Structure

Physi-Chem Properties

Molecular Weight:  256.07
Volume:  264.953
LogP:  2.598
LogD:  1.377
LogS:  -3.598
# Rotatable Bonds:  2
TPSA:  44.76
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.528
Synthetic Accessibility Score:  5.348
Fsp3:  0.267
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.642
MDCK Permeability:  2.6615502065396868e-05
Pgp-inhibitor:  0.01
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.195
20% Bioavailability (F20%):  0.995
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.252
Plasma Protein Binding (PPB):  99.60922241210938%
Volume Distribution (VD):  2.128
Pgp-substrate:  5.577776908874512%

ADMET: Metabolism

CYP1A2-inhibitor:  0.609
CYP1A2-substrate:  0.096
CYP2C19-inhibitor:  0.906
CYP2C19-substrate:  0.347
CYP2C9-inhibitor:  0.903
CYP2C9-substrate:  0.047
CYP2D6-inhibitor:  0.742
CYP2D6-substrate:  0.077
CYP3A4-inhibitor:  0.933
CYP3A4-substrate:  0.537

ADMET: Excretion

Clearance (CL):  8.129
Half-life (T1/2):  0.186

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.997
Drug-inuced Liver Injury (DILI):  0.983
AMES Toxicity:  0.985
Rat Oral Acute Toxicity:  0.974
Maximum Recommended Daily Dose:  0.942
Skin Sensitization:  0.927
Carcinogencity:  0.965
Eye Corrosion:  0.04
Eye Irritation:  0.09
Respiratory Toxicity:  0.952

Download Data

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

  Natural Product: NPC474723

Natural Product ID:  NPC474723
Common Name*:   [(2Z,5S)-2-Hexa-2,4-Diynylidene-1,6-Dioxaspiro[4.4]Nona-3,7-Dien-9-Yl] Acetate
IUPAC Name:   [(2Z,5S)-2-hexa-2,4-diynylidene-1,6-dioxaspiro[4.4]nona-3,7-dien-9-yl] acetate
Synonyms:  
Standard InCHIKey:  XQVRVLVORPSYNU-PGGAVIIOSA-N
Standard InCHI:  InChI=1S/C15H12O4/c1-3-4-5-6-7-13-8-10-15(19-13)14(9-11-17-15)18-12(2)16/h7-11,14H,1-2H3/b13-7-/t14?,15-/m0/s1
SMILES:  CC#CC#CC=C1C=CC2(O1)C(C=CO2)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL480307
PubChem CID:   44575224
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000254] Ethers
          • [CHEMONTID:0001656] Acetals
            • [CHEMONTID:0004472] Ketals

*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
NPO3028 Plagius flosculosus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[16499337]
NPO3028 Plagius flosculosus Species Asteraceae 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
NPT15 Cell Line Jurkat Homo sapiens IC50 = 4100.0 nM PMID[507607]
NPT15 Cell Line Jurkat Homo sapiens IC50 = 5200.0 nM PMID[507607]
NPT116 Cell Line HL-60 Homo sapiens IC50 = 4200.0 nM PMID[507607]

