Structure

Physi-Chem Properties

Molecular Weight:  782.45
Volume:  775.587
LogP:  2.269
LogD:  1.922
LogS:  -3.732
# Rotatable Bonds:  7
TPSA:  236.06
# H-Bond Aceptor:  14
# H-Bond Donor:  9
# Rings:  7
# Heavy Atoms:  14

MedChem Properties

QED Drug-Likeness Score:  0.104
Synthetic Accessibility Score:  5.97
Fsp3:  0.927
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.761
MDCK Permeability:  3.390583151485771e-05
Pgp-inhibitor:  0.954
Pgp-substrate:  0.055
Human Intestinal Absorption (HIA):  0.903
20% Bioavailability (F20%):  0.133
30% Bioavailability (F30%):  0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.036
Plasma Protein Binding (PPB):  79.1919937133789%
Volume Distribution (VD):  0.385
Pgp-substrate:  10.993659973144531%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.863
CYP2C19-inhibitor:  0.001
CYP2C19-substrate:  0.478
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.009
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.069
CYP3A4-inhibitor:  0.155
CYP3A4-substrate:  0.039

ADMET: Excretion

Clearance (CL):  0.978
Half-life (T1/2):  0.654

ADMET: Toxicity

hERG Blockers:  0.033
Human Hepatotoxicity (H-HT):  0.218
Drug-inuced Liver Injury (DILI):  0.021
AMES Toxicity:  0.136
Rat Oral Acute Toxicity:  0.079
Maximum Recommended Daily Dose:  0.8
Skin Sensitization:  0.128
Carcinogencity:  0.018
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.957

Download Data

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

  Natural Product: NPC138325

Natural Product ID:  NPC138325
Common Name*:   (6Z,9Z,12Z,15Z,18Z)-1,6,9,12,15,18-Henicosahexaene
IUPAC Name:   (6Z,9Z,12Z,15Z,18Z)-henicosa-1,6,9,12,15,18-hexaene
Synonyms:  
Standard InCHIKey:  FDYJPTFUAQLZOU-DYXXURTGSA-N
Standard InCHI:  InChI=1S/C21H32/c1-3-5-7-9-11-13-15-17-19-21-20-18-16-14-12-10-8-6-4-2/h3,6,8,11-14,17-20H,1,4-5,7,9-10,15-16,21H2,2H3/b8-6-,13-11-,14-12-,19-17-,20-18-
SMILES:  CC/C=CC/C=CC/C=CC/C=CC/C=CCCCC=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3120704
PubChem CID:   11460308
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 = 5000.0 nM PMID[495830]

☑ 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 NPC138325 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 NPC34671
0.8966 High Similarity NPC151719
0.8929 High Similarity NPC115959
0.8929 High Similarity NPC123965
0.8387 Intermediate Similarity NPC305759
0.8387 Intermediate Similarity NPC173592
0.8387 Intermediate Similarity NPC99088
0.8333 Intermediate Similarity NPC471327
0.8276 Intermediate Similarity NPC138113
0.8125 Intermediate Similarity NPC182392
0.8 Intermediate Similarity NPC60288
0.7931 Intermediate Similarity NPC76765
0.7931 Intermediate Similarity NPC179103
0.7742 Intermediate Similarity NPC206088
0.7742 Intermediate Similarity NPC66577
0.7742 Intermediate Similarity NPC196831
0.75 Intermediate Similarity NPC88325
0.7353 Intermediate Similarity NPC92224
0.7333 Intermediate Similarity NPC288991
0.7333 Intermediate Similarity NPC262789
0.7333 Intermediate Similarity NPC64176
0.7308 Intermediate Similarity NPC178306
0.7273 Intermediate Similarity NPC62779
0.7241 Intermediate Similarity NPC287191
0.7241 Intermediate Similarity NPC266539
0.7241 Intermediate Similarity NPC31891
0.7241 Intermediate Similarity NPC266144
0.7188 Intermediate Similarity NPC3649
0.7188 Intermediate Similarity NPC100879
0.697 Remote Similarity NPC213749
0.6944 Remote Similarity NPC266298
0.6923 Remote Similarity NPC225855
0.6897 Remote Similarity NPC38513
0.6857 Remote Similarity NPC282119
0.6538 Remote Similarity NPC33192
0.6486 Remote Similarity NPC92863
0.6486 Remote Similarity NPC34873
0.6486 Remote Similarity NPC155880
0.6486 Remote Similarity NPC45727
0.6486 Remote Similarity NPC40434
0.6486 Remote Similarity NPC180840
0.6486 Remote Similarity NPC48638
0.6471 Remote Similarity NPC13217
0.641 Remote Similarity NPC269823
0.6341 Remote Similarity NPC138935
0.6316 Remote Similarity NPC15934
0.6316 Remote Similarity NPC217923
0.625 Remote Similarity NPC256766
0.625 Remote Similarity NPC213538
0.6216 Remote Similarity NPC34764
0.6216 Remote Similarity NPC185839
0.6216 Remote Similarity NPC76145
0.6216 Remote Similarity NPC190810
0.619 Remote Similarity NPC76976
0.6154 Remote Similarity NPC183670
0.6154 Remote Similarity NPC329762
0.6154 Remote Similarity NPC103236
0.6154 Remote Similarity NPC27444
0.6098 Remote Similarity NPC270796
0.6098 Remote Similarity NPC116934
0.6053 Remote Similarity NPC229262
0.6053 Remote Similarity NPC239039
0.6053 Remote Similarity NPC297643
0.6053 Remote Similarity NPC139717
0.6047 Remote Similarity NPC323445
0.6047 Remote Similarity NPC163751
0.6047 Remote Similarity NPC110234
0.6047 Remote Similarity NPC44363
0.6 Remote Similarity NPC144023
0.6 Remote Similarity NPC120926
0.6 Remote Similarity NPC469713
0.6 Remote Similarity NPC33489
0.6 Remