Intermediate Similarity NPC329686
0.7 Intermediate Similarity NPC46248
0.7 Intermediate Similarity NPC249801
0.6964 Remote Similarity NPC284224
0.6957 Remote Similarity NPC182392
0.6957 Remote Similarity NPC58957
0.6949 Remote Similarity NPC181872
0.6935 Remote Similarity NPC470320
0.6935 Remote Similarity NPC226592
0.6923 Remote Similarity NPC140501
0.6923 Remote Similarity NPC160628
0.6909 Remote Similarity NPC29234
0.6863 Remote Similarity NPC252978
0.6852 Remote Similarity NPC475153
0.6833 Remote Similarity NPC222852
0.6833 Remote Similarity NPC122239
0.6786 Remote Similarity NPC35756
0.6786 Remote Similarity NPC473705
0.6774 Remote Similarity NPC55068
0.6739 Remote Similarity NPC62779
0.6739 Remote Similarity NPC250734
0.6731 Remote Similarity NPC145755
0.6731 Remote Similarity NPC267514
0.6724 Remote Similarity NPC317899
0.6721 Remote Similarity NPC327112
0.6721 Remote Similarity NPC471081
0.6667 Remote Similarity NPC217188
0.6667 Remote Similarity NPC471958
0.6667 Remote Similarity NPC226848
0.6613 Remote Similarity NPC477829
0.661 Remote Similarity NPC249645
0.661 Remote Similarity NPC55412
0.6607 Remote Similarity NPC244038
0.6604 Remote Similarity NPC474202
0.6604 Remote Similarity NPC474362
0.6562 Remote Similarity NPC255863
0.6562 Remote Similarity NPC136164
0.6562 Remote Similarity NPC308844
0.6562 Remote Similarity NPC245947
0.6557 Remote Similarity NPC473866
0.6557 Remote Similarity NPC329424
0.6557 Remote Similarity NPC474267
0.6557 Remote Similarity NPC475931
0.6552 Remote Similarity NPC269615
0.6545 Remote Similarity NPC267110
0.6531 Remote Similarity NPC34873
0.6531 Remote Similarity NPC40434
0.65 Remote Similarity NPC11130
0.65 Remote Similarity NPC474577
0.65 Remote Similarity NPC121034
0.6491 Remote Similarity NPC208638
0.6458 Remote Similarity NPC79544
0.6452 Remote Similarity NPC130807
0.6441 Remote Similarity NPC232247
0.6441 Remote Similarity NPC251666
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
0.6393 Remote Similarity NPC469373
0.6383 Remote Similarity NPC81989
0.6379 Remote Similarity NPC475723
0.6364 Remote Similarity NPC26500
0.6364 Remote Similarity NPC99619
0.6346 Remote Similarity NPC31121
0.6333 Remote Similarity NPC324224
0.6333 Remote Similarity NPC48891
0.6333 Remote Similarity NPC472808

  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 NPC249670 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
0.6923 Remote Similarity NPD4265 Approved
0.6774 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6721 Remote Similarity NPD4246 Clinical (unspecified phase)
0.661 Remote Similarity NPD4219 Approved
0.6087 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5909 Remote Similarity NPD3197 Phase 1
0.5902 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5902 Remote Similarity NPD342 Phase 1
0.5882 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5873 Remote Similarity NPD585 Clinical (unspecified phase)
0.5846 Remote Similarity NPD368 Approved
0.5769 Remote Similarity NPD5331 Approved
0.5769 Remote Similarity NPD5332 Approved
0.5753 Remote Similarity NPD8264 Approved
0.5714 Remote Similarity NPD39 Approved
0.569 Remote Similarity NPD4220 Pre-registration

  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