Structure

Physi-Chem Properties

Molecular Weight:  280.12
Volume:  302.265
LogP:  3.474
LogD:  2.868
LogS:  -4.035
# Rotatable Bonds:  9
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.291
Synthetic Accessibility Score:  4.437
Fsp3:  0.438
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -3.973
MDCK Permeability:  4.421899939188734e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.699
Plasma Protein Binding (PPB):  92.0777816772461%
Volume Distribution (VD):  1.326
Pgp-substrate:  3.794499397277832%

ADMET: Metabolism

CYP1A2-inhibitor:  0.492
CYP1A2-substrate:  0.138
CYP2C19-inhibitor:  0.697
CYP2C19-substrate:  0.804
CYP2C9-inhibitor:  0.225
CYP2C9-substrate:  0.082
CYP2D6-inhibitor:  0.744
CYP2D6-substrate:  0.285
CYP3A4-inhibitor:  0.906
CYP3A4-substrate:  0.292

ADMET: Excretion

Clearance (CL):  7.783
Half-life (T1/2):  0.572

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.76
Drug-inuced Liver Injury (DILI):  0.859
AMES Toxicity:  0.595
Rat Oral Acute Toxicity:  0.277
Maximum Recommended Daily Dose:  0.817
Skin Sensitization:  0.892
Carcinogencity:  0.781
Eye Corrosion:  0.454
Eye Irritation:  0.865
Respiratory Toxicity:  0.938

Download Data

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

  Natural Product: NPC477424

Natural Product ID:  NPC477424
Common Name*:   [(3Z,9Z,11E)-6-chlorotetradeca-3,9,11-trien-1-yn-7-yl] acetate
IUPAC Name:   [(3Z,9Z,11E)-6-chlorotetradeca-3,9,11-trien-1-yn-7-yl] acetate
Synonyms:  
Standard InCHIKey:  GJNIZHUDNBTUTM-FLZUSWORSA-N
Standard InCHI:  InChI=1S/C16H21ClO2/c1-4-6-8-9-11-13-16(19-14(3)18)15(17)12-10-7-5-2/h2,6-11,15-16H,4,12-13H2,1,3H3/b8-6+,10-7-,11-9-
SMILES:  CC/C=C/C=C\CC(C(C/C=C\C#C)Cl)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   45270506
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001093] Carboxylic acid derivatives
          • [CHEMONTID:0001238] Carboxylic acid esters

*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
NPO26797 Laurencia glandulifera Species Rhodomelaceae Eukaryota n.a. the island of Crete in the south Aegean Sea n.a. PMID[19138151]
NPO26797 Laurencia glandulifera Species Rhodomelaceae 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
NPT139 Cell Line HT-29 Homo sapiens IC50 >= 10000 nM PMID[19138151]
NPT83 Cell Line MCF7 Homo sapiens IC50 >= 10000 nM PMID[19138151]
NPT306 Cell Line PC-3 Homo sapiens IC50 >= 10000 nM PMID[19138151]
NPT165 Cell Line HeLa Homo sapiens IC50 >= 10000 nM PMID[19138151]
NPT762 Cell Line A-431 Homo sapiens IC50 >= 10000 nM PMID[19138151]

