Structure

Physi-Chem Properties

Molecular Weight:  436.33
Volume:  521.288
LogP:  6.639
LogD:  4.886
LogS:  -4.05
# Rotatable Bonds:  19
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.131
Synthetic Accessibility Score:  4.192
Fsp3:  0.6
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:  -5.141
MDCK Permeability:  1.0304280294803903e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.971
20% Bioavailability (F20%):  0.997
30% Bioavailability (F30%):  0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  96.29866790771484%
Volume Distribution (VD):  0.529
Pgp-substrate:  0.4845682382583618%

ADMET: Metabolism

CYP1A2-inhibitor:  0.346
CYP1A2-substrate:  0.165
CYP2C19-inhibitor:  0.87
CYP2C19-substrate:  0.191
CYP2C9-inhibitor:  0.712
CYP2C9-substrate:  0.998
CYP2D6-inhibitor:  0.541
CYP2D6-substrate:  0.164
CYP3A4-inhibitor:  0.633
CYP3A4-substrate:  0.063

ADMET: Excretion

Clearance (CL):  2.676
Half-life (T1/2):  0.269

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.193
Drug-inuced Liver Injury (DILI):  0.045
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.683
Maximum Recommended Daily Dose:  0.999
Skin Sensitization:  0.982
Carcinogencity:  0.101
Eye Corrosion:  0.12
Eye Irritation:  0.942
Respiratory Toxicity:  0.944

Download Data

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

  Natural Product: NPC477727

Natural Product ID:  NPC477727
Common Name*:   (4E,15E,26E)-triaconta-4,15,26-trien-1,12,29-triyne-3,28-diol
IUPAC Name:   (4E,15E,26E)-triaconta-4,15,26-trien-1,12,29-triyne-3,28-diol
Synonyms:  
Standard InCHIKey:  KNPRZNJIIPJQLW-RRCZHBAJSA-N
Standard InCHI:  InChI=1S/C30H44O2/c1-3-29(31)27-25-23-21-19-17-15-13-11-9-7-5-6-8-10-12-14-16-18-20-22-24-26-28-30(32)4-2/h1-2,5-6,25-32H,7-9,11,13-24H2/b6-5+,27-25+,28-26+
SMILES:  C#CC(/C=C/CCCCCCCCC/C=C/CC#CCCCCCC/C=C/C(C#C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   44558969
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
NPO32667 Petrosia sp. Species Petrosiidae Eukaryota n.a. (15-25 m depth) off Komun Island, Korea 1995-JUL PMID[10217707]
NPO32667 Petrosia sp. Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[10346968]
NPO32667 Petrosia sp. Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[11170665]
NPO32667 Petrosia sp. Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[11754614]
NPO32667 Petrosia sp. Species Petrosiidae Eukaryota n.a. Indonesia 1996 PMID[18327911]
NPO32667 Petrosia sp. Species Petrosiidae Eukaryota n.a. Miyako sea-knoll, southwestern Japan (2525.64' N, 12542.48' E), at a depth of 415 m 2009-OCT PMID[21534590]
NPO32667 Petrosia sp. Species Petrosiidae Eukaryota n.a. American Samoa n.a. PMID[23368996]
NPO32667 Petrosia sp. Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[26821210]
NPO32667 Petrosia sp. Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[9917297]

☑ 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
NPT81 Cell Line A549 Homo sapiens ED50 = 1.4 ug/ml PMID[10217707]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 = 0.1 ug/ml PMID[10217707]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 = 0.2 ug/ml PMID[10217707]
NPT574 Cell Line XF498 Homo sapiens ED50 = 1.2 ug/ml PMID[10217707]
NPT148 Cell Line HCT-15 Homo sapiens ED50 = 1.2 ug/ml PMID[10217707]

