Structure

Physi-Chem Properties

Molecular Weight:  256.15
Volume:  299.077
LogP:  4.495
LogD:  2.7
LogS:  -5.16
# Rotatable Bonds:  8
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.289
Synthetic Accessibility Score:  3.432
Fsp3:  0.412
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  3
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.25
MDCK Permeability:  2.693795431696344e-05
Pgp-inhibitor:  0.095
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.021
30% Bioavailability (F30%):  0.863

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  101.89556121826172%
Volume Distribution (VD):  1.881
Pgp-substrate:  0.9245836138725281%

ADMET: Metabolism

CYP1A2-inhibitor:  0.945
CYP1A2-substrate:  0.153
CYP2C19-inhibitor:  0.876
CYP2C19-substrate:  0.463
CYP2C9-inhibitor:  0.747
CYP2C9-substrate:  0.112
CYP2D6-inhibitor:  0.253
CYP2D6-substrate:  0.061
CYP3A4-inhibitor:  0.85
CYP3A4-substrate:  0.196

ADMET: Excretion

Clearance (CL):  5.739
Half-life (T1/2):  0.327

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.741
Drug-inuced Liver Injury (DILI):  0.982
AMES Toxicity:  0.485
Rat Oral Acute Toxicity:  0.924
Maximum Recommended Daily Dose:  0.864
Skin Sensitization:  0.96
Carcinogencity:  0.487
Eye Corrosion:  0.976
Eye Irritation:  0.99
Respiratory Toxicity:  0.897

Download Data

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

  Natural Product: NPC474391

Natural Product ID:  NPC474391
Common Name*:   Heptadeca-1,8(Z)-Diene-4,6-Diyne-3,10-Dione
IUPAC Name:   (8Z)-heptadeca-1,8-dien-4,6-diyne-3,10-dione
Synonyms:  
Standard InCHIKey:  HPXDLSZVGXBKTQ-QINSGFPZSA-N
Standard InCHI:  InChI=1S/C17H20O2/c1-3-5-6-7-11-14-17(19)15-12-9-8-10-13-16(18)4-2/h4,12,15H,2-3,5-7,11,14H2,1H3/b15-12-
SMILES:  CCCCCCCC(=O)C=CC#CC#CC(=O)C=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL465850
PubChem CID:   14753644
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0003131] Alpha,beta-unsaturated carbonyl compounds
            • [CHEMONTID:0003672] Alpha,beta-unsaturated ketones
              • [CHEMONTID:0001363] Enones

*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
NPO23488 Seseli mairei Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[2095375]
NPO23488 Seseli mairei Species Apiaceae Eukaryota n.a. root n.a. PMID[2095375]
NPO23488 Seseli mairei 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
NPT180 Cell Line HCT-8 Homo sapiens ED50 = 3.7 ug ml-1 PMID[540344]
NPT91 Cell Line KB Homo sapiens ED50 > 10.0 ug ml-1 PMID[540344]
NPT168 Cell Line P388 Mus musculus ED50 > 10.0 ug ml-1 PMID[540344]
NPT137 Cell Line L1210 Mus musculus ED50 > 10.0 ug ml-1 PMID[540344]