☑ 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 NPC474723 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 NPC474729
0.8621 High Similarity NPC151923
0.8621 High Similarity NPC9611
0.8281 Intermediate Similarity NPC90463
0.7619 Intermediate Similarity NPC223804
0.7385 Intermediate Similarity NPC474711
0.7385 Intermediate Similarity NPC474588
0.7302 Intermediate Similarity NPC474913
0.7143 Intermediate Similarity NPC159535
0.7143 Intermediate Similarity NPC151761
0.7101 Intermediate Similarity NPC476589
0.7077 Intermediate Similarity NPC474869
0.7059 Intermediate Similarity NPC475073
0.6923 Remote Similarity NPC245002
0.6825 Remote Similarity NPC106531
0.6765 Remote Similarity NPC98519
0.6765 Remote Similarity NPC130953
0.6724 Remote Similarity NPC57923
0.6721 Remote Similarity NPC90490
0.6716 Remote Similarity NPC189700
0.6667 Remote Similarity NPC225272
0.6618 Remote Similarity NPC133600
0.6618 Remote Similarity NPC222852
0.6615 Remote Similarity NPC269615
0.6613 Remote Similarity NPC82446
0.6585 Remote Similarity NPC30915
0.6571 Remote Similarity NPC473737
0.6571 Remote Similarity NPC210303
0.6571 Remote Similarity NPC44343
0.6571 Remote Similarity NPC179087
0.6567 Remote Similarity NPC471279
0.6567 Remote Similarity NPC471277
0.6543 Remote Similarity NPC474028
0.6543 Remote Similarity NPC474439
0.6528 Remote Similarity NPC276299
0.6522 Remote Similarity NPC26223
0.6522 Remote Similarity NPC309408
0.6508 Remote Similarity NPC275316
0.6479 Remote Similarity NPC471460
0.6463 Remote Similarity NPC475714
0.6429 Remote Similarity NPC15193
0.6418 Remote Similarity NPC221763
0.6418 Remote Similarity NPC150717
0.6389 Remote Similarity NPC131174
0.6389 Remote Similarity NPC182794
0.6377 Remote Similarity NPC474267
0.6377 Remote Similarity NPC302564
0.6351 Remote Similarity NPC477117
0.6351 Remote Similarity NPC280374
0.6338 Remote Similarity NPC132243
0.6324 Remote Similarity NPC44542
0.6324 Remote Similarity NPC472445
0.6324 Remote Similarity NPC212730
0.6324 Remote Similarity NPC265551
0.6322 Remote Similarity NPC475995
0.6322 Remote Similarity NPC474098
0.6301 Remote Similarity NPC470033
0.6286 Remote Similarity NPC299730
0.6282 Remote Similarity NPC478191
0.6282 Remote Similarity NPC478196
0.6282 Remote Similarity NPC478192
0.6282 Remote Similarity NPC478195
0.6282 Remote Similarity NPC478193
0.6282 Remote Similarity NPC478194
0.6269 Remote Similarity NPC478117
0.625 Remote Similarity NPC471611
0.625 Remote Similarity NPC470808
0.625 Remote Similarity NPC25747
0.625 Remote Similarity NPC475618
0.625 Remote Similarity NPC308457
0.625 Remote Similarity NPC148233
0.6232 Remote Similarity NPC474084
0.6212 Remote Similarity NPC477781
0.6212 Remote Similarity NPC477780
0.619 Remote Similarity NPC475706
0.6184 Remote Similarity NPC59558
0.6176 Remote Similarity NPC230296
0.6176 Remote Similarity NPC86948
0.6164 Remote Similarity NPC476586
0.6164 Remote Similarity NPC470123
0.6164 Remote Similarity NPC7940
0.6164 Remote Similarity NPC96414
0.6164 Remote Similarity NPC19769
0.6164 Remote Similarity NPC133904
0.6164 Remote Similarity NPC220766
0.6164 Remote Similarity NPC273600
0.6154 Remote Similarity NPC470686
0.6143 Remote Similarity NPC286189
0.6133 Remote Similarity NPC63873
0.6133 Remote Similarity NPC474823
0.6129 Remote Similarity NPC47946
0.6129 Remote Similarity NPC26600
0.6125 Remote Similarity NPC10572
0.6125 Remote Similarity NPC68156
0.6119 Remote Similarity NPC478120
0.6118 Remote Similarity NPC474424
0.6111 Remote Similarity NPC476584
0.6104 Remote Similarity NPC178575
0.6094 Remote Similarity NPC234084
0.6087 Remote Similarity NPC474825
0.6081 Remote Similarity NPC37382
0.6081 Remote Similarity NPC201356
0.6081 Remote Similarity NPC478101