☑ 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 NPC477727 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 NPC199286
1.0 High Similarity NPC471281
0.9787 High Similarity NPC55383
0.9787 High Similarity NPC471959
0.9787 High Similarity NPC89824
0.9787 High Similarity NPC9273
0.9787 High Similarity NPC165447
0.9787 High Similarity NPC224148
0.9787 High Similarity NPC256656
0.9787 High Similarity NPC76198
0.9787 High Similarity NPC197272
0.9787 High Similarity NPC475477
0.9787 High Similarity NPC329608
0.9787 High Similarity NPC294278
0.9787 High Similarity NPC477723
0.9787 High Similarity NPC170776
0.9783 High Similarity NPC471280
0.9783 High Similarity NPC471275
0.9783 High Similarity NPC125122
0.9783 High Similarity NPC471276
0.9574 High Similarity NPC249670
0.9574 High Similarity NPC474642
0.9574 High Similarity NPC473913
0.9362 High Similarity NPC248884
0.9362 High Similarity NPC31194
0.9362 High Similarity NPC85079
0.9348 High Similarity NPC124183
0.9348 High Similarity NPC35141
0.92 High Similarity NPC473532
0.92 High Similarity NPC48058
0.9167 High Similarity NPC72699
0.902 High Similarity NPC477726
0.902 High Similarity NPC473910
0.902 High Similarity NPC473721
0.902 High Similarity NPC477725
0.902 High Similarity NPC473896
0.902 High Similarity NPC473735
0.902 High Similarity NPC474513
0.902 High Similarity NPC470963
0.902 High Similarity NPC475353
0.902 High Similarity NPC146551
0.902 High Similarity NPC473725
0.898 High Similarity NPC151782
0.8958 High Similarity NPC153538
0.8936 High Similarity NPC55063
0.8936 High Similarity NPC19834
0.8913 High Similarity NPC101616
0.8846 High Similarity NPC473847
0.8846 High Similarity NPC477661
0.8846 High Similarity NPC311648
0.8846 High Similarity NPC470964
0.8846 High Similarity NPC475384
0.8846 High Similarity NPC161838
0.8846 High Similarity NPC470966
0.8846 High Similarity NPC471960
0.8846 High Similarity NPC470969
0.8846 High Similarity NPC470968
0.8846 High Similarity NPC470967
0.8723 High Similarity NPC269074
0.8679 High Similarity NPC470970
0.8679 High Similarity NPC594
0.8679 High Similarity NPC48968
0.8654 High Similarity NPC474644
0.8654 High Similarity NPC471239
0.8654 High Similarity NPC152668
0.86 High Similarity NPC93639
0.8491 Intermediate Similarity NPC474643
0.8491 Intermediate Similarity NPC473865
0.8478 Intermediate Similarity NPC149668
0.8462 Intermediate Similarity NPC256209
0.8462 Intermediate Similarity NPC49059
0.8431 Intermediate Similarity NPC142092
0.8364 Intermediate Similarity NPC473652
0.8269 Intermediate Similarity NPC26102
0.8269 Intermediate Similarity NPC477724
0.8269 Intermediate Similarity NPC187361
0.8235 Intermediate Similarity NPC59408
0.8235 Intermediate Similarity NPC129263
0.8235 Intermediate Similarity NPC71053
0.8214 Intermediate Similarity NPC471278
0.8163 Intermediate Similarity NPC180575
0.8163 Intermediate Similarity NPC157096
0.8113 Intermediate Similarity NPC110732
0.8085 Intermediate Similarity NPC304151
0.807 Intermediate Similarity NPC168407
0.807 Intermediate Similarity NPC475984
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
0.8 Intermediate Similarity NPC193975
0.7931 Intermediate Similarity NPC470965
0.7925 Intermediate Similarity NPC34577
0.7885 Intermediate Similarity NPC474495
0.7885 Intermediate Similarity NPC473672
0.7843 Intermediate Similarity NPC302310
0.7755 Intermediate Similarity NPC108195
0.7679 Intermediate Similarity NPC265551
0.7679 Intermediate Similarity NPC212730
0.7593 Intermediate Similarity NPC61177
0.7458 Intermediate Similarity NPC271282
0.7458 Intermediate Similarity NPC325929
