Structure

Physi-Chem Properties

Molecular Weight:  232.15
Volume:  269.758
LogP:  4.06
LogD:  2.525
LogS:  -4.022
# Rotatable Bonds:  7
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.539
Synthetic Accessibility Score:  2.961
Fsp3:  0.533
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.647
MDCK Permeability:  4.2670799302868545e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.022
20% Bioavailability (F20%):  0.029
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.004
Plasma Protein Binding (PPB):  100.83721160888672%
Volume Distribution (VD):  0.301
Pgp-substrate:  0.9308740496635437%

ADMET: Metabolism

CYP1A2-inhibitor:  0.442
CYP1A2-substrate:  0.352
CYP2C19-inhibitor:  0.893
CYP2C19-substrate:  0.533
CYP2C9-inhibitor:  0.885
CYP2C9-substrate:  0.996
CYP2D6-inhibitor:  0.116
CYP2D6-substrate:  0.867
CYP3A4-inhibitor:  0.518
CYP3A4-substrate:  0.045

ADMET: Excretion

Clearance (CL):  1.853
Half-life (T1/2):  0.816

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.819
Drug-inuced Liver Injury (DILI):  0.976
AMES Toxicity:  0.637
Rat Oral Acute Toxicity:  0.051
Maximum Recommended Daily Dose:  0.026
Skin Sensitization:  0.946
Carcinogencity:  0.605
Eye Corrosion:  0.978
Eye Irritation:  0.979
Respiratory Toxicity:  0.893

Download Data

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

  Natural Product: NPC28205

Natural Product ID:  NPC28205
Common Name*:   (E)-Pentadec-10-En-6,8-Diynoic Acid
IUPAC Name:   (E)-pentadec-10-en-6,8-diynoic acid
Synonyms:  
Standard InCHIKey:  VLPCQMHZJMTSIW-AATRIKPKSA-N
Standard InCHI:  InChI=1S/C15H20O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15(16)17/h5-6H,2-4,11-14H2,1H3,(H,16,17)/b6-5+
SMILES:  CCCC/C=C/C#CC#CCCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL448670
PubChem CID:   10443953
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0002949] Long-chain fatty acids

*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
NPO32503 heisteria acuminata Species Erythropalaceae Eukaryota bark n.a. n.a. PMID[9584394]

☑ 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
NPT2 Others Unspecified Inhibition = 56.0 % PMID[545632]
NPT2 Others Unspecified Inhibition = 44.0 % PMID[545632]
NPT2 Others Unspecified Inhibition = 14.0 % PMID[545632]

