Structure

Physi-Chem Properties

Molecular Weight:  266.19
Volume:  301.117
LogP:  3.838
LogD:  2.957
LogS:  -3.33
# Rotatable Bonds:  9
TPSA:  49.69
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.383
Synthetic Accessibility Score:  3.714
Fsp3:  0.625
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.25
MDCK Permeability:  0.00011193181126145646
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.887
Plasma Protein Binding (PPB):  97.21939849853516%
Volume Distribution (VD):  1.041
Pgp-substrate:  2.76460599899292%

ADMET: Metabolism

CYP1A2-inhibitor:  0.949
CYP1A2-substrate:  0.139
CYP2C19-inhibitor:  0.947
CYP2C19-substrate:  0.596
CYP2C9-inhibitor:  0.836
CYP2C9-substrate:  0.035
CYP2D6-inhibitor:  0.208
CYP2D6-substrate:  0.043
CYP3A4-inhibitor:  0.917
CYP3A4-substrate:  0.271

ADMET: Excretion

Clearance (CL):  11.64
Half-life (T1/2):  0.736

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.849
Drug-inuced Liver Injury (DILI):  0.924
AMES Toxicity:  0.706
Rat Oral Acute Toxicity:  0.206
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.919
Carcinogencity:  0.928
Eye Corrosion:  0.037
Eye Irritation:  0.829
Respiratory Toxicity:  0.73

Download Data

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

  Natural Product: NPC121034

Natural Product ID:  NPC121034
Common Name*:   Petroraspailyne A2
IUPAC Name:   (2S)-3-[(1Z,5Z)-11-methyldodeca-1,5-dien-3-ynoxy]propane-1,2-diol
Synonyms:   Petroraspailyne A2
Standard InCHIKey:  MACMPNKFCAKIDK-NMMJBCQNSA-N
Standard InCHI:  InChI=1S/C16H26O3/c1-15(2)11-9-7-5-3-4-6-8-10-12-19-14-16(18)13-17/h3-4,10,12,15-18H,5,7,9,11,13-14H2,1-2H3/b4-3-,12-10-/t16-/m0/s1
SMILES:  OC[C@@H](CO/C=CC#C/C=CCCCCC(C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL453792
PubChem CID:   10038569
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000175] Glycerolipids
        • [CHEMONTID:0003264] Glycerol vinyl ethers

*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
NPT111 Cell Line K562 Homo sapiens LC50 = 57.0 ug.mL-1 PMID[464550]