0.7458 Intermediate Similarity NPC66460
0.7447 Intermediate Similarity NPC15934
0.7419 Intermediate Similarity NPC473752
0.7391 Intermediate Similarity NPC216416
0.7368 Intermediate Similarity NPC44542
0.7368 Intermediate Similarity NPC471279
0.7368 Intermediate Similarity NPC471277
0.7358 Intermediate Similarity NPC473768
0.7347 Intermediate Similarity NPC206906
0.7333 Intermediate Similarity NPC29697
0.7273 Intermediate Similarity NPC474496
0.7255 Intermediate Similarity NPC276825
0.72 Intermediate Similarity NPC116934
0.7174 Intermediate Similarity NPC213767
0.717 Intermediate Similarity NPC475153
0.7143 Intermediate Similarity NPC269823
0.7069 Intermediate Similarity NPC472445
0.7059 Intermediate Similarity NPC138935
0.7037 Intermediate Similarity NPC474460
0.7037 Intermediate Similarity NPC475071
0.7037 Intermediate Similarity NPC182102
0.7037 Intermediate Similarity NPC26960
0.7 Intermediate Similarity NPC213538
0.7 Intermediate Similarity NPC256766
0.6981 Remote Similarity NPC471958
0.6964 Remote Similarity NPC284224
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
0.6923 Remote Similarity NPC76976
0.6909 Remote Similarity NPC29234
0.6885 Remote Similarity NPC477829
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
0.6735 Remote Similarity NPC103213
0.6735 Remote Similarity NPC255042
0.6735 Remote Similarity NPC182840
0.6735 Remote Similarity NPC29091
0.6735 Remote Similarity NPC306850
0.6724 Remote Similarity NPC329686
0.6724 Remote Similarity NPC317899
0.6721 Remote Similarity NPC327112
0.6667 Remote Similarity NPC249801
0.6667 Remote Similarity NPC217188
0.6667 Remote Similarity NPC475723
0.6667 Remote Similarity NPC46248
0.6667 Remote Similarity NPC226848
0.6667 Remote Similarity NPC31121
0.6604 Remote Similarity NPC474202
0.6604 Remote Similarity NPC474362
0.6596 Remote Similarity NPC58957
0.6596 Remote Similarity NPC182392
0.6562 Remote Similarity NPC255863
0.6562 Remote Similarity NPC136164
0.6562 Remote Similarity NPC308844
0.6562 Remote Similarity NPC245947
0.6557 Remote Similarity NPC329424
0.6557 Remote Similarity NPC473866
0.6557 Remote Similarity NPC474267
0.6557 Remote Similarity NPC475931
0.6552 Remote Similarity NPC269615
0.6545 Remote Similarity NPC267110
0.6538 Remote Similarity NPC252978
0.65 Remote Similarity NPC474577
0.65 Remote Similarity NPC121034
0.6452 Remote Similarity NPC130807
0.6452 Remote Similarity NPC471081
0.6441 Remote Similarity NPC227135
0.6429 Remote Similarity NPC288381
0.6429 Remote Similarity NPC20934
0.6429 Remote Similarity NPC473487
0.6415 Remote Similarity NPC145755
0.6415 Remote Similarity NPC267514
0.6415 Remote Similarity NPC473539
0.6415 Remote Similarity NPC474413
0.6393 Remote Similarity NPC469373
0.6383 Remote Similarity NPC250734
0.6364 Remote Similarity NPC26500
0.6364 Remote Similarity NPC99619
0.6333 Remote Similarity NPC249645
0.6333 Remote Similarity NPC324224
0.6333 Remote Similarity NPC55412
0.6333 Remote Similarity NPC472808
0.6316 Remote Similarity NPC200772
0.6316 Remote Similarity NPC244038
0.6304 Remote Similarity NPC196831
0.629 Remote Similarity NPC322002
0.629 Remote Similarity NPC322186
0.6271 Remote Similarity NPC189677
0.6271 Remote Similarity NPC300121
0.623 Remote Similarity NPC11130

  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 NPC477727 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)
0.6333 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)
0.5882 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
0.5645 Remote Similarity NPD342 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