☑ 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 NPC474391 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
0.8511 High Similarity NPC145755
0.8511 High Similarity NPC267514
0.8261 Intermediate Similarity NPC7754
0.8261 Intermediate Similarity NPC270170
0.8235 Intermediate Similarity NPC477458
0.8 Intermediate Similarity NPC471958
0.7895 Intermediate Similarity NPC235242
0.7843 Intermediate Similarity NPC145311
0.7647 Intermediate Similarity NPC324812
0.76 Intermediate Similarity NPC474202
0.76 Intermediate Similarity NPC474362
0.75 Intermediate Similarity NPC473733
0.7458 Intermediate Similarity NPC168407
0.7451 Intermediate Similarity NPC100380
0.7447 Intermediate Similarity NPC217923
0.7414 Intermediate Similarity NPC274927
0.7414 Intermediate Similarity NPC106851
0.7391 Intermediate Similarity NPC220061
0.7358 Intermediate Similarity NPC15325
0.7288 Intermediate Similarity NPC122521
0.7288 Intermediate Similarity NPC174447
0.7288 Intermediate Similarity NPC251042
0.7288 Intermediate Similarity NPC229252
0.7288 Intermediate Similarity NPC143857
0.7255 Intermediate Similarity NPC239754
0.7255 Intermediate Similarity NPC191337
0.7234 Intermediate Similarity NPC155880
0.7234 Intermediate Similarity NPC92863
0.7222 Intermediate Similarity NPC234829
0.7193 Intermediate Similarity NPC179764
0.7193 Intermediate Similarity NPC187777
0.7193 Intermediate Similarity NPC325977
0.7167 Intermediate Similarity NPC40082
0.7143 Intermediate Similarity NPC300121
0.7119 Intermediate Similarity NPC473652
0.7115 Intermediate Similarity NPC163751
0.7115 Intermediate Similarity NPC262558
0.7115 Intermediate Similarity NPC8610
0.7115 Intermediate Similarity NPC44363
0.7115 Intermediate Similarity NPC110234
0.7059 Intermediate Similarity NPC477686
0.7059 Intermediate Similarity NPC25771
0.7037 Intermediate Similarity NPC224227
0.7018 Intermediate Similarity NPC274290
0.7018 Intermediate Similarity NPC275472
0.7018 Intermediate Similarity NPC473863
0.7018 Intermediate Similarity NPC54766
0.7018 Intermediate Similarity NPC471239
0.6964 Remote Similarity NPC284224
0.6964 Remote Similarity NPC474141
0.6964 Remote Similarity NPC296311
0.6939 Remote Similarity NPC113082
0.6909 Remote Similarity NPC262968
0.6897 Remote Similarity NPC477201
0.6885 Remote Similarity NPC97322
0.6863 Remote Similarity NPC301972
0.6863 Remote Similarity NPC292463
0.6842 Remote Similarity NPC322461
0.6833 Remote Similarity NPC259261
0.6825 Remote Similarity NPC251118
0.6825 Remote Similarity NPC176215
0.6825 Remote Similarity NPC296436
0.6792 Remote Similarity NPC471752
0.6786 Remote Similarity NPC471751
0.6786 Remote Similarity NPC161366
0.678 Remote Similarity NPC192843
0.678 Remote Similarity NPC225929
0.678 Remote Similarity NPC115385
0.678 Remote Similarity NPC193695
0.6774 Remote Similarity NPC477707
0.6774 Remote Similarity NPC477830
0.6774 Remote Similarity NPC143168
0.6774 Remote Similarity NPC53109
0.6774 Remote Similarity NPC288253
0.6731 Remote Similarity NPC471753
0.6727 Remote Similarity NPC118788
0.6727 Remote Similarity NPC32351
0.6727 Remote Similarity NPC228776
0.6724 Remote Similarity NPC477984
0.6724 Remote Similarity NPC474672
0.6721 Remote Similarity NPC25853
0.6719 Remote Similarity NPC16119
0.6667 Remote Similarity NPC94991
0.6667 Remote Similarity NPC7029
0.6667 Remote Similarity NPC30215
0.6667 Remote Similarity NPC298710
0.6667 Remote Similarity NPC39633
0.6667 Remote Similarity NPC67920
0.6667 Remote Similarity NPC266295
0.6667 Remote Similarity NPC287397
0.6667 Remote Similarity NPC474400
0.6667 Remote Similarity NPC294548
0.6667 Remote Similarity NPC61177
0.6667 Remote Similarity NPC34622
0.6667 Remote Similarity NPC139029
0.6667 Remote Similarity NPC309606
0.6667 Remote Similarity NPC139545
0.6667 Remote Similarity NPC1813
0.6667 Remote Similarity NPC45283
0.6667 Remote Similarity NPC311852
0.6667 Remote Similarity NPC36061
0.6615 Remote Similarity NPC474619
0.6613 Remote Similarity NPC475795
0.6607 Remote Similarity NPC28205
0.6607 Remote Similarity NPC284212
0.6607 Remote Similarity NPC470412
0.6607 Remote Similarity NPC470410
0.6562 Remote Similarity NPC98897
0.6557 Remote Similarity NPC96551
0.6557 Remote Similarity NPC329550
0.6557 Remote Similarity NPC285594
0.6552 Remote Similarity NPC261831
0.6552 Remote Similarity NPC6095
0.6552 Remote Similarity NPC202850
0.6552 Remote Similarity NPC290563
0.6552 Remote Similarity NPC88966
0.6552 Remote Similarity NPC281972
0.6552 Remote Similarity NPC424
0.6552 Remote Similarity NPC32467
0.6552 Remote Similarity NPC154245
0.6552 Remote Similarity NPC63396
0.6552 Remote Similarity NPC85813
0.6552 Remote Similarity NPC87564
0.6552 Remote Similarity NPC25417
0.6538 Remote Similarity NPC216921
0.6531 Remote Similarity NPC130923
0.6531 Remote Similarity NPC180840
0.6515 Remote Similarity NPC260474
0.6515 Remote Similarity NPC476614
0.6515 Remote Similarity NPC87141
0.6515 Remote Similarity NPC188292
0.6508 Remote Similarity NPC167256
0.6508 Remote Similarity NPC32285
0.6508 Remote Similarity NPC57463
0.6508 Remote Similarity NPC151728
0.65 Remote Similarity NPC193975
0.65 Remote Similarity NPC281230
0.6491 Remote Similarity NPC18357
0.6491 Remote Similarity NPC92114
0.6491 Remote Similarity NPC281245
0.6491 Remote Similarity NPC473705
0.6481 Remote Similarity NPC4079
0.6481 Remote Similarity NPC14917
0.6481 Remote Similarity NPC236355
0.6471 Remote Similarity NPC33489
0.6471 Remote Similarity NPC186531
0.6441 Remote Similarity NPC28779
0.6441 Remote Similarity NPC10316
0.6441 Remote Similarity NPC200845
0.6441 Remote Similarity NPC188789
0.6441 Remote Similarity NPC228473
0.6441 Remote Similarity NPC128061
0.6441 Remote Similarity NPC223677
0.6441 Remote Similarity NPC45626
0.6429 Remote Similarity NPC58970
0.6429 Remote Similarity NPC59051
0.6429 Remote Similarity NPC163984
0.6429 Remote Similarity NPC176819
0.6418 Remote Similarity NPC262673
0.6418 Remote Similarity NPC143396
0.6418 Remote Similarity NPC256846
0.6406 Remote Similarity NPC226592
0.6406 Remote Similarity NPC473902
0.6406 Remote Similarity NPC470320
0.6406 Remote Similarity NPC150162
0.6406 Remote Similarity NPC4638
0.6406 Remote Similarity NPC212210
0.6393 Remote Similarity NPC267817
0.6393 Remote Similarity NPC329819
0.6393 Remote Similarity NPC34416
0.6379 Remote Similarity NPC71761
0.6379 Remote Similarity NPC321062
0.6379 Remote Similarity NPC37644
0.6379 Remote Similarity NPC70387
0.6379 Remote Similarity NPC268564
0.6364 Remote Similarity NPC243272
0.6333 Remote Similarity NPC20603
0.6333 Remote Similarity NPC18951
0.6327 Remote Similarity NPC24833
0.6327 Remote Similarity NPC185839
0.6324 Remote Similarity NPC94743
0.6324 Remote Similarity NPC291062
0.6316 Remote Similarity NPC64866
0.6316 Remote Similarity NPC27438
0.6308 Remote Similarity NPC133904
0.6296 Remote Similarity NPC166788
0.629 Remote Similarity NPC472304
0.629 Remote Similarity NPC143834
0.629 Remote Similarity NPC276764
0.6275 Remote Similarity NPC111474
0.6275 Remote Similarity NPC48930
0.6271 Remote Similarity NPC48058
0.6269 Remote Similarity NPC263382
0.6269 Remote Similarity NPC125578
0.6269 Remote Similarity NPC218477
0.6269 Remote Similarity NPC155198
0.6269 Remote Similarity NPC134385
0.6269 Remote Similarity NPC146376
0.625 Remote Similarity NPC165695
0.625 Remote Similarity NPC5413