☑ 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 NPC28205 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
0.9583 High Similarity NPC284212
0.9216 High Similarity NPC473863
0.9216 High Similarity NPC274290
0.9167 High Similarity NPC5413
0.9167 High Similarity NPC149821
0.9149 High Similarity NPC42304
0.9038 High Similarity NPC187777
0.9038 High Similarity NPC179764
0.8958 High Similarity NPC207292
0.8846 High Similarity NPC54766
0.8627 High Similarity NPC281245
0.8627 High Similarity NPC92114
0.8627 High Similarity NPC129458
0.8571 High Similarity NPC91495
0.8542 High Similarity NPC117572
0.8519 High Similarity NPC225929
0.8462 Intermediate Similarity NPC1813
0.8462 Intermediate Similarity NPC70387
0.8462 Intermediate Similarity NPC10081
0.8462 Intermediate Similarity NPC294548
0.8462 Intermediate Similarity NPC225066
0.8462 Intermediate Similarity NPC321062
0.8462 Intermediate Similarity NPC139029
0.8462 Intermediate Similarity NPC36061
0.8364 Intermediate Similarity NPC267817
0.8302 Intermediate Similarity NPC290563
0.8302 Intermediate Similarity NPC85813
0.8302 Intermediate Similarity NPC261831
0.8302 Intermediate Similarity NPC281972
0.8302 Intermediate Similarity NPC154245
0.8302 Intermediate Similarity NPC424
0.8302 Intermediate Similarity NPC88966
0.8302 Intermediate Similarity NPC25417
0.8302 Intermediate Similarity NPC87564
0.8302 Intermediate Similarity NPC32467
0.8302 Intermediate Similarity NPC6095
0.8269 Intermediate Similarity NPC303765
0.8269 Intermediate Similarity NPC18357
0.8235 Intermediate Similarity NPC59051
0.8148 Intermediate Similarity NPC45626
0.8077 Intermediate Similarity NPC48162
0.8077 Intermediate Similarity NPC470411
0.8077 Intermediate Similarity NPC470410
0.8077 Intermediate Similarity NPC470412
0.807 Intermediate Similarity NPC235242
0.8036 Intermediate Similarity NPC329819
0.8 Intermediate Similarity NPC477201
0.8 Intermediate Similarity NPC18951
0.7885 Intermediate Similarity NPC224227
0.7843 Intermediate Similarity NPC180534
0.7755 Intermediate Similarity NPC270796
0.7736 Intermediate Similarity NPC262968
0.7692 Intermediate Similarity NPC163345
0.7679 Intermediate Similarity NPC325977
0.7667 Intermediate Similarity NPC226592
0.7667 Intermediate Similarity NPC470320
0.7636 Intermediate Similarity NPC322461
0.7636 Intermediate Similarity NPC137538
0.7593 Intermediate Similarity NPC161366
0.7586 Intermediate Similarity NPC274927
0.7586 Intermediate Similarity NPC106851
0.7586 Intermediate Similarity NPC329550
0.75 Intermediate Similarity NPC477984
0.75 Intermediate Similarity NPC52264
0.75 Intermediate Similarity NPC474672
0.7458 Intermediate Similarity NPC251042
0.7458 Intermediate Similarity NPC122521
0.7458 Intermediate Similarity NPC174447
0.7458 Intermediate Similarity NPC243532
0.7455 Intermediate Similarity NPC309606
0.7455 Intermediate Similarity NPC39633
0.7455 Intermediate Similarity NPC139545
0.7447 Intermediate Similarity NPC73245
0.7414 Intermediate Similarity NPC34416
0.7407 Intermediate Similarity NPC178586
0.7368 Intermediate Similarity NPC327388
0.7333 Intermediate Similarity NPC477829
0.7333 Intermediate Similarity NPC201939
0.7333 Intermediate Similarity NPC40082
0.7273 Intermediate Similarity NPC216407
0.7241 Intermediate Similarity NPC323597
0.7241 Intermediate Similarity NPC211752
0.7241 Intermediate Similarity NPC323498
0.7241 Intermediate Similarity NPC323436
0.7193 Intermediate Similarity NPC28779
0.7193 Intermediate Similarity NPC10316
0.7193 Intermediate Similarity NPC128061
0.7193 Intermediate Similarity NPC223677
0.7193 Intermediate Similarity NPC200845
0.7193 Intermediate Similarity NPC228473
0.717 Intermediate Similarity NPC216130
0.7167 Intermediate Similarity NPC328311
0.7167 Intermediate Similarity NPC327112
0.7143 Intermediate Similarity NPC71761
0.7143 Intermediate Similarity NPC284224
0.7119 Intermediate Similarity NPC469373
0.7097 Intermediate Similarity NPC68343
0.7097 Intermediate Similarity NPC328089
0.7049 Intermediate Similarity NPC320305
0.7049 Intermediate Similarity NPC125312
0.7049 Intermediate Similarity NPC328776
0.7049 Intermediate Similarity NPC321838
0.7049 Intermediate Similarity NPC113293
0.7049 Intermediate Similarity NPC174560
0.7018 Intermediate Similarity NPC87394
0.7 Intermediate Similarity NPC163746
0.7 Intermediate Similarity NPC103286
0.7 Intermediate Similarity NPC329249
0.6984 Remote Similarity NPC326268
0.6984 Remote Similarity NPC323045
0.6984 Remote Similarity NPC245947
0.6984 Remote Similarity NPC317881
0.6984 Remote Similarity NPC318420
0.6984 Remote Similarity NPC136164
0.6984 Remote Similarity NPC320642
0.6984 Remote Similarity NPC255863
0.6935 Remote Similarity NPC29697
0.6897 Remote Similarity NPC67367
0.6885 Remote Similarity NPC81896
0.6885 Remote Similarity NPC321919
0.6875 Remote Similarity NPC158179
0.6863 Remote Similarity NPC71317
0.6863 Remote Similarity NPC129972
0.6863 Remote Similarity NPC301528
0.6825 Remote Similarity NPC234767
0.6792 Remote Similarity NPC474362
0.6792 Remote Similarity NPC474202
0.6774 Remote Similarity NPC325929
0.6774 Remote Similarity NPC475984
0.6774 Remote Similarity NPC271282
0.6774 Remote Similarity NPC66460
0.6769 Remote Similarity NPC99619
0.6769 Remote Similarity NPC330426
0.6769 Remote Similarity NPC148192
0.6769 Remote Similarity NPC26500
0.6769 Remote Similarity NPC22101
0.6769 Remote Similarity NPC104537
0.6769 Remote Similarity NPC271921
0.6769 Remote Similarity NPC49863
0.6769 Remote Similarity NPC60120
0.6769 Remote Similarity NPC127091
0.6735 Remote Similarity NPC155880
0.6735 Remote Similarity NPC92863
0.6731 Remote Similarity NPC255837
0.6731 Remote Similarity NPC19305
0.6727 Remote Similarity NPC207815
0.6724 Remote Similarity NPC300121
0.6721 Remote Similarity NPC318306
0.6721 Remote Similarity NPC322002
0.6719 Remote Similarity NPC323477
0.6667 Remote Similarity NPC470965
0.6667 Remote Similarity NPC170167
0.6667 Remote Similarity NPC472445
0.6667 Remote Similarity NPC48218
0.6667 Remote Similarity NPC53302
0.6667 Remote Similarity NPC324981
0.6667 Remote Similarity NPC477779
0.6667 Remote Similarity NPC322457
0.6667 Remote Similarity NPC473559
0.6667 Remote Similarity NPC476614
0.6667 Remote Similarity NPC141481
0.6618 Remote Similarity NPC477981
0.6618 Remote Similarity NPC477983
0.6615 Remote Similarity NPC308294
0.6615 Remote Similarity NPC142423
0.6615 Remote Similarity NPC328653
0.6613 Remote Similarity NPC229252
0.6613 Remote Similarity NPC143857
0.6607 Remote Similarity NPC474391
0.6607 Remote Similarity NPC473487
0.6604 Remote Similarity NPC8219
0.6604 Remote Similarity NPC108195
0.6567 Remote Similarity NPC317583
0.6567 Remote Similarity NPC143396
0.6515 Remote Similarity NPC25298
0.6515 Remote Similarity NPC473829
0.6515 Remote Similarity NPC475443
0.65 Remote Similarity NPC324224
0.65 Remote Similarity NPC472808
0.6491 Remote Similarity NPC477458
0.6491 Remote Similarity NPC477777
0.6491 Remote Similarity NPC244452
0.6491 Remote Similarity NPC129263
0.6481 Remote Similarity NPC172042
0.6481 Remote Similarity NPC276825
0.6471 Remote Similarity NPC42526
0.6471 Remote Similarity NPC476660
0.6462 Remote Similarity NPC476657
0.6462 Remote Similarity NPC476655
0.6462 Remote Similarity NPC476654
0.6452 Remote Similarity NPC222852
0.6452 Remote Similarity NPC474267
0.6441 Remote Similarity NPC110732
0.6441 Remote Similarity NPC256209
0.6441 Remote Similarity NPC474127
0.6441 Remote Similarity NPC49059
0.6429 Remote Similarity NPC302310
0.6415 Remote Similarity NPC252978
0.6406 Remote Similarity NPC477707
0.6406 Remote Similarity NPC54925

