Structure

Physi-Chem Properties

Molecular Weight:  246.16
Volume:  287.054
LogP:  4.754
LogD:  2.655
LogS:  -4.507
# Rotatable Bonds:  8
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.523
Synthetic Accessibility Score:  2.912
Fsp3:  0.562
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:  -4.991
MDCK Permeability:  5.201850945013575e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.032
20% Bioavailability (F20%):  0.052
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  101.16240692138672%
Volume Distribution (VD):  0.359
Pgp-substrate:  1.0418812036514282%

ADMET: Metabolism

CYP1A2-inhibitor:  0.596
CYP1A2-substrate:  0.22
CYP2C19-inhibitor:  0.876
CYP2C19-substrate:  0.429
CYP2C9-inhibitor:  0.844
CYP2C9-substrate:  0.987
CYP2D6-inhibitor:  0.026
CYP2D6-substrate:  0.151
CYP3A4-inhibitor:  0.682
CYP3A4-substrate:  0.048

ADMET: Excretion

Clearance (CL):  3.787
Half-life (T1/2):  0.806

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.733
Drug-inuced Liver Injury (DILI):  0.973
AMES Toxicity:  0.427
Rat Oral Acute Toxicity:  0.087
Maximum Recommended Daily Dose:  0.031
Skin Sensitization:  0.947
Carcinogencity:  0.504
Eye Corrosion:  0.986
Eye Irritation:  0.986
Respiratory Toxicity:  0.867

Download Data

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

  Natural Product: NPC274290

Natural Product ID:  NPC274290
Common Name*:   (Z)-Hexadec-11-En-7,9-Diynoic Acid
IUPAC Name:   (Z)-hexadec-11-en-7,9-diynoic acid
Synonyms:  
Standard InCHIKey:  ZYKRBUYXWXJLBD-WAYWQWQTSA-N
Standard InCHI:  InChI=1S/C16H22O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h5-6H,2-4,11-15H2,1H3,(H,17,18)/b6-5-
SMILES:  CCCC/C=CC#CC#CCCCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL510276
PubChem CID:   10422039
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 = 51.0 % PMID[481346]
NPT2 Others Unspecified Inhibition = 36.0 % PMID[481346]
NPT2 Others Unspecified Inhibition = 45.0 % PMID[481346]

☑ 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 NPC274290 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 NPC473863
0.9808 High Similarity NPC179764
0.9808 High Similarity NPC187777
0.9615 High Similarity NPC54766
0.9259 High Similarity NPC225929
0.9231 High Similarity NPC294548
0.9231 High Similarity NPC1813
0.9231 High Similarity NPC70387
0.9231 High Similarity NPC321062
0.9231 High Similarity NPC36061
0.9231 High Similarity NPC139029
0.9216 High Similarity NPC28205
0.9216 High Similarity NPC284212
0.9091 High Similarity NPC267817
0.9057 High Similarity NPC32467
0.9057 High Similarity NPC85813
0.9057 High Similarity NPC281972
0.9057 High Similarity NPC154245
0.9057 High Similarity NPC290563
0.9057 High Similarity NPC424
0.9057 High Similarity NPC87564
0.9057 High Similarity NPC6095
0.9057 High Similarity NPC88966
0.9057 High Similarity NPC25417
0.9057 High Similarity NPC261831
0.9038 High Similarity NPC18357
0.9038 High Similarity NPC281245
0.8846 High Similarity NPC470412
0.8846 High Similarity NPC470410
0.8824 High Similarity NPC149821
0.8824 High Similarity NPC5413
0.8772 High Similarity NPC235242
0.8727 High Similarity NPC18951
0.8727 High Similarity NPC477201
0.8679 High Similarity NPC92114
0.8654 High Similarity NPC224227
0.8627 High Similarity NPC207292
0.8491 Intermediate Similarity NPC262968
0.8431 Intermediate Similarity NPC42304
0.8333 Intermediate Similarity NPC470320
0.8333 Intermediate Similarity NPC129458
0.8333 Intermediate Similarity NPC161366
0.8333 Intermediate Similarity NPC226592
0.8302 Intermediate Similarity NPC59051
0.8276 Intermediate Similarity NPC274927
0.8276 Intermediate Similarity NPC106851
0.8269 Intermediate Similarity NPC180534
0.8269 Intermediate Similarity NPC91495
0.8235 Intermediate Similarity NPC117572
0.8214 Intermediate Similarity NPC45626
0.8182 Intermediate Similarity NPC225066
0.8182 Intermediate Similarity NPC309606
0.8182 Intermediate Similarity NPC39633
0.8182 Intermediate Similarity NPC139545
0.8182 Intermediate Similarity NPC10081
0.8136 Intermediate Similarity NPC251042
0.8136 Intermediate Similarity NPC122521
0.8136 Intermediate Similarity NPC243532
0.8136 Intermediate Similarity NPC174447
0.8103 Intermediate Similarity NPC329819
0.8 Intermediate Similarity NPC303765
0.8 Intermediate Similarity NPC201939
0.8 Intermediate Similarity NPC477829
0.8 Intermediate Similarity NPC40082
0.7895 Intermediate Similarity NPC10316
0.7895 Intermediate Similarity NPC228473
0.7895 Intermediate Similarity NPC200845
0.7895 Intermediate Similarity NPC128061
0.7895 Intermediate Similarity NPC28779
0.7895 Intermediate Similarity NPC223677
0.7857 Intermediate Similarity NPC71761
0.7818 Intermediate Similarity NPC48162
0.7797 Intermediate Similarity NPC34416
0.7759 Intermediate Similarity NPC325977
0.7742 Intermediate Similarity NPC328089
0.7742 Intermediate Similarity NPC68343
0.7719 Intermediate Similarity NPC87394
0.7705 Intermediate Similarity NPC174560
0.7705 Intermediate Similarity NPC125312
0.7619 Intermediate Similarity NPC136164
0.7619 Intermediate Similarity NPC318420
0.7619 Intermediate Similarity NPC255863
0.7619 Intermediate Similarity NPC245947
0.7619 Intermediate Similarity NPC326268
0.7593 Intermediate Similarity NPC216130
0.7586 Intermediate Similarity NPC52264
0.7586 Intermediate Similarity NPC474672
0.7586 Intermediate Similarity NPC477984
0.75 Intermediate Similarity NPC255837
0.75 Intermediate Similarity NPC470411
0.75 Intermediate Similarity NPC19305
0.75 Intermediate Similarity NPC270796
0.75 Intermediate Similarity NPC469373
0.7419 Intermediate Similarity NPC321838
0.7419 Intermediate Similarity NPC320305
0.7419 Intermediate Similarity NPC328776
0.7414 Intermediate Similarity NPC137538
0.7414 Intermediate Similarity NPC322461
0.7385 Intermediate Similarity NPC271921
0.7385 Intermediate Similarity NPC330426
0.7385 Intermediate Similarity NPC104537
0.7385 Intermediate Similarity NPC99619
0.7385 Intermediate Similarity NPC127091
0.7385 Intermediate Similarity NPC148192
0.7385 Intermediate Similarity NPC22101
0.7385 Intermediate Similarity NPC26500
0.7377 Intermediate Similarity NPC329550
0.7358 Intermediate Similarity NPC8219
0.7302 Intermediate Similarity NPC29697
0.7273 Intermediate Similarity NPC476614
0.7273 Intermediate Similarity NPC324981
0.7273 Intermediate Similarity NPC48218
0.7273 Intermediate Similarity NPC141481
0.7273 Intermediate Similarity NPC473559
0.7258 Intermediate Similarity NPC143857
0.7258 Intermediate Similarity NPC229252
0.7258 Intermediate Similarity NPC327112
0.7258 Intermediate Similarity NPC328311
0.7241 Intermediate Similarity NPC284224
0.7231 Intermediate Similarity NPC142423
0.7231 Intermediate Similarity NPC308294
0.7188 Intermediate Similarity NPC234767
0.7167 Intermediate Similarity NPC327388
0.7164 Intermediate Similarity NPC317583
0.7164 Intermediate Similarity NPC143396
0.7143 Intermediate Similarity NPC163345
0.7143 Intermediate Similarity NPC475984
0.7143 Intermediate Similarity NPC271282
0.7143 Intermediate Similarity NPC66460
0.7143 Intermediate Similarity NPC325929
0.7143 Intermediate Similarity NPC207815
0.7121 Intermediate Similarity NPC60120
0.7121 Intermediate Similarity NPC475443
0.7121 Intermediate Similarity NPC473829
0.7115 Intermediate Similarity NPC103286
0.7115 Intermediate Similarity NPC163746
0.7059 Intermediate Similarity NPC476660
0.7059 Intermediate Similarity NPC42526
0.7049 Intermediate Similarity NPC323436
0.7049 Intermediate Similarity NPC323597
0.7049 Intermediate Similarity NPC211752
0.7049 Intermediate Similarity NPC323498
0.7031 Intermediate Similarity NPC470965
0.7031 Intermediate Similarity NPC54925
0.7031 Intermediate Similarity NPC477707
0.7018 Intermediate Similarity NPC474391
0.7015 Intermediate Similarity NPC53302
0.6981 Remote Similarity NPC71317
0.6981 Remote Similarity NPC129972
0.6981 Remote Similarity NPC301528
0.6912 Remote Similarity NPC473772
0.6897 Remote Similarity NPC178586
0.6897 Remote Similarity NPC129263
0.6897 Remote Similarity NPC477458
0.6892 Remote Similarity NPC200446
0.6875 Remote Similarity NPC113293
0.6863 Remote Similarity NPC73245
0.6857 Remote Similarity NPC325627
0.6849 Remote Similarity NPC469495
0.6842 Remote Similarity NPC304162
0.6833 Remote Similarity NPC49059
0.6833 Remote Similarity NPC256209
0.6825 Remote Similarity NPC474267
0.6825 Remote Similarity NPC329249
0.6818 Remote Similarity NPC320642
0.6818 Remote Similarity NPC323045
0.6818 Remote Similarity NPC317881
0.6812 Remote Similarity NPC67183
0.6792 Remote Similarity NPC171736
0.6792 Remote Similarity NPC149184
0.6792 Remote Similarity NPC307783
0.6792 Remote Similarity NPC216630
0.6792 Remote Similarity NPC196924
0.6792 Remote Similarity NPC209970
0.678 Remote Similarity NPC216407
0.6769 Remote Similarity NPC477830
0.6761 Remote Similarity NPC55527
0.6761 Remote Similarity NPC476046
0.6761 Remote Similarity NPC103958
0.6761 Remote Similarity NPC227396
0.6761 Remote Similarity NPC241854
0.6761 Remote Similarity NPC283908
0.6761 Remote Similarity NPC3753
0.6761 Remote Similarity NPC237591
0.6761 Remote Similarity NPC183503
0.6761 Remote Similarity NPC92558
0.6761 Remote Similarity NPC251970
0.6761 Remote Similarity NPC474321
0.6761 Remote Similarity NPC161923
0.6757 Remote Similarity NPC209995
0.6731 Remote Similarity NPC261080
0.6731 Remote Similarity NPC301585
0.6731 Remote Similarity NPC201844
0.6731 Remote Similarity NPC113928
0.6731 Remote Similarity NPC301696
0.6731 Remote Similarity NPC154186
0.6731 Remote Similarity NPC279026
0.6731 Remote Similarity NPC14227
0.6727 Remote Similarity NPC108195
0.6719 Remote Similarity NPC81896

