Structure

Physi-Chem Properties

Molecular Weight:  246.16
Volume:  287.054
LogP:  2.381
LogD:  2.838
LogS:  -4.41
# Rotatable Bonds:  9
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.373
Synthetic Accessibility Score:  4.076
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.882
MDCK Permeability:  9.653334018366877e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.97
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  0.971

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.212
Plasma Protein Binding (PPB):  91.25313568115234%
Volume Distribution (VD):  0.834
Pgp-substrate:  1.213257908821106%

ADMET: Metabolism

CYP1A2-inhibitor:  0.46
CYP1A2-substrate:  0.357
CYP2C19-inhibitor:  0.87
CYP2C19-substrate:  0.824
CYP2C9-inhibitor:  0.56
CYP2C9-substrate:  0.981
CYP2D6-inhibitor:  0.528
CYP2D6-substrate:  0.379
CYP3A4-inhibitor:  0.248
CYP3A4-substrate:  0.151

ADMET: Excretion

Clearance (CL):  2.211
Half-life (T1/2):  0.614

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.234
Drug-inuced Liver Injury (DILI):  0.226
AMES Toxicity:  0.05
Rat Oral Acute Toxicity:  0.967
Maximum Recommended Daily Dose:  0.998
Skin Sensitization:  0.954
Carcinogencity:  0.105
Eye Corrosion:  0.142
Eye Irritation:  0.936
Respiratory Toxicity:  0.972

Download Data

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

  Natural Product: NPC471280

Natural Product ID:  NPC471280
Common Name*:   (4E,12E)-Hexadeca-4,12-Dien-1,15-Diyne-3,14-Diol
IUPAC Name:   (4E,12E)-hexadeca-4,12-dien-1,15-diyne-3,14-diol
Synonyms:  
Standard InCHIKey:  YUTFLVQSQJNSGY-PHEQNACWSA-N
Standard InCHI:  InChI=1S/C16H22O2/c1-3-15(17)13-11-9-7-5-6-8-10-12-14-16(18)4-2/h1-2,11-18H,5-10H2/b13-11+,14-12+
SMILES:  C#CC(C=CCCCCCCC=CC(C#C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2408395
PubChem CID:   71745538
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 = 9400.0 nM PMID[474043]

☑ 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 NPC471280 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 NPC471275
1.0 High Similarity NPC471276
1.0 High Similarity NPC125122
0.9783 High Similarity NPC471281
0.9783 High Similarity NPC199286
0.9783 High Similarity NPC477727
0.9574 High Similarity NPC89824
0.9574 High Similarity NPC170776
0.9574 High Similarity NPC329608
0.9574 High Similarity NPC256656
0.9574 High Similarity NPC197272
0.9574 High Similarity NPC224148
0.9574 High Similarity NPC477723
0.9574 High Similarity NPC76198
0.9574 High Similarity NPC55383
0.9574 High Similarity NPC9273
0.9574 High Similarity NPC471959
0.9574 High Similarity NPC294278
0.9574 High Similarity NPC165447
0.9574 High Similarity NPC475477
0.9565 High Similarity NPC248884
0.9565 High Similarity NPC31194
0.9565 High Similarity NPC85079
0.9556 High Similarity NPC35141
0.9556 High Similarity NPC124183
0.9362 High Similarity NPC473913
0.9362 High Similarity NPC474642
0.9362 High Similarity NPC72699
0.9362 High Similarity NPC249670
0.9167 High Similarity NPC151782
0.9149 High Similarity NPC153538
0.913 High Similarity NPC19834
0.913 High Similarity NPC55063
0.9111 High Similarity NPC101616
0.9 High Similarity NPC473532
0.9 High Similarity NPC48058
0.8913 High Similarity NPC269074
0.8824 High Similarity NPC473725
0.8824 High Similarity NPC473910
0.8824 High Similarity NPC475353
0.8824 High Similarity NPC471239
0.8824 High Similarity NPC473735
0.8824 High Similarity NPC473721
0.8824 High Similarity NPC474513
0.8824 High Similarity NPC477725
0.8824 High Similarity NPC470963
0.8824 High Similarity NPC477726
0.8824 High Similarity NPC473896
0.8824 High Similarity NPC146551
0.8776 High Similarity NPC93639
0.8667 High Similarity NPC149668
0.8654 High Similarity NPC470966
0.8654 High Similarity NPC470968
0.8654 High Similarity NPC475384
0.8654 High Similarity NPC161838
0.8654 High Similarity NPC470969
0.8654 High Similarity NPC471960
0.8654 High Similarity NPC470967
0.8654 High Similarity NPC311648
0.8654 High Similarity NPC473847
0.8654 High Similarity NPC477661
0.8654 High Similarity NPC470964
0.8627 High Similarity NPC256209
0.8627 High Similarity NPC49059
0.86 High Similarity NPC142092
0.8491 Intermediate Similarity NPC594
0.8491 Intermediate Similarity NPC48968
0.8491 Intermediate Similarity NPC470970
0.8462 Intermediate Similarity NPC152668
0.8462 Intermediate Similarity NPC474644
0.84 Intermediate Similarity NPC71053
0.84 Intermediate Similarity NPC129263
0.84 Intermediate Similarity NPC59408
0.8333 Intermediate Similarity NPC180575
0.8333 Intermediate Similarity NPC157096
0.8302 Intermediate Similarity NPC473865
0.8302 Intermediate Similarity NPC474643
0.8269 Intermediate Similarity NPC110732
0.8261 Intermediate Similarity NPC304151
0.8222 Intermediate Similarity NPC329762
0.8222 Intermediate Similarity NPC27444
0.8222 Intermediate Similarity NPC103236
0.82 Intermediate Similarity NPC291437
0.82 Intermediate Similarity NPC328784
0.8182 Intermediate Similarity NPC473652
0.8148 Intermediate Similarity NPC193975
0.8077 Intermediate Similarity NPC34577
0.8077 Intermediate Similarity NPC26102
0.8077 Intermediate Similarity NPC477724
0.8077 Intermediate Similarity NPC187361
0.8036 Intermediate Similarity NPC471278
0.8 Intermediate Similarity NPC302310
0.7917 Intermediate Similarity NPC108195
0.7895 Intermediate Similarity NPC168407
0.7895 Intermediate Similarity NPC475984
0.7818 Intermediate Similarity NPC212730
0.7818 Intermediate Similarity NPC265551
0.7759 Intermediate Similarity NPC470965
0.7736 Intermediate Similarity NPC61177
0.7692 Intermediate Similarity NPC474495
0.7692 Intermediate Similarity NPC473672
0.7609 Intermediate Similarity NPC15934
0.7586 Intermediate Similarity NPC271282
0.7586 Intermediate Similarity NPC325929
0.7586 Intermediate Similarity NPC66460
0.7556 Intermediate Similarity NPC216416
0.75 Intermediate Similarity NPC206906
0.75 Intermediate Similarity NPC473768
0.75 Intermediate Similarity NPC44542
0.7458 Intermediate Similarity NPC29697
0.74 Intermediate Similarity NPC276825
0.7333 Intermediate Similarity NPC213767
0.7308 Intermediate Similarity NPC475153
0.7258 Intermediate Similarity NPC473752
0.7193 Intermediate Similarity NPC471277
0.7193 Intermediate Similarity NPC472445
0.7193 Intermediate Similarity NPC471279
0.717 Intermediate Similarity NPC475071
0.7091 Intermediate Similarity NPC474496
0.7091 Intermediate Similarity NPC284224
0.7049 Intermediate Similarity NPC470320
0.7049 Intermediate Similarity NPC226592
0.7037 Intermediate Similarity NPC29234
0.7 Intermediate Similarity NPC477829
0.7 Intermediate Similarity NPC116934
0.6949 Remote Similarity NPC222852
0.6939 Remote Similarity NPC269823
0.6909 Remote Similarity NPC473705
0.6909 Remote Similarity NPC35756
0.6889 Remote Similarity NPC62779
0.6875 Remote Similarity NPC255042
0.6875 Remote Similarity NPC103213
0.6875 Remote Similarity NPC182840
0.6875 Remote Similarity NPC306850
0.6875 Remote Similarity NPC29091
0.6863 Remote Similarity NPC138935
0.6852 Remote Similarity NPC182102
0.6852 Remote Similarity NPC26960
0.6852 Remote Similarity NPC474460
0.6842 Remote Similarity NPC317899
0.68 Remote Similarity NPC249801
0.68 Remote Similarity NPC213538
0.68 Remote Similarity NPC46248
0.68 Remote Similarity NPC31121
0.68 Remote Similarity NPC256766
0.6792 Remote Similarity NPC471958
0.6786 Remote Similarity NPC475723
0.6786 Remote Similarity NPC217188
0.678 Remote Similarity NPC181872
0.6739 Remote Similarity NPC58957
0.6731 Remote Similarity NPC140501
0.6731 Remote Similarity NPC474202
0.6731 Remote Similarity NPC76976
0.6731 Remote Similarity NPC160628
0.6731 Remote Similarity NPC474362
0.6667 Remote Similarity NPC252978
0.6667 Remote Similarity NPC122239
0.6667 Remote Similarity NPC474267
0.6667 Remote Similarity NPC269615
0.6667 Remote Similarity NPC473866
0.6667 Remote Similarity NPC267110
0.6613 Remote Similarity NPC55068
0.661 Remote Similarity NPC474577
0.661 Remote Similarity NPC121034
0.6557 Remote Similarity NPC327112
0.6552 Remote Similarity NPC329686
0.6552 Remote Similarity NPC227135
0.6545 Remote Similarity NPC473487
0.6545 Remote Similarity NPC20934
0.6545 Remote Similarity NPC288381
0.6538 Remote Similarity NPC267514
0.6538 Remote Similarity NPC474413
0.6538 Remote Similarity NPC145755
0.6538 Remote Similarity NPC473539
0.6522 Remote Similarity NPC250734
0.65 Remote Similarity NPC226848
0.65 Remote Similarity NPC469373
0.6444 Remote Similarity NPC196831
0.6441 Remote Similarity NPC472808
0.6441 Remote Similarity NPC324224
0.6441 Remote Similarity NPC249645
0.6441 Remote Similarity NPC55412
0.6429 Remote Similarity NPC200772
0.6429 Remote Similarity NPC244038
0.6406 Remote Similarity NPC136164
0.6406 Remote Similarity NPC308844
0.6406 Remote Similarity NPC245947
0.6406 Remote Similarity NPC255863
0.6393 Remote Similarity NPC329424
0.6393 Remote Similarity NPC475931
0.6383 Remote Similarity NPC182392
0.6379 Remote Similarity NPC189677
0.6379 Remote Similarity NPC300121
0.6327 Remote Similarity NPC34873
0.6327 Remote Similarity NPC40434
0.6316 Remote Similarity NPC106531
0.629 Remote Similarity NPC471081
0.629 Remote Similarity NPC130807
0.6271 Remote Similarity NPC232247
0.6271 Remote Similarity NPC251666

  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 NPC471280 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
0.6731 Remote Similarity NPD4265 Approved
0.6613 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6557 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6441 Remote Similarity NPD4219 Approved
0.6 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5968 Remote Similarity NPD585 Clinical (unspecified phase)
0.5942 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5938 Remote Similarity NPD368 Approved
0.5789 Remote Similarity NPD4220 Pre-registration
0.5758 Remote Similarity NPD3197 Phase 1
0.5738 Remote Similarity NPD342 Phase 1
0.5735 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5641 Remote Similarity NPD5332 Approved
0.5641 Remote Similarity NPD5331 Approved
0.5616 Remote Similarity NPD8264 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