  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 NPC28205 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
0.9167 High Similarity NPD3173 Approved
0.8542 High Similarity NPD3174 Discontinued
0.8542 High Similarity NPD4222 Approved
0.8462 Intermediate Similarity NPD3172 Approved
0.8302 Intermediate Similarity NPD4266 Approved
0.8302 Intermediate Similarity NPD3194 Approved
0.8302 Intermediate Similarity NPD3195 Phase 2
0.8302 Intermediate Similarity NPD3196 Approved
0.8163 Intermediate Similarity NPD39 Approved
0.7843 Intermediate Similarity NPD622 Approved
0.7755 Intermediate Similarity NPD5326 Phase 3
0.7736 Intermediate Similarity NPD29 Approved
0.7736 Intermediate Similarity NPD28 Approved
0.717 Intermediate Similarity NPD5343 Approved
0.7167 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.7097 Intermediate Similarity NPD3197 Phase 1
0.6769 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6604 Remote Similarity NPD6097 Approved
0.6604 Remote Similarity NPD6096 Approved
0.6557 Remote Similarity NPD6109 Phase 1
0.6275 Remote Similarity NPD633 Phase 3
0.6275 Remote Similarity NPD9448 Phase 2
0.6154 Remote Similarity NPD9635 Discontinued
0.614 Remote Similarity NPD4220 Pre-registration
0.6038 Remote Similarity NPD2270 Approved
0.5962 Remote Similarity NPD9655 Approved
0.5932 Remote Similarity NPD6927 Phase 3
0.5909 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5897 Remote Similarity NPD5331 Approved
0.5897 Remote Similarity NPD5332 Approved
0.5882 Remote Similarity NPD7331 Phase 2
0.5867 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5867 Remote Similarity NPD3732 Approved
0.5818 Remote Similarity NPD9411 Phase 1
0.5806 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5733 Remote Similarity NPD4756 Discovery
0.5714 Remote Similarity NPD5368 Approved
0.5714 Remote Similarity NPD4252 Approved
0.5714 Remote Similarity NPD3199 Clinical (unspecified phase)
0.566 Remote Similarity NPD9450 Approved
0.566 Remote Similarity NPD77 Approved
0.566 Remote Similarity NPD5783 Phase 3
0.5658 Remote Similarity NPD4268 Approved
0.5658 Remote Similarity NPD4271 Approved
0.5645 Remote Similarity NPD8971 Approved
0.5641 Remote Similarity NPD5369 Approved
0.5614 Remote Similarity NPD4265 Approved
0.5614 Remote Similarity NPD634 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