Structure

Physi-Chem Properties

Molecular Weight:  238.23
Volume:  288.81
LogP:  4.893
LogD:  4.013
LogS:  -3.338
# Rotatable Bonds:  13
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.237
Synthetic Accessibility Score:  2.275
Fsp3:  0.812
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.806
MDCK Permeability:  2.303795554325916e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.998
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.884
Plasma Protein Binding (PPB):  89.37782287597656%
Volume Distribution (VD):  3.734
Pgp-substrate:  2.9560770988464355%

ADMET: Metabolism

CYP1A2-inhibitor:  0.353
CYP1A2-substrate:  0.27
CYP2C19-inhibitor:  0.392
CYP2C19-substrate:  0.08
CYP2C9-inhibitor:  0.249
CYP2C9-substrate:  0.936
CYP2D6-inhibitor:  0.44
CYP2D6-substrate:  0.715
CYP3A4-inhibitor:  0.409
CYP3A4-substrate:  0.074

ADMET: Excretion

Clearance (CL):  3.835
Half-life (T1/2):  0.742

ADMET: Toxicity

hERG Blockers:  0.385
Human Hepatotoxicity (H-HT):  0.032
Drug-inuced Liver Injury (DILI):  0.033
AMES Toxicity:  0.162
Rat Oral Acute Toxicity:  0.021
Maximum Recommended Daily Dose:  0.043
Skin Sensitization:  0.976
Carcinogencity:  0.291
Eye Corrosion:  0.988
Eye Irritation:  0.989
Respiratory Toxicity:  0.938

Download Data

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

  Natural Product: NPC239754

Natural Product ID:  NPC239754
Common Name*:   (Z)-Hexadec-11-Enal
IUPAC Name:   (Z)-hexadec-11-enal
Synonyms:  
Standard InCHIKey:  AMTITFMUKRZZEE-WAYWQWQTSA-N
Standard InCHI:  InChI=1S/C16H30O/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17/h5-6,16H,2-4,7-15H2,1H3/b6-5-
SMILES:  CCCC/C=CCCCCCCCCCC=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3185124
PubChem CID:   5364495
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000298] Fatty aldehydes

*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
NPO5777 Pimelobacter simplex Species 0cardioidaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22091 Geitlerinema acutissimum Species Coleofasciculaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO23637 Ramalina ecklonii Species Ramalinaceae 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
NPT2 Others Unspecified "" Potency n.a. 61130.6 nM PubChem BioAssay data set
NPT2 Others Unspecified "" Potency n.a. 34665.4 nM PubChem BioAssay data set

