Structure

Physi-Chem Properties

Molecular Weight:  286.27
Volume:  358.59
LogP:  4.351
LogD:  4.379
LogS:  -2.759
# Rotatable Bonds:  14
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.232
Synthetic Accessibility Score:  2.946
Fsp3:  0.524
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:  -4.995
MDCK Permeability:  9.667854465078562e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.028
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.048
Plasma Protein Binding (PPB):  100.57029724121094%
Volume Distribution (VD):  3.537
Pgp-substrate:  0.6530406475067139%

ADMET: Metabolism

CYP1A2-inhibitor:  0.42
CYP1A2-substrate:  0.775
CYP2C19-inhibitor:  0.529
CYP2C19-substrate:  0.231
CYP2C9-inhibitor:  0.458
CYP2C9-substrate:  0.953
CYP2D6-inhibitor:  0.825
CYP2D6-substrate:  0.966
CYP3A4-inhibitor:  0.863
CYP3A4-substrate:  0.128

ADMET: Excretion

Clearance (CL):  3.75
Half-life (T1/2):  0.914

ADMET: Toxicity

hERG Blockers:  0.094
Human Hepatotoxicity (H-HT):  0.261
Drug-inuced Liver Injury (DILI):  0.005
AMES Toxicity:  0.918
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.398
Skin Sensitization:  0.977
Carcinogencity:  0.751
Eye Corrosion:  0.401
Eye Irritation:  0.939
Respiratory Toxicity:  0.93

Download Data

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

  Natural Product: NPC34671

Natural Product ID:  NPC34671
Common Name*:   (6Z,9Z,12Z,15Z)-1,6,9,12,15-Henicosapentaene
IUPAC Name:   (6Z,9Z,12Z,15Z)-henicosa-1,6,9,12,15-pentaene
Synonyms:  
Standard InCHIKey:  WMMKRRHSYGLRHN-MAZCIEHSSA-N
Standard InCHI:  InChI=1S/C21H34/c1-3-5-7-9-11-13-15-17-19-21-20-18-16-14-12-10-8-6-4-2/h3,11-14,17-20H,1,4-10,15-16,21H2,2H3/b13-11-,14-12-,19-17-,20-18-
SMILES:  CCCCC/C=CC/C=CC/C=CC/C=CCCCC=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3120703
PubChem CID:   21597700
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004475] Unsaturated hydrocarbons
        • [CHEMONTID:0004476] Unsaturated aliphatic hydrocarbons

*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
NPO12641 Stereospermum chelonoides Species Bignoniaceae 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
NPT2620 Individual Protein Seed linoleate 9S-lipoxygenase Glycine max IC50 = 40000.0 nM PMID[479217]

