Structure

Physi-Chem Properties

Molecular Weight:  342.18
Volume:  383.205
LogP:  3.563
LogD:  2.359
LogS:  -4.515
# Rotatable Bonds:  11
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.277
Synthetic Accessibility Score:  3.912
Fsp3:  0.429
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:  -4.182
MDCK Permeability:  2.8038628443027847e-05
Pgp-inhibitor:  0.262
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.096
20% Bioavailability (F20%):  0.047
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  99.19422912597656%
Volume Distribution (VD):  1.2
Pgp-substrate:  3.284898281097412%

ADMET: Metabolism

CYP1A2-inhibitor:  0.902
CYP1A2-substrate:  0.155
CYP2C19-inhibitor:  0.949
CYP2C19-substrate:  0.457
CYP2C9-inhibitor:  0.94
CYP2C9-substrate:  0.994
CYP2D6-inhibitor:  0.942
CYP2D6-substrate:  0.912
CYP3A4-inhibitor:  0.934
CYP3A4-substrate:  0.236

ADMET: Excretion

Clearance (CL):  1.772
Half-life (T1/2):  0.143

ADMET: Toxicity

hERG Blockers:  0.019
Human Hepatotoxicity (H-HT):  0.967
Drug-inuced Liver Injury (DILI):  0.976
AMES Toxicity:  0.881
Rat Oral Acute Toxicity:  0.038
Maximum Recommended Daily Dose:  0.13
Skin Sensitization:  0.957
Carcinogencity:  0.543
Eye Corrosion:  0.831
Eye Irritation:  0.923
Respiratory Toxicity:  0.463

Download Data

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

  Natural Product: NPC474913

Natural Product ID:  NPC474913
Common Name*:   Heptadeca-8,10,12-Trien-4,6-Diyne-1,14-Diyl Diacetate
IUPAC Name:   [(8E,10E,12E)-14-acetyloxyheptadeca-8,10,12-trien-4,6-diynyl] acetate
Synonyms:  
Standard InCHIKey:  WXSAEKWPSCLCGV-SRUHFADLSA-N
Standard InCHI:  InChI=1S/C21H26O4/c1-4-16-21(25-20(3)23)17-14-12-10-8-6-5-7-9-11-13-15-18-24-19(2)22/h6,8,10,12,14,17,21H,4,13,15-16,18H2,1-3H3/b8-6+,12-10+,17-14+
SMILES:  CCCC(C=CC=CC=CC#CC#CCCCOC(=O)C)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL487400
PubChem CID:   44559587
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001722] Fatty alcohol 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
NPO18052 Cicuta maculata Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[3572419]
NPO18052 Cicuta maculata Species Apiaceae 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
NPT91 Cell Line KB Homo sapiens ED50 > 4.0 ug ml-1 PMID[521352]

