Structure

Physi-Chem Properties

Molecular Weight:  652.52
Volume:  787.478
LogP:  11.397
LogD:  5.861
LogS:  -3.767
# Rotatable Bonds:  30
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.046
Synthetic Accessibility Score:  4.518
Fsp3:  0.609
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.2
MDCK Permeability:  6.283899438130902e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.884
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.0
Plasma Protein Binding (PPB):  106.32831573486328%
Volume Distribution (VD):  3.174
Pgp-substrate:  0.23619425296783447%

ADMET: Metabolism

CYP1A2-inhibitor:  0.101
CYP1A2-substrate:  0.112
CYP2C19-inhibitor:  0.655
CYP2C19-substrate:  0.056
CYP2C9-inhibitor:  0.188
CYP2C9-substrate:  1.0
CYP2D6-inhibitor:  0.132
CYP2D6-substrate:  0.059
CYP3A4-inhibitor:  0.727
CYP3A4-substrate:  0.032

ADMET: Excretion

Clearance (CL):  1.933
Half-life (T1/2):  0.073

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.469
Drug-inuced Liver Injury (DILI):  0.955
AMES Toxicity:  0.06
Rat Oral Acute Toxicity:  0.635
Maximum Recommended Daily Dose:  1.0
Skin Sensitization:  0.991
Carcinogencity:  0.154
Eye Corrosion:  0.977
Eye Irritation:  0.931
Respiratory Toxicity:  0.996