☑ 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 NPC121034 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
0.9636 High Similarity NPC473866
0.8868 High Similarity NPC29234
0.8364 Intermediate Similarity NPC295765
0.8214 Intermediate Similarity NPC475560
0.7544 Intermediate Similarity NPC93639
0.7455 Intermediate Similarity NPC157096
0.7377 Intermediate Similarity NPC52012
0.7333 Intermediate Similarity NPC227135
0.7333 Intermediate Similarity NPC474644
0.7333 Intermediate Similarity NPC281590
0.7313 Intermediate Similarity NPC273508
0.7313 Intermediate Similarity NPC209327
0.7273 Intermediate Similarity NPC201948
0.7258 Intermediate Similarity NPC181872
0.7213 Intermediate Similarity NPC474643
0.7213 Intermediate Similarity NPC473865
0.7193 Intermediate Similarity NPC302310
0.7193 Intermediate Similarity NPC153538
0.7188 Intermediate Similarity NPC64971
0.7083 Intermediate Similarity NPC470899
0.7069 Intermediate Similarity NPC72699
0.7069 Intermediate Similarity NPC473768
0.7031 Intermediate Similarity NPC469694
0.7 Intermediate Similarity NPC477983
0.7 Intermediate Similarity NPC477981
0.6949 Remote Similarity NPC151782
0.6949 Remote Similarity NPC59408
0.6949 Remote Similarity NPC71053
0.6912 Remote Similarity NPC473357
0.6912 Remote Similarity NPC193029
0.6897 Remote Similarity NPC85079
0.6897 Remote Similarity NPC31194
0.6897 Remote Similarity NPC248884
0.6875 Remote Similarity NPC278202
0.6875 Remote Similarity NPC475931
0.6842 Remote Similarity NPC124183
0.6842 Remote Similarity NPC55063
0.6842 Remote Similarity NPC35141
0.6842 Remote Similarity NPC19834
0.6833 Remote Similarity NPC142092
0.6786 Remote Similarity NPC101616
0.6786 Remote Similarity NPC108195
0.6774 Remote Similarity NPC329686
0.6769 Remote Similarity NPC258788
0.6765 Remote Similarity NPC250977
0.6727 Remote Similarity NPC31121
0.6714 Remote Similarity NPC472947
0.6667 Remote Similarity NPC276825
0.6667 Remote Similarity NPC476709
0.6615 Remote Similarity NPC122239
0.6613 Remote Similarity NPC110732
0.6613 Remote Similarity NPC256209
0.6613 Remote Similarity NPC49059
0.661 Remote Similarity NPC471275
0.661 Remote Similarity NPC125122
0.661 Remote Similarity NPC471276
0.661 Remote Similarity NPC475153
0.661 Remote Similarity NPC471280
0.6575 Remote Similarity NPC471525
0.6571 Remote Similarity NPC477980
0.6562 Remote Similarity NPC474577
0.6557 Remote Similarity NPC35756
0.6522 Remote Similarity NPC267027
0.6522 Remote Similarity NPC477982
0.6515 Remote Similarity NPC321919
0.6515 Remote Similarity NPC81896
0.65 Remote Similarity NPC26960
0.65 Remote Similarity NPC249670
0.65 Remote Similarity NPC291437
0.65 Remote Similarity NPC199286
0.65 Remote Similarity NPC471281
0.65 Remote Similarity NPC328784
0.65 Remote Similarity NPC474642
0.65 Remote Similarity NPC474460
0.65 Remote Similarity NPC288381
0.65 Remote Similarity NPC477727
0.65 Remote Similarity NPC20934
0.65 Remote Similarity NPC182102
0.65 Remote Similarity NPC473913
0.6494 Remote Similarity NPC200446
0.6479 Remote Similarity NPC16964
0.6471 Remote Similarity NPC476658
0.6462 Remote Similarity NPC155025
0.6462 Remote Similarity NPC226848
0.6452 Remote Similarity NPC284224
0.6452 Remote Similarity NPC474496
0.6452 Remote Similarity NPC26102
0.6452 Remote Similarity NPC477724
0.6452 Remote Similarity NPC187361
0.6447 Remote Similarity NPC218817
0.6447 Remote Similarity NPC469495
0.6447 Remote Similarity NPC11796
0.6429 Remote Similarity NPC149668
0.6393 Remote Similarity NPC165447
0.6393 Remote Similarity NPC224148
0.6393 Remote Similarity NPC76198
0.6393 Remote Similarity NPC9273
0.6393 Remote Similarity NPC471959
0.6393 Remote Similarity NPC475477
0.6393 Remote Similarity NPC329608
0.6393 Remote Similarity NPC294278
0.6393 Remote Similarity NPC55383
0.6393 Remote Similarity NPC477723
0.6393 Remote Similarity NPC197272
0.6393 Remote Similarity NPC474495
0.6393 Remote Similarity NPC473672
0.6393 Remote Similarity NPC170776
0.6393 Remote Similarity NPC256656
0.6393 Remote Similarity NPC89824
0.6389 Remote Similarity NPC473361
0.6389 Remote Similarity NPC329904
0.6389 Remote Similarity NPC189745
0.6389 Remote Similarity NPC129630