☑ 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 NPC477424 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
0.7606 Intermediate Similarity NPC477421
0.7581 Intermediate Similarity NPC26310
0.7302 Intermediate Similarity NPC44542
0.7286 Intermediate Similarity NPC323677
0.7286 Intermediate Similarity NPC477429
0.7258 Intermediate Similarity NPC474913
0.7077 Intermediate Similarity NPC222852
0.7049 Intermediate Similarity NPC106531
0.7031 Intermediate Similarity NPC472445
0.6825 Remote Similarity NPC269615
0.6769 Remote Similarity NPC471279
0.6769 Remote Similarity NPC471277
0.6716 Remote Similarity NPC477430
0.6667 Remote Similarity NPC469373
0.662 Remote Similarity NPC225272
0.6615 Remote Similarity NPC327388
0.6575 Remote Similarity NPC477423
0.6567 Remote Similarity NPC474267
0.6557 Remote Similarity NPC207815
0.6533 Remote Similarity NPC77724
0.6515 Remote Similarity NPC323498
0.6515 Remote Similarity NPC323597
0.6515 Remote Similarity NPC212730
0.6515 Remote Similarity NPC265551
0.6515 Remote Similarity NPC211752
0.6486 Remote Similarity NPC473306
0.6471 Remote Similarity NPC299730
0.6471 Remote Similarity NPC471278
0.6377 Remote Similarity NPC325929
0.6377 Remote Similarity NPC66460
0.6377 Remote Similarity NPC271282
0.6349 Remote Similarity NPC178586
0.6324 Remote Similarity NPC329249
0.6324 Remote Similarity NPC478095
0.6316 Remote Similarity NPC123357
0.6316 Remote Similarity NPC477422
0.6308 Remote Similarity NPC137538
0.629 Remote Similarity NPC163345
0.629 Remote Similarity NPC302310
0.6286 Remote Similarity NPC44343
0.6286 Remote Similarity NPC179087
0.6286 Remote Similarity NPC210303
0.6286 Remote Similarity NPC29697
0.625 Remote Similarity NPC146811
0.625 Remote Similarity NPC226511
0.6234 Remote Similarity NPC52781
0.6232 Remote Similarity NPC26223
0.6212 Remote Similarity NPC152668
0.6212 Remote Similarity NPC474513
0.6212 Remote Similarity NPC470963
0.6212 Remote Similarity NPC52264
0.6212 Remote Similarity NPC146551
0.6197 Remote Similarity NPC476658
0.6176 Remote Similarity NPC478096
0.6154 Remote Similarity NPC284224
0.6145 Remote Similarity NPC475732
0.6145 Remote Similarity NPC30915
0.6143 Remote Similarity NPC328776
0.6143 Remote Similarity NPC320305
0.6125 Remote Similarity NPC473947
0.6119 Remote Similarity NPC324224
0.6119 Remote Similarity NPC311648
0.6119 Remote Similarity NPC470964
0.6119 Remote Similarity NPC472808
0.6111 Remote Similarity NPC182794
0.6111 Remote Similarity NPC476654
0.6111 Remote Similarity NPC476655
0.6111 Remote Similarity NPC476657
0.6102 Remote Similarity NPC187922
0.6094 Remote Similarity NPC71053
0.6094 Remote Similarity NPC59408
0.6087 Remote Similarity NPC159650
0.6087 Remote Similarity NPC22897
0.6087 Remote Similarity NPC322186
0.6029 Remote Similarity NPC594
0.6029 Remote Similarity NPC323436
0.6029 Remote Similarity NPC48968
0.6027 Remote Similarity NPC476656
0.6027 Remote Similarity NPC476659
0.6 Remote Similarity NPC321919
0.6 Remote Similarity NPC328311
0.6 Remote Similarity NPC327112
0.6 Remote Similarity NPC184461
0.6 Remote Similarity NPC81896
0.6 Remote Similarity NPC316572
0.5972 Remote Similarity NPC308457
0.5972 Remote Similarity NPC328089
0.5972 Remote Similarity NPC148233
0.5972 Remote Similarity NPC25747
0.5972 Remote Similarity NPC68343
0.597 Remote Similarity NPC200845
0.597 Remote Similarity NPC10316
0.597 Remote Similarity NPC223677
0.597 Remote Similarity NPC128061
0.597 Remote Similarity NPC474672
0.597 Remote Similarity NPC28779
0.597 Remote Similarity NPC228473
0.5968 Remote Similarity NPC197467
0.5938 Remote Similarity NPC291437
0.5938 Remote Similarity NPC301482
0.5938 Remote Similarity NPC328784
0.5938 Remote Similarity NPC289388
0.593 Remote Similarity NPC475405
0.5926 Remote Similarity NPC477088
0.5921 Remote Similarity NPC476037
0.5921 Remote Similarity NPC476012