☑ 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 NPC34671 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
0.963 High Similarity NPC138325
0.931 High Similarity NPC151719
0.8667 High Similarity NPC471327
0.8621 High Similarity NPC115959
0.8621 High Similarity NPC123965
0.8438 Intermediate Similarity NPC182392
0.8276 Intermediate Similarity NPC179103
0.8276 Intermediate Similarity NPC76765
0.8125 Intermediate Similarity NPC99088
0.8125 Intermediate Similarity NPC305759
0.8125 Intermediate Similarity NPC173592
0.8065 Intermediate Similarity NPC196831
0.8 Intermediate Similarity NPC138113
0.7857 Intermediate Similarity NPC88325
0.7742 Intermediate Similarity NPC60288
0.7647 Intermediate Similarity NPC92224
0.7586 Intermediate Similarity NPC266144
0.7586 Intermediate Similarity NPC31891
0.7586 Intermediate Similarity NPC266539
0.7586 Intermediate Similarity NPC287191
0.7576 Intermediate Similarity NPC62779
0.75 Intermediate Similarity NPC206088
0.75 Intermediate Similarity NPC100879
0.75 Intermediate Similarity NPC3649
0.75 Intermediate Similarity NPC66577
0.7241 Intermediate Similarity NPC38513
0.7222 Intermediate Similarity NPC266298
0.7143 Intermediate Similarity NPC282119
0.7097 Intermediate Similarity NPC288991
0.7097 Intermediate Similarity NPC262789
0.7097 Intermediate Similarity NPC64176
0.7037 Intermediate Similarity NPC178306
0.6765 Remote Similarity NPC213749
0.6757 Remote Similarity NPC92863
0.6757 Remote Similarity NPC155880
0.6667 Remote Similarity NPC225855
0.6579 Remote Similarity NPC15934
0.6579 Remote Similarity NPC217923
0.6486 Remote Similarity NPC76145
0.6486 Remote Similarity NPC34764
0.6486 Remote Similarity NPC190810
0.6429 Remote Similarity NPC76976
0.641 Remote Similarity NPC329762
0.641 Remote Similarity NPC27444
0.641 Remote Similarity NPC103236
0.641 Remote Similarity NPC183670
0.6316 Remote Similarity NPC45727
0.6316 Remote Similarity NPC297643
0.6316 Remote Similarity NPC34873
0.6316 Remote Similarity NPC239039
0.6316 Remote Similarity NPC40434
0.6316 Remote Similarity NPC229262
0.6316 Remote Similarity NPC180840
0.6316 Remote Similarity NPC139717
0.6316 Remote Similarity NPC48638
0.6296 Remote Similarity NPC33192
0.6286 Remote Similarity NPC13217
0.6279 Remote Similarity NPC44363
0.6279 Remote Similarity NPC163751
0.6279 Remote Similarity NPC110234
0.6279 Remote Similarity NPC323445
0.625 Remote Similarity NPC218918
0.625 Remote Similarity NPC33489
0.625 Remote Similarity NPC144023
0.625 Remote Similarity NPC120926
0.625 Remote Similarity NPC269823
0.619 Remote Similarity NPC145755
0.619 Remote Similarity NPC108195
0.619 Remote Similarity NPC138935
0.619 Remote Similarity NPC267514
0.6176 Remote Similarity NPC16561
0.6154 Remote Similarity NPC33761
0.6136 Remote Similarity NPC91495
0.6136 Remote Similarity NPC124851
0.6098 Remote Similarity NPC177470
0.6098 Remote Similarity NPC256766
0.6098 Remote Similarity NPC213538
0.6098 Remote Similarity NPC298710
0.6098 Remote Similarity NPC149668
0.6098 Remote Similarity NPC287397
0.6098 Remote Similarity NPC208936
0.6098 Remote Similarity NPC67920
0.6098 Remote Similarity NPC304151
0.6053 Remote Similarity NPC185839
0.6047 Remote Similarity NPC49088
0.6047 Remote Similarity NPC269074
0.6047 Remote Similarity NPC276825
0.6047 Remote Similarity NPC239754
0.6 Remote Similarity NPC98284
0.6 Remote Similarity NPC17810
0.5952 Remote Similarity NPC116934
0.5952 Remote Similarity NPC270796
0.5952 Remote Similarity NPC252978
0.5909 Remote Similarity NPC55063
0.5909 Remote Similarity NPC19834
0.5909 Remote Similarity NPC180575
0.587 Remote Similarity NPC249670
0.587 Remote Similarity NPC474642
0.587 Remote Similarity NPC473913
0.587 Remote Similarity NPC59051
0.5854 Remote Similarity NPC188596
0.5854 Remote Similarity NPC469969
0.5854 Remote Similarity NPC469713
0.5814 Remote Similarity NPC101616
0.5789 Remote Similarity NPC38497
0.5778 Remote Similarity NPC471958
0.5758 Remote Similarity NPC225191
0.5758 Remote Similarity NPC10183
0.5758 Remote Similarity NPC179860
0.5758 Remote Similarity NPC19070
0.5758 Remote Similarity NPC51067
0.575 Remote Similarity NPC103213
0.575 Remote Similarity NPC171978
0.575 Remote Similarity NPC29091
0.575 Remote Similarity NPC255042
0.575 Remote Similarity NPC277382
0.575 Remote Similarity NPC182840
0.5745 Remote Similarity NPC262968
0.5745 Remote Similarity NPC261571
0.5745 Remote Similarity NPC477458
0.5714 Remote Similarity NPC108494
0.5714 Remote Similarity NPC67761
0.5714 Remote Similarity NPC194586
0.5714 Remote Similarity NPC209279
0.5714 Remote Similarity NPC206906
0.5714 Remote Similarity NPC473912
0.5714 Remote Similarity NPC51758
0.5714 Remote Similarity NPC180871
0.5714 Remote Similarity NPC68889
0.5714 Remote Similarity NPC88079
0.5682 Remote Similarity NPC191337
0.5682 Remote Similarity NPC474202
0.5682 Remote Similarity NPC160628
0.5682 Remote Similarity NPC140501
0.5682 Remote Similarity NPC117572
0.5682 Remote Similarity NPC474362
0.5667 Remote Similarity NPC96619
0.5652 Remote Similarity NPC31194
0.5652 Remote Similarity NPC248884
0.5652 Remote Similarity NPC85079
0.5652 Remote Similarity NPC153538
0.5652 Remote Similarity NPC5413
0.5652 Remote Similarity NPC207815
0.5652 Remote Similarity NPC302310
0.5652 Remote Similarity NPC22765
0.5652 Remote Similarity NPC17518
0.5652 Remote Similarity NPC149821
0.5641 Remote Similarity NPC201753
0.5641 Remote Similarity NPC279300
0.5625 Remote Similarity NPC49494
0.5625 Remote Similarity NPC188341
0.5625 Remote Similarity NPC92114
0.5625 Remote Similarity NPC208638
0.561 Remote Similarity NPC323278
0.561 Remote Similarity NPC12319
0.561 Remote Similarity NPC56917
0.561 Remote Similarity NPC18205

  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 NPC34671 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
0.6579 Remote Similarity NPD5783 Phase 3
0.6486 Remote Similarity NPD319 Phase 1
0.6429 Remote Similarity NPD39 Approved
0.6047 Remote Similarity NPD3174 Discontinued
0.6 Remote Similarity NPD8262 Approved
0.5952 Remote Similarity NPD5326 Phase 3
0.5814 Remote Similarity NPD6096 Approved
0.5814 Remote Similarity NPD6097 Approved
0.5806 Remote Similarity NPD8834 Discontinued
0.5778 Remote Similarity NPD5343 Approved
0.5745 Remote Similarity NPD28 Approved
0.5745 Remote Similarity NPD29 Approved
0.5682 Remote Similarity NPD4265 Approved
0.5682 Remote Similarity NPD4222 Approved
0.5652 Remote Similarity NPD3173 Approved
0.561 Remote Similarity NPD1153 Clinical (unspecified phase)

  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