  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 NPC274290 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
0.9231 High Similarity NPD3172 Approved
0.9057 High Similarity NPD4266 Approved
0.9057 High Similarity NPD3196 Approved
0.9057 High Similarity NPD3194 Approved
0.9057 High Similarity NPD3195 Phase 2
0.8824 High Similarity NPD3173 Approved
0.8491 Intermediate Similarity NPD28 Approved
0.8491 Intermediate Similarity NPD29 Approved
0.8269 Intermediate Similarity NPD622 Approved
0.8235 Intermediate Similarity NPD4222 Approved
0.8235 Intermediate Similarity NPD3174 Discontinued
0.7885 Intermediate Similarity NPD39 Approved
0.7742 Intermediate Similarity NPD3197 Phase 1
0.75 Intermediate Similarity NPD5326 Phase 3
0.7258 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.6964 Remote Similarity NPD5343 Approved
0.6792 Remote Similarity NPD2270 Approved
0.6731 Remote Similarity NPD9448 Phase 2
0.6731 Remote Similarity NPD633 Phase 3
0.6618 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6515 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6471 Remote Similarity NPD7331 Phase 2
0.6429 Remote Similarity NPD3199 Clinical (unspecified phase)
0.6429 Remote Similarity NPD6097 Approved
0.6429 Remote Similarity NPD6096 Approved
0.6415 Remote Similarity NPD9655 Approved
0.6406 Remote Similarity NPD6109 Phase 1
0.64 Remote Similarity NPD3732 Approved
0.6267 Remote Similarity NPD4756 Discovery
0.6234 Remote Similarity NPD5368 Approved
0.6226 Remote Similarity NPD3206 Approved
0.6203 Remote Similarity NPD5332 Approved
0.6203 Remote Similarity NPD5331 Approved
0.619 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6184 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6154 Remote Similarity NPD5369 Approved
0.6076 Remote Similarity NPD4269 Approved
0.6076 Remote Similarity NPD6435 Approved
0.6076 Remote Similarity NPD4270 Approved
0.6034 Remote Similarity NPD634 Phase 3
0.6026 Remote Similarity NPD4252 Approved
0.6 Remote Similarity NPD4220 Pre-registration
0.6 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6 Remote Similarity NPD5362 Discontinued
0.6 Remote Similarity NPD7154 Phase 3
0.6 Remote Similarity NPD8039 Approved
0.5974 Remote Similarity NPD4268 Approved
0.5974 Remote Similarity NPD4271 Approved
0.5857 Remote Similarity NPD7341 Phase 2
0.5854 Remote Similarity NPD5363 Approved
0.5823 Remote Similarity NPD4821 Approved
0.5823 Remote Similarity NPD4819 Approved
0.5823 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5823 Remote Similarity NPD4820 Approved
0.5823 Remote Similarity NPD4822 Approved
0.5806 Remote Similarity NPD6927 Phase 3
0.5783 Remote Similarity NPD4623 Approved
0.5783 Remote Similarity NPD5786 Approved
0.5783 Remote Similarity NPD4519 Discontinued
0.5775 Remote Similarity NPD3704 Approved
0.575 Remote Similarity NPD857 Phase 3
0.5714 Remote Similarity NPD9635 Discontinued
0.5714 Remote Similarity NPD3186 Phase 1
0.5663 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5647 Remote Similarity NPD4518 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