Download Data

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

  Natural Product: NPC329608

Natural Product ID:  NPC329608
Common Name*:   petrotetrayndiol A
IUPAC Name:   (3S,4E,14S,17E,21E,27E,43Z)-hexatetraconta-4,17,21,27,43-pentaen-1,12,15,45-tetrayne-3,14-diol
Synonyms:  
Standard InCHIKey:  SIVHBQCTWBWNEN-XVNKNYJPSA-N
Standard InCHI:  InChI=1S/C46H68O2/c1-3-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27-28-29-30-34-37-40-43-46(48)44-41-38-35-32-31-33-36-39-42-45(47)4-2/h1-2,5-6,21-22,27-28,34,37,39,42,45-48H,7-20,23-26,29-33,35-36,38H2/b6-5-,22-21+,28-27+,37-34+,42-39+/t45-,46-/m1/s1
SMILES:  C#C/C=C\CCCCCCCCCCCCCC/C=C/CCCC/C=C/CC/C=C/C#C[C@H](C#CCCCCCC/C=C/[C@@H](C#C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   44559095
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 = 1.6 ug/ml PMID[10217707]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 = 0.5 ug/ml PMID[10217707]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 = 0.9 ug/ml PMID[10217707]
NPT574 Cell Line XF498 Homo sapiens ED50 = 1.7 ug/ml PMID[10217707]
NPT148 Cell Line HCT-15 Homo sapiens ED50 = 1 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 NPC329608 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 NPC475477
1.0 High Similarity NPC165447
1.0 High Similarity NPC9273
1.0 High Similarity NPC89824
1.0 High Similarity NPC477723
1.0 High Similarity NPC471959
1.0 High Similarity NPC197272
1.0 High Similarity NPC76198
1.0 High Similarity NPC224148
1.0 High Similarity NPC170776
1.0 High Similarity NPC294278
1.0 High Similarity NPC256656
0.9787 High Similarity NPC471281
0.9787 High Similarity NPC199286
0.9787 High Similarity NPC477727
0.9583 High Similarity NPC55383
0.9574 High Similarity NPC471280
0.9574 High Similarity NPC125122
0.9574 High Similarity NPC471276
0.9574 High Similarity NPC471275
0.94 High Similarity NPC473532
0.94 High Similarity NPC48058
0.9375 High Similarity NPC473913
0.9375 High Similarity NPC474642
0.9375 High Similarity NPC249670
0.9216 High Similarity NPC473735
0.9216 High Similarity NPC473725
0.9216 High Similarity NPC473721
0.9216 High Similarity NPC473896
0.9216 High Similarity NPC473910
0.9216 High Similarity NPC475353
0.9167 High Similarity NPC85079
0.9167 High Similarity NPC248884
0.9167 High Similarity NPC31194
0.9149 High Similarity NPC35141
0.9149 High Similarity NPC124183
0.9038 High Similarity NPC473847
0.9038 High Similarity NPC161838
0.9038 High Similarity NPC470966
0.9038 High Similarity NPC470964
0.9038 High Similarity NPC471960
0.9038 High Similarity NPC470969
0.9038 High Similarity NPC470967
0.9038 High Similarity NPC475384
0.9038 High Similarity NPC470968
0.9038 High Similarity NPC477661
0.9038 High Similarity NPC311648
0.898 High Similarity NPC72699
0.8868 High Similarity NPC470970
0.8868 High Similarity NPC48968
0.8868 High Similarity NPC594
0.8846 High Similarity NPC474513
0.8846 High Similarity NPC146551
0.8846 High Similarity NPC470963
0.8846 High Similarity NPC477726
0.8846 High Similarity NPC152668
0.8846 High Similarity NPC477725
0.88 High Similarity NPC151782
0.8776 High Similarity NPC153538
0.875 High Similarity NPC19834
0.875 High Similarity NPC55063
0.8723 High Similarity NPC101616
0.8545 High Similarity NPC473652
0.8542 High Similarity NPC269074
0.8491 Intermediate Similarity NPC474644
0.8491 Intermediate Similarity NPC471239
0.8462 Intermediate Similarity NPC187361
0.8462 Intermediate Similarity NPC477724
0.8462 Intermediate Similarity NPC26102
0.8431 Intermediate Similarity NPC93639
0.8333 Intermediate Similarity NPC474643
0.8333 Intermediate Similarity NPC473865
0.8302 Intermediate Similarity NPC256209
0.8302 Intermediate Similarity NPC49059
0.8298 Intermediate Similarity NPC149668
0.8269 Intermediate Similarity NPC142092
0.8246 Intermediate Similarity NPC168407
0.8103 Intermediate Similarity NPC470965
0.8077 Intermediate Similarity NPC129263
0.8077 Intermediate Similarity NPC71053
0.8077 Intermediate Similarity NPC59408
0.807 Intermediate Similarity NPC471278
0.8 Intermediate Similarity NPC180575
0.8 Intermediate Similarity NPC157096
0.7963 Intermediate Similarity NPC110732
0.7931 Intermediate Similarity NPC475984
0.7917 Intermediate Similarity NPC304151
0.7885 Intermediate Similarity NPC328784
0.7885 Intermediate Similarity NPC291437
0.7872 Intermediate Similarity NPC329762
0.7872 Intermediate Similarity NPC27444
0.7872 Intermediate Similarity NPC103236
0.7857 Intermediate Similarity NPC193975
0.7778 Intermediate Similarity NPC34577
0.7736 Intermediate Similarity NPC473672
0.7736 Intermediate Similarity NPC474495