☑ 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 NPC474913 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
0.8704 High Similarity NPC269615
0.8679 High Similarity NPC106531
0.8596 High Similarity NPC474267
0.8596 High Similarity NPC222852
0.8571 High Similarity NPC471277
0.8571 High Similarity NPC472445
0.8571 High Similarity NPC471279
0.8448 Intermediate Similarity NPC299730
0.8246 Intermediate Similarity NPC44542
0.8246 Intermediate Similarity NPC265551
0.8246 Intermediate Similarity NPC212730
0.7931 Intermediate Similarity NPC474869
0.7833 Intermediate Similarity NPC471278
0.7736 Intermediate Similarity NPC197467
0.7705 Intermediate Similarity NPC66460
0.7705 Intermediate Similarity NPC271282
0.7705 Intermediate Similarity NPC325929
0.7656 Intermediate Similarity NPC225272
0.7647 Intermediate Similarity NPC57923
0.7581 Intermediate Similarity NPC29697
0.7547 Intermediate Similarity NPC47946
0.7547 Intermediate Similarity NPC26600
0.7541 Intermediate Similarity NPC26223
0.75 Intermediate Similarity NPC478096
0.75 Intermediate Similarity NPC146811
0.7455 Intermediate Similarity NPC135698
0.7419 Intermediate Similarity NPC26810
0.7419 Intermediate Similarity NPC55376
0.7377 Intermediate Similarity NPC478095
0.7321 Intermediate Similarity NPC291437
0.7321 Intermediate Similarity NPC328784
0.7302 Intermediate Similarity NPC474729
0.7302 Intermediate Similarity NPC44343
0.7302 Intermediate Similarity NPC179087
0.7302 Intermediate Similarity NPC210303
0.7302 Intermediate Similarity NPC474723
0.7258 Intermediate Similarity NPC477424
0.7213 Intermediate Similarity NPC469373
0.7188 Intermediate Similarity NPC148233
0.7188 Intermediate Similarity NPC308457
0.7188 Intermediate Similarity NPC25747
0.7143 Intermediate Similarity NPC15912
0.7119 Intermediate Similarity NPC478120
0.7097 Intermediate Similarity NPC22897
0.7097 Intermediate Similarity NPC97570
0.7097 Intermediate Similarity NPC329249
0.7097 Intermediate Similarity NPC322186
0.7097 Intermediate Similarity NPC159650
0.7091 Intermediate Similarity NPC128280
0.7077 Intermediate Similarity NPC478099
0.7077 Intermediate Similarity NPC182794
0.7077 Intermediate Similarity NPC478098
0.7059 Intermediate Similarity NPC476012
0.7059 Intermediate Similarity NPC476037
0.7049 Intermediate Similarity NPC48968
0.7049 Intermediate Similarity NPC594
0.7049 Intermediate Similarity NPC294938
0.7049 Intermediate Similarity NPC129150
0.7031 Intermediate Similarity NPC473737
0.7018 Intermediate Similarity NPC236338
0.7018 Intermediate Similarity NPC275316
0.7018 Intermediate Similarity NPC27264
0.7 Intermediate Similarity NPC146551
0.7 Intermediate Similarity NPC470963
0.7 Intermediate Similarity NPC152668
0.7 Intermediate Similarity NPC474513
0.6984 Remote Similarity NPC328311
0.6984 Remote Similarity NPC79756
0.697 Remote Similarity NPC124586
0.697 Remote Similarity NPC478101
0.6957 Remote Similarity NPC316185
0.6957 Remote Similarity NPC293114
0.6949 Remote Similarity NPC477781
0.6949 Remote Similarity NPC477780
0.6935 Remote Similarity NPC223679
0.6935 Remote Similarity NPC254095
0.6909 Remote Similarity NPC270706
0.6897 Remote Similarity NPC148056
0.6897 Remote Similarity NPC59408
0.6897 Remote Similarity NPC71053
0.6885 Remote Similarity NPC245002
0.6885 Remote Similarity NPC324224
0.6885 Remote Similarity NPC311648
0.6885 Remote Similarity NPC470964
0.6885 Remote Similarity NPC86948
0.6885 Remote Similarity NPC221763
0.6885 Remote Similarity NPC472808
0.6875 Remote Similarity NPC475984
0.6875 Remote Similarity NPC151648
0.6875 Remote Similarity NPC15193
0.6866 Remote Similarity NPC478097
0.6866 Remote Similarity NPC478100
0.6857 Remote Similarity NPC284006
0.6857 Remote Similarity NPC329914
0.6857 Remote Similarity NPC329890
0.6842 Remote Similarity NPC207815
0.6842 Remote Similarity NPC302310
0.6833 Remote Similarity NPC151761
0.6833 Remote Similarity NPC110732
0.6833 Remote Similarity NPC159535
0.6825 Remote Similarity NPC82465
0.6825 Remote Similarity NPC322002
0.6825 Remote Similarity NPC318306
0.6825 Remote Similarity NPC286189
0.6818 Remote Similarity NPC96414
0.6818 Remote Similarity NPC19769
0.6818 Remote Similarity NPC282760
0.6818 Remote Similarity NPC220766
0.6812 Remote Similarity NPC59558
0.6812 Remote Similarity NPC473361