0.5915 Remote Similarity NPC201939
0.5915 Remote Similarity NPC26810
0.5915 Remote Similarity NPC475984
0.5909 Remote Similarity NPC61177
0.5909 Remote Similarity NPC71761
0.5882 Remote Similarity NPC245002
0.5867 Remote Similarity NPC474823
0.5867 Remote Similarity NPC477431
0.5862 Remote Similarity NPC475712
0.5857 Remote Similarity NPC322002
0.5857 Remote Similarity NPC329424
0.5857 Remote Similarity NPC286189
0.5857 Remote Similarity NPC318306
0.5846 Remote Similarity NPC244452
0.5844 Remote Similarity NPC293114
0.5844 Remote Similarity NPC316185
0.5833 Remote Similarity NPC474723
0.5833 Remote Similarity NPC470965
0.5833 Remote Similarity NPC54925
0.5833 Remote Similarity NPC57923
0.5833 Remote Similarity NPC474729
0.5833 Remote Similarity NPC473737
0.5821 Remote Similarity NPC110732
0.5821 Remote Similarity NPC478120
0.5821 Remote Similarity NPC322461
0.5821 Remote Similarity NPC300121
0.5814 Remote Similarity NPC477428
0.5811 Remote Similarity NPC477982
0.5811 Remote Similarity NPC124586
0.5806 Remote Similarity NPC276825
0.5806 Remote Similarity NPC26600
0.5806 Remote Similarity NPC47946
0.5797 Remote Similarity NPC193975
0.5797 Remote Similarity NPC474869
0.5797 Remote Similarity NPC225929
0.5789 Remote Similarity NPC329656
0.5789 Remote Similarity NPC475004
0.5789 Remote Similarity NPC473772
0.5789 Remote Similarity NPC476059
0.5789 Remote Similarity NPC473603
0.5781 Remote Similarity NPC135698
0.5781 Remote Similarity NPC477778
0.5781 Remote Similarity NPC15912
0.5781 Remote Similarity NPC473551
0.5775 Remote Similarity NPC243532
0.5775 Remote Similarity NPC143857
0.5775 Remote Similarity NPC229252
0.5769 Remote Similarity NPC329914
0.5769 Remote Similarity NPC284006
0.5769 Remote Similarity NPC329890
0.5758 Remote Similarity NPC142092
0.5758 Remote Similarity NPC170167
0.5753 Remote Similarity NPC477456
0.5753 Remote Similarity NPC477457
0.5753 Remote Similarity NPC470320
0.5735 Remote Similarity NPC478117
0.5733 Remote Similarity NPC478100
0.5733 Remote Similarity NPC478097
0.5733 Remote Similarity NPC49863
0.5714 Remote Similarity NPC157096
0.5714 Remote Similarity NPC474204
0.5714 Remote Similarity NPC475310
0.5714 Remote Similarity NPC329904
0.5714 Remote Similarity NPC473361
0.5714 Remote Similarity NPC476660
0.5696 Remote Similarity NPC92558
0.5696 Remote Similarity NPC315843
0.5696 Remote Similarity NPC107654
0.5694 Remote Similarity NPC55376
0.5694 Remote Similarity NPC151648
0.5694 Remote Similarity NPC113293
0.5694 Remote Similarity NPC321838
0.5694 Remote Similarity NPC477829
0.5692 Remote Similarity NPC275316
0.5692 Remote Similarity NPC27264
0.5676 Remote Similarity NPC131174
0.5676 Remote Similarity NPC323477
0.5676 Remote Similarity NPC133904
0.5676 Remote Similarity NPC19769
0.5676 Remote Similarity NPC320642
0.5676 Remote Similarity NPC96414
0.5676 Remote Similarity NPC317881
0.5676 Remote Similarity NPC323045
0.5676 Remote Similarity NPC478098
0.5676 Remote Similarity NPC136164
0.5676 Remote Similarity NPC318420
0.5676 Remote Similarity NPC245947
0.5676 Remote Similarity NPC326268
0.5676 Remote Similarity NPC255863
0.5676 Remote Similarity NPC478099
0.5676 Remote Similarity NPC220766
0.5672 Remote Similarity NPC309606
0.5672 Remote Similarity NPC139545
0.5672 Remote Similarity NPC39633

  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 NPC477424 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
0.6441 Remote Similarity NPD6097 Approved
0.6441 Remote Similarity NPD6096 Approved
0.6393 Remote Similarity NPD5343 Approved
0.6 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5942 Remote Similarity NPD6109 Phase 1
0.5846 Remote Similarity NPD6927 Phase 3
0.5806 Remote Similarity NPD3174 Discontinued
0.5806 Remote Similarity NPD39 Approved
0.5733 Remote Similarity NPD4247 Clinical (unspecified phase)

  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