  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 NPC474391 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
0.7636 Intermediate Similarity NPD4627 Clinical (unspecified phase)
0.6909 Remote Similarity NPD29 Approved
0.6909 Remote Similarity NPD28 Approved
0.6774 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6719 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6667 Remote Similarity NPD3172 Approved
0.6604 Remote Similarity NPD3174 Discontinued
0.6552 Remote Similarity NPD3194 Approved
0.6552 Remote Similarity NPD3195 Phase 2
0.6552 Remote Similarity NPD3196 Approved
0.6552 Remote Similarity NPD4266 Approved
0.64 Remote Similarity NPD5783 Phase 3
0.625 Remote Similarity NPD3173 Approved
0.6212 Remote Similarity NPD7331 Phase 2
0.6087 Remote Similarity NPD4691 Approved
0.6056 Remote Similarity NPD4058 Approved
0.6 Remote Similarity NPD39 Approved
0.6 Remote Similarity NPD4222 Approved
0.5942 Remote Similarity NPD4137 Phase 3
0.5909 Remote Similarity NPD3197 Phase 1
0.5857 Remote Similarity NPD4747 Approved
0.5833 Remote Similarity NPD4687 Approved
0.5821 Remote Similarity NPD7341 Phase 2
0.5789 Remote Similarity NPD5343 Approved
0.5789 Remote Similarity NPD622 Approved
0.5775 Remote Similarity NPD5276 Approved
0.5735 Remote Similarity NPD3704 Approved
0.5652 Remote Similarity NPD3709 Clinical (unspecified phase)
0.5636 Remote Similarity NPD5326 Phase 3
0.5625 Remote Similarity NPD287 Approved
0.5616 Remote Similarity NPD5733 Approved
0.56 Remote Similarity NPD4756 Discovery

  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