0.6081 Remote Similarity NPC146811
0.6081 Remote Similarity NPC124586
0.6081 Remote Similarity NPC475675
0.6081 Remote Similarity NPC475555
0.6081 Remote Similarity NPC191233
0.6076 Remote Similarity NPC210258
0.6076 Remote Similarity NPC206507
0.6076 Remote Similarity NPC147621
0.6061 Remote Similarity NPC191643
0.6056 Remote Similarity NPC471278
0.6053 Remote Similarity NPC475004
0.6053 Remote Similarity NPC470693
0.6034 Remote Similarity NPC226511
0.6032 Remote Similarity NPC197467
0.6027 Remote Similarity NPC114464
0.6026 Remote Similarity NPC316851
0.6 Remote Similarity NPC478096
0.6 Remote Similarity NPC478100
0.6 Remote Similarity NPC15789
0.6 Remote Similarity NPC187770
0.5976 Remote Similarity NPC271632
0.5974 Remote Similarity NPC473361
0.5974 Remote Similarity NPC329904
0.5972 Remote Similarity NPC151648
0.597 Remote Similarity NPC327103
0.5952 Remote Similarity NPC251026
0.5949 Remote Similarity NPC107654
0.5949 Remote Similarity NPC472173
0.5946 Remote Similarity NPC282760
0.5946 Remote Similarity NPC478099
0.5946 Remote Similarity NPC478098
0.5932 Remote Similarity NPC200147
0.5921 Remote Similarity NPC238223
0.5921 Remote Similarity NPC475760
0.5921 Remote Similarity NPC470032
0.5921 Remote Similarity NPC287705
0.5915 Remote Similarity NPC478095
0.5915 Remote Similarity NPC159650
0.5915 Remote Similarity NPC22897
0.5915 Remote Similarity NPC322186
0.5915 Remote Similarity NPC97570
0.5909 Remote Similarity NPC475739
0.589 Remote Similarity NPC2328
0.5882 Remote Similarity NPC142111
0.5882 Remote Similarity NPC218486
0.5882 Remote Similarity NPC473315
0.5875 Remote Similarity NPC161038
0.5875 Remote Similarity NPC477421
0.5875 Remote Similarity NPC315552
0.5867 Remote Similarity NPC248125
0.5857 Remote Similarity NPC319423
0.5846 Remote Similarity NPC135698
0.5844 Remote Similarity NPC475982
0.5843 Remote Similarity NPC242877
0.5843 Remote Similarity NPC64913
0.5833 Remote Similarity NPC123357
0.5833 Remote Similarity NPC477424
0.5833 Remote Similarity NPC476585
0.5823 Remote Similarity NPC474705
0.5814 Remote Similarity NPC473308
0.5811 Remote Similarity NPC477457
0.5811 Remote Similarity NPC477456
0.5802 Remote Similarity NPC470705
0.5797 Remote Similarity NPC173157
0.5795 Remote Similarity NPC45409
0.5789 Remote Similarity NPC203335
0.5789 Remote Similarity NPC478097
0.5789 Remote Similarity NPC132286
0.5783 Remote Similarity NPC99651
0.5769 Remote Similarity NPC476037
0.5769 Remote Similarity NPC476012
0.5758 Remote Similarity NPC236338
0.5753 Remote Similarity NPC66460
0.5753 Remote Similarity NPC55376
0.5753 Remote Similarity NPC271282
0.5753 Remote Similarity NPC26810
0.5753 Remote Similarity NPC325929
0.575 Remote Similarity NPC474280
0.575 Remote Similarity NPC315843
0.575 Remote Similarity NPC472174
0.5747 Remote Similarity NPC130030
0.5733 Remote Similarity NPC471565
0.5733 Remote Similarity NPC471566
0.5732 Remote Similarity NPC473825
0.5732 Remote Similarity NPC275530
0.5714 Remote Similarity NPC51846
0.5696 Remote Similarity NPC475762
0.5696 Remote Similarity NPC133098
0.5696 Remote Similarity NPC293114
0.5696 Remote Similarity NPC316185
0.5696 Remote Similarity NPC84038
0.5694 Remote Similarity NPC329249
0.5692 Remote Similarity NPC128520
0.5682 Remote Similarity NPC208473
0.5676 Remote Similarity NPC29697
0.5676 Remote Similarity NPC474774
0.5645 Remote Similarity NPC187922

  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 NPC474723 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
0.6 Remote Similarity NPD69 Approved
0.6 Remote Similarity NPD9119 Approved
0.5857 Remote Similarity NPD9118 Approved
0.5672 Remote Similarity NPD6927 Phase 3

  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