0.7692 Intermediate Similarity NPC302310
0.76 Intermediate Similarity NPC108195
0.7581 Intermediate Similarity NPC473752
0.7544 Intermediate Similarity NPC265551
0.7544 Intermediate Similarity NPC212730
0.7455 Intermediate Similarity NPC61177
0.7333 Intermediate Similarity NPC271282
0.7333 Intermediate Similarity NPC325929
0.7333 Intermediate Similarity NPC66460
0.7292 Intermediate Similarity NPC15934
0.7241 Intermediate Similarity NPC471277
0.7241 Intermediate Similarity NPC471279
0.7241 Intermediate Similarity NPC44542
0.7234 Intermediate Similarity NPC216416
0.7222 Intermediate Similarity NPC473768
0.7213 Intermediate Similarity NPC29697
0.72 Intermediate Similarity NPC206906
0.72 Intermediate Similarity NPC213538
0.72 Intermediate Similarity NPC256766
0.717 Intermediate Similarity NPC471958
0.7143 Intermediate Similarity NPC474496
0.7115 Intermediate Similarity NPC276825
0.7059 Intermediate Similarity NPC116934
0.7037 Intermediate Similarity NPC475153
0.7021 Intermediate Similarity NPC213767
0.7 Intermediate Similarity NPC269823
0.6949 Remote Similarity NPC472445
0.6923 Remote Similarity NPC138935
0.6909 Remote Similarity NPC475071
0.6909 Remote Similarity NPC182102
0.6909 Remote Similarity NPC26960
0.6909 Remote Similarity NPC474460
0.6842 Remote Similarity NPC284224
0.6833 Remote Similarity NPC181872
0.6825 Remote Similarity NPC226592
0.6825 Remote Similarity NPC470320
0.6792 Remote Similarity NPC76976
0.6792 Remote Similarity NPC160628
0.6792 Remote Similarity NPC140501
0.6786 Remote Similarity NPC29234
0.6774 Remote Similarity NPC477829
0.6721 Remote Similarity NPC222852
0.6721 Remote Similarity NPC122239
0.6667 Remote Similarity NPC55068
0.6667 Remote Similarity NPC35756
0.6667 Remote Similarity NPC473705
0.6613 Remote Similarity NPC327112
0.661 Remote Similarity NPC329686
0.661 Remote Similarity NPC317899
0.66 Remote Similarity NPC182840
0.66 Remote Similarity NPC103213
0.66 Remote Similarity NPC29091
0.66 Remote Similarity NPC255042
0.66 Remote Similarity NPC306850
0.6596 Remote Similarity NPC62779
0.6557 Remote Similarity NPC226848
0.6552 Remote Similarity NPC475723
0.6552 Remote Similarity NPC217188
0.6538 Remote Similarity NPC249801
0.6538 Remote Similarity NPC31121
0.6538 Remote Similarity NPC46248
0.6481 Remote Similarity NPC474362
0.6481 Remote Similarity NPC474202
0.6462 Remote Similarity NPC245947
0.6462 Remote Similarity NPC255863
0.6462 Remote Similarity NPC136164
0.6462 Remote Similarity NPC308844
0.6458 Remote Similarity NPC58957
0.6458 Remote Similarity NPC182392
0.6452 Remote Similarity NPC329424
0.6452 Remote Similarity NPC473866
0.6452 Remote Similarity NPC475931
0.6452 Remote Similarity NPC474267
0.6441 Remote Similarity NPC269615
0.6429 Remote Similarity NPC267110
0.6415 Remote Similarity NPC252978
0.6393 Remote Similarity NPC474577
0.6393 Remote Similarity NPC121034
0.6349 Remote Similarity NPC471081
0.6349 Remote Similarity NPC130807
0.6333 Remote Similarity NPC227135
0.6324 Remote Similarity NPC103712
0.6324 Remote Similarity NPC291196
0.6316 Remote Similarity NPC20934
0.6316 Remote Similarity NPC288381
0.6316 Remote Similarity NPC473487
0.6296 Remote Similarity NPC267514
0.6296 Remote Similarity NPC145755
0.6296 Remote Similarity NPC474413
0.6296 Remote Similarity NPC473539
0.629 Remote Similarity NPC469373
0.6269 Remote Similarity NPC26500
0.6269 Remote Similarity NPC99619
0.625 Remote Similarity NPC250734
0.623 Remote Similarity NPC55412
0.623 Remote Similarity NPC472808
0.623 Remote Similarity NPC249645
0.623 Remote Similarity NPC324224
0.6207 Remote Similarity NPC200772
0.6207 Remote Similarity NPC244038
0.619 Remote Similarity NPC322186
0.619 Remote Similarity NPC322002
0.617 Remote Similarity NPC196831
0.6167 Remote Similarity NPC300121

  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 NPC329608 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
0.6792 Remote Similarity NPD4265 Approved
0.6667 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6613 Remote Similarity NPD4246 Clinical (unspecified phase)
0.623 Remote Similarity NPD4219 Approved
0.6 Remote Similarity NPD3212 Clinical (unspecified phase)
0.589 Remote Similarity NPD8264 Approved
0.5821 Remote Similarity NPD3197 Phase 1
0.5806 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5797 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5781 Remote Similarity NPD585 Clinical (unspecified phase)
0.5758 Remote Similarity NPD368 Approved
0.5696 Remote Similarity NPD5332 Approved
0.5696 Remote Similarity NPD5331 Approved
0.5614 Remote Similarity NPD39 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