0.6812 Remote Similarity NPC329904
0.678 Remote Similarity NPC142092
0.678 Remote Similarity NPC151919
0.6774 Remote Similarity NPC193975
0.6774 Remote Similarity NPC293437
0.6774 Remote Similarity NPC223804
0.6774 Remote Similarity NPC135863
0.6774 Remote Similarity NPC249850
0.6769 Remote Similarity NPC470965
0.6769 Remote Similarity NPC217940
0.6769 Remote Similarity NPC474774
0.6765 Remote Similarity NPC474823
0.6765 Remote Similarity NPC475760
0.6765 Remote Similarity NPC63873
0.6765 Remote Similarity NPC477117
0.6761 Remote Similarity NPC107654
0.6761 Remote Similarity NPC315843
0.6761 Remote Similarity NPC470686
0.6727 Remote Similarity NPC12907
0.6724 Remote Similarity NPC15789
0.6721 Remote Similarity NPC478117
0.6719 Remote Similarity NPC327112
0.6719 Remote Similarity NPC19241
0.6716 Remote Similarity NPC201356
0.6716 Remote Similarity NPC248125
0.6716 Remote Similarity NPC191233
0.6716 Remote Similarity NPC284447
0.6714 Remote Similarity NPC186531
0.6667 Remote Similarity NPC151481
0.6667 Remote Similarity NPC284224
0.6667 Remote Similarity NPC21946
0.6667 Remote Similarity NPC476658
0.6667 Remote Similarity NPC475004
0.6667 Remote Similarity NPC61177
0.6667 Remote Similarity NPC470693
0.6667 Remote Similarity NPC226066
0.6667 Remote Similarity NPC477456
0.6667 Remote Similarity NPC470808
0.6667 Remote Similarity NPC477457
0.6667 Remote Similarity NPC260396
0.6618 Remote Similarity NPC194871
0.6618 Remote Similarity NPC122627
0.6618 Remote Similarity NPC203335
0.6613 Remote Similarity NPC327388
0.6613 Remote Similarity NPC96663
0.6613 Remote Similarity NPC150717
0.661 Remote Similarity NPC151782
0.6604 Remote Similarity NPC123357
0.6575 Remote Similarity NPC188860
0.6567 Remote Similarity NPC476655
0.6567 Remote Similarity NPC471566
0.6567 Remote Similarity NPC318420
0.6567 Remote Similarity NPC476654
0.6567 Remote Similarity NPC320642
0.6567 Remote Similarity NPC471565
0.6567 Remote Similarity NPC133904
0.6567 Remote Similarity NPC476657
0.6567 Remote Similarity NPC326268
0.6567 Remote Similarity NPC131174
0.6562 Remote Similarity NPC474588
0.6562 Remote Similarity NPC329424
0.6562 Remote Similarity NPC474711
0.6562 Remote Similarity NPC133600
0.6557 Remote Similarity NPC300121
0.6557 Remote Similarity NPC9611
0.6557 Remote Similarity NPC151923
0.6552 Remote Similarity NPC82446
0.6552 Remote Similarity NPC248884
0.6552 Remote Similarity NPC31194
0.6552 Remote Similarity NPC153538
0.6552 Remote Similarity NPC85079
0.6552 Remote Similarity NPC91765
0.6538 Remote Similarity NPC226511
0.6528 Remote Similarity NPC92558
0.6522 Remote Similarity NPC218477
0.6522 Remote Similarity NPC238223
0.6515 Remote Similarity NPC2328
0.6515 Remote Similarity NPC68110
0.6508 Remote Similarity NPC323498
0.6508 Remote Similarity NPC211752
0.6508 Remote Similarity NPC323597
0.6491 Remote Similarity NPC180575
0.6491 Remote Similarity NPC124183
0.6491 Remote Similarity NPC35141
0.6486 Remote Similarity NPC233071
0.6479 Remote Similarity NPC475762
0.6471 Remote Similarity NPC37382
0.6471 Remote Similarity NPC476659
0.6471 Remote Similarity NPC476656
0.6471 Remote Similarity NPC276299

  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 NPC474913 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
0.75 Intermediate Similarity NPD6927 Phase 3
0.7037 Intermediate Similarity NPD6097 Approved
0.7037 Intermediate Similarity NPD6096 Approved
0.6964 Remote Similarity NPD5343 Approved
0.6719 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6667 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6567 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6552 Remote Similarity NPD4220 Pre-registration
0.6406 Remote Similarity NPD6109 Phase 1
0.6377 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6154 Remote Similarity NPD585 Clinical (unspecified phase)
0.6076 Remote Similarity NPD5209 Approved
0.6034 Remote Similarity NPD4222 Approved
0.6034 Remote Similarity NPD3174 Discontinued
0.6034 Remote Similarity NPD39 Approved
0.6 Remote Similarity NPD8039 Approved
0.5965 Remote Similarity NPD5326 Phase 3
0.5902 Remote Similarity NPD2268 Discontinued
0.5854 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5741 Remote Similarity NPD9115 Approved
0.5738 Remote Similarity NPD3173 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