0.6379 Remote Similarity NPC269074
0.6379 Remote Similarity NPC24824
0.6379 Remote Similarity NPC165651
0.6379 Remote Similarity NPC210560
0.6377 Remote Similarity NPC308844
0.6377 Remote Similarity NPC176215
0.6377 Remote Similarity NPC476654
0.6377 Remote Similarity NPC473722
0.6377 Remote Similarity NPC476657
0.6377 Remote Similarity NPC471200
0.6377 Remote Similarity NPC476655
0.6377 Remote Similarity NPC296436
0.6364 Remote Similarity NPC329762
0.6364 Remote Similarity NPC222852
0.6364 Remote Similarity NPC103236
0.6364 Remote Similarity NPC27444
0.6364 Remote Similarity NPC209995
0.6351 Remote Similarity NPC190859
0.6351 Remote Similarity NPC104644
0.6351 Remote Similarity NPC107654
0.6349 Remote Similarity NPC473532
0.6338 Remote Similarity NPC272961
0.6316 Remote Similarity NPC476703
0.6308 Remote Similarity NPC193975
0.6308 Remote Similarity NPC44542
0.6308 Remote Similarity NPC265551
0.6308 Remote Similarity NPC212730
0.6286 Remote Similarity NPC272125
0.6286 Remote Similarity NPC137163
0.6286 Remote Similarity NPC326310
0.6286 Remote Similarity NPC476659
0.6286 Remote Similarity NPC311736
0.6286 Remote Similarity NPC476656
0.6286 Remote Similarity NPC83965
0.6271 Remote Similarity NPC180575
0.6269 Remote Similarity NPC471081
0.6269 Remote Similarity NPC99487
0.625 Remote Similarity NPC329989
0.625 Remote Similarity NPC473910
0.625 Remote Similarity NPC475353
0.625 Remote Similarity NPC477726
0.625 Remote Similarity NPC473735
0.625 Remote Similarity NPC473896
0.625 Remote Similarity NPC239373
0.625 Remote Similarity NPC477725
0.625 Remote Similarity NPC232247
0.625 Remote Similarity NPC473721
0.625 Remote Similarity NPC473725
0.625 Remote Similarity NPC251666
0.6234 Remote Similarity NPC477089
0.6232 Remote Similarity NPC475221
0.6232 Remote Similarity NPC300593
0.623 Remote Similarity NPC329773
0.6212 Remote Similarity NPC41180
0.6212 Remote Similarity NPC329819
0.6212 Remote Similarity NPC152438
0.6197 Remote Similarity NPC104537
0.6197 Remote Similarity NPC127091
0.6197 Remote Similarity NPC472253
0.6197 Remote Similarity NPC73603
0.6197 Remote Similarity NPC148192
0.6197 Remote Similarity NPC22101
0.6197 Remote Similarity NPC271921
0.6197 Remote Similarity NPC472255
0.6197 Remote Similarity NPC259299
0.6197 Remote Similarity NPC330426
0.6197 Remote Similarity NPC163290
0.619 Remote Similarity NPC217188
0.619 Remote Similarity NPC61177
0.6184 Remote Similarity NPC236228
0.6184 Remote Similarity NPC256720
0.6184 Remote Similarity NPC170148
0.6176 Remote Similarity NPC68679
0.6176 Remote Similarity NPC55376
0.6176 Remote Similarity NPC225342
0.6176 Remote Similarity NPC475251
0.6176 Remote Similarity NPC274704
0.6176 Remote Similarity NPC321867
0.6176 Remote Similarity NPC207007
0.6154 Remote Similarity NPC470967
0.6154 Remote Similarity NPC161838
0.6154 Remote Similarity NPC477661
0.6154 Remote Similarity NPC473847
0.6154 Remote Similarity NPC471960
0.6154 Remote Similarity NPC470969
0.6154 Remote Similarity NPC470966
0.6154 Remote Similarity NPC475384

  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 NPC121034 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
0.6212 Remote Similarity NPD585 Clinical (unspecified phase)
0.6176 Remote Similarity NPD368 Approved
0.597 Remote Similarity NPD6109 Phase 1
0.5909 Remote Similarity NPD4219 Approved
0.5854 Remote Similarity NPD7154 Phase 3
0.5833 Remote Similarity NPD4265 Approved
0.5775 Remote Similarity NPD3197 Phase 1
0.5769 Remote Similarity NPD6933 Approved
0.5758 Remote Similarity NPD342 Phase 1
0.575 Remote Similarity NPD6683 Phase 2
0.5733 Remote Similarity NPD7144 Approved
0.5733 Remote Similarity NPD7143 Approved
0.5696 Remote Similarity NPD6932 Approved
0.5663 Remote Similarity NPD6110 Phase 1
0.5658 Remote Similarity NPD7151 Approved
0.5658 Remote Similarity NPD7150 Approved
0.5658 Remote Similarity NPD7152 Approved
0.5641 Remote Similarity NPD8264 Approved
0.5634 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5625 Remote Similarity NPD7145 Approved
0.561 Remote Similarity NPD6898 Phase 1
0.56 Remote Similarity NPD6922 Approved
0.56 Remote Similarity NPD6923 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