☑ 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 NPC239754 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
0.9767 High Similarity NPC44363
0.9767 High Similarity NPC110234
0.9767 High Similarity NPC163751
0.881 High Similarity NPC48930
0.8542 High Similarity NPC234829
0.8 Intermediate Similarity NPC298710
0.8 Intermediate Similarity NPC67920
0.8 Intermediate Similarity NPC287397
0.7917 Intermediate Similarity NPC324812
0.7778 Intermediate Similarity NPC33489
0.7708 Intermediate Similarity NPC276009
0.7708 Intermediate Similarity NPC195246
0.7708 Intermediate Similarity NPC22098
0.76 Intermediate Similarity NPC224227
0.7547 Intermediate Similarity NPC28779
0.7547 Intermediate Similarity NPC223677
0.7547 Intermediate Similarity NPC200845
0.7547 Intermediate Similarity NPC10316
0.7547 Intermediate Similarity NPC128061
0.7547 Intermediate Similarity NPC188789
0.75 Intermediate Similarity NPC71761
0.75 Intermediate Similarity NPC92863
0.75 Intermediate Similarity NPC139545
0.75 Intermediate Similarity NPC309606
0.75 Intermediate Similarity NPC155880
0.75 Intermediate Similarity NPC39633
0.7451 Intermediate Similarity NPC477458
0.7451 Intermediate Similarity NPC262968
0.7447 Intermediate Similarity NPC106819
0.7333 Intermediate Similarity NPC33761
0.7255 Intermediate Similarity NPC474391
0.7234 Intermediate Similarity NPC208936
0.7222 Intermediate Similarity NPC228473
0.717 Intermediate Similarity NPC1813
0.717 Intermediate Similarity NPC139029
0.717 Intermediate Similarity NPC36061
0.717 Intermediate Similarity NPC294548
0.7059 Intermediate Similarity NPC145311
0.7037 Intermediate Similarity NPC25417
0.7037 Intermediate Similarity NPC209431
0.7037 Intermediate Similarity NPC88966
0.7037 Intermediate Similarity NPC87564
0.7037 Intermediate Similarity NPC281972
0.7037 Intermediate Similarity NPC32467
0.7037 Intermediate Similarity NPC6095
0.7037 Intermediate Similarity NPC100809
0.7037 Intermediate Similarity NPC424
0.7037 Intermediate Similarity NPC85813
0.7037 Intermediate Similarity NPC154245
0.7037 Intermediate Similarity NPC290563
0.7037 Intermediate Similarity NPC261831
0.7 Intermediate Similarity NPC100380
0.7 Intermediate Similarity NPC268039
0.6981 Remote Similarity NPC281245
0.6981 Remote Similarity NPC22182
0.6981 Remote Similarity NPC92114
0.6977 Remote Similarity NPC49615
0.6939 Remote Similarity NPC114841
0.6923 Remote Similarity NPC59051
0.6905 Remote Similarity NPC262505
0.6905 Remote Similarity NPC254713
0.6905 Remote Similarity NPC261991
0.6905 Remote Similarity NPC49151
0.6905 Remote Similarity NPC179831
0.6897 Remote Similarity NPC143857
0.6897 Remote Similarity NPC243532
0.6897 Remote Similarity NPC229252
0.6889 Remote Similarity NPC279300
0.6863 Remote Similarity NPC216130
0.6852 Remote Similarity NPC321062
0.6852 Remote Similarity NPC70387
0.6809 Remote Similarity NPC18205
0.6809 Remote Similarity NPC12319
0.6809 Remote Similarity NPC101147
0.6809 Remote Similarity NPC323278
0.6786 Remote Similarity NPC477201
0.6786 Remote Similarity NPC18951
0.6786 Remote Similarity NPC187777
0.6786 Remote Similarity NPC179764
0.678 Remote Similarity NPC201939
0.6739 Remote Similarity NPC180840
0.6731 Remote Similarity NPC149821
0.6731 Remote Similarity NPC207815
0.6731 Remote Similarity NPC5413
0.6731 Remote Similarity NPC163345
0.6727 Remote Similarity NPC95581
0.6727 Remote Similarity NPC250539
0.6724 Remote Similarity NPC473652
0.6667 Remote Similarity NPC75204
0.6667 Remote Similarity NPC225929
0.6667 Remote Similarity NPC161366
0.6667 Remote Similarity NPC54925
0.6607 Remote Similarity NPC474672
0.6607 Remote Similarity NPC54766
0.6607 Remote Similarity NPC473863
0.6607 Remote Similarity NPC274290
0.66 Remote Similarity NPC108195
0.66 Remote Similarity NPC25771
0.66 Remote Similarity NPC267514
0.66 Remote Similarity NPC145755
0.6596 Remote Similarity NPC217923
0.6557 Remote Similarity NPC470320
0.6557 Remote Similarity NPC68343
0.6557 Remote Similarity NPC328089
0.6545 Remote Similarity NPC284224
0.6545 Remote Similarity NPC61177
0.6538 Remote Similarity NPC207292
0.6538 Remote Similarity NPC91495
0.6531 Remote Similarity NPC149668
0.6522 Remote Similarity NPC185839
0.6522 Remote Similarity NPC220061
0.6512 Remote Similarity NPC151719
0.6508 Remote Similarity NPC193770
0.6481 Remote Similarity NPC27438
0.6481 Remote Similarity NPC30433
0.6471 Remote Similarity NPC269074
0.6471 Remote Similarity NPC117572
0.6471 Remote Similarity NPC76976
0.6452 Remote Similarity NPC296436
0.6452 Remote Similarity NPC318420
0.6452 Remote Similarity NPC326268
0.6452 Remote Similarity NPC136164
0.6452 Remote Similarity NPC255863
0.6452 Remote Similarity NPC176215
0.6452 Remote Similarity NPC245947
0.6444 Remote Similarity NPC72258
0.6441 Remote Similarity NPC274927
0.6441 Remote Similarity NPC106851
0.6429 Remote Similarity NPC202850
0.6429 Remote Similarity NPC137538
0.6429 Remote Similarity NPC63396
0.6406 Remote Similarity NPC155198
0.64 Remote Similarity NPC252978
0.64 Remote Similarity NPC301972
0.64 Remote Similarity NPC292463
0.6379 Remote Similarity NPC230823
0.6379 Remote Similarity NPC321568
0.6379 Remote Similarity NPC208749
0.6379 Remote Similarity NPC267626
0.6379 Remote Similarity NPC22019
0.6379 Remote Similarity NPC49575
0.6379 Remote Similarity NPC281986
0.6379 Remote Similarity NPC55004
0.6346 Remote Similarity NPC19834
0.6346 Remote Similarity NPC262558
0.6346 Remote Similarity NPC8610
0.6346 Remote Similarity NPC55063
0.6333 Remote Similarity NPC251042
0.6333 Remote Similarity NPC174447
0.6333 Remote Similarity NPC235242
0.6333 Remote Similarity NPC122521
0.6316 Remote Similarity NPC275472
0.6316 Remote Similarity NPC477984
0.6316 Remote Similarity NPC52264
0.6308 Remote Similarity NPC261398
0.6304 Remote Similarity NPC301919
0.6304 Remote Similarity NPC38497
0.6296 Remote Similarity NPC32351
0.6296 Remote Similarity NPC15325
0.629 Remote Similarity NPC226592
0.6271 Remote Similarity NPC94991
0.6271 Remote Similarity NPC266295
0.6271 Remote Similarity NPC30215
0.625 Remote Similarity NPC475443
0.625 Remote Similarity NPC15934
0.625 Remote Similarity NPC290350
0.625 Remote Similarity NPC473829
0.625 Remote Similarity NPC26500
0.625 Remote Similarity NPC474141
0.625 Remote Similarity NPC104537
0.625 Remote Similarity NPC217188
0.625 Remote Similarity NPC4370
0.625 Remote Similarity NPC271921
0.625 Remote Similarity NPC99619
0.625 Remote Similarity NPC148192
0.625 Remote Similarity NPC127091
0.625 Remote Similarity NPC330426
0.625 Remote Similarity NPC22101
0.623 Remote Similarity NPC328776
0.623 Remote Similarity NPC320305
0.623 Remote Similarity NPC168407
0.623 Remote Similarity NPC40082
0.623 Remote Similarity NPC321838
0.6226 Remote Similarity NPC180534
0.6226 Remote Similarity NPC91962
0.6207 Remote Similarity NPC327388
0.6207 Remote Similarity NPC473733
0.6207 Remote Similarity NPC325977
0.619 Remote Similarity NPC133904
0.619 Remote Similarity NPC32279
0.6182 Remote Similarity NPC284212
0.6182 Remote Similarity NPC28205
0.6182 Remote Similarity NPC48162
0.617 Remote Similarity NPC8416
0.617 Remote Similarity NPC254764
0.617 Remote Similarity NPC69245
0.6167 Remote Similarity NPC259261
0.6154 Remote Similarity NPC324981
0.6154 Remote Similarity NPC48218
0.6154 Remote Similarity NPC191337

  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 NPC239754 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
0.7451 Intermediate Similarity NPD28 Approved
0.7451 Intermediate Similarity NPD29 Approved
0.717 Intermediate Similarity NPD3172 Approved
0.7143 Intermediate Similarity NPD3174 Discontinued
0.7037 Intermediate Similarity NPD3196 Approved
0.7037 Intermediate Similarity NPD3195 Phase 2
0.7037 Intermediate Similarity NPD3194 Approved
0.7037 Intermediate Similarity NPD4266 Approved
0.6863 Remote Similarity NPD5343 Approved
0.6731 Remote Similarity NPD3173 Approved
0.66 Remote Similarity NPD6097 Approved
0.66 Remote Similarity NPD6096 Approved
0.6596 Remote Similarity NPD5783 Phase 3
0.6557 Remote Similarity NPD3197 Phase 1
0.6471 Remote Similarity NPD39 Approved
0.6471 Remote Similarity NPD4222 Approved
0.6316 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6226 Remote Similarity NPD622 Approved
0.6094 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6078 Remote Similarity NPD5326 Phase 3
0.6066 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5893 Remote Similarity NPD6927 Phase 3
0.5634 Remote Similarity NPD8039 Approved
0.5625 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5606 Remote Similarity NPD7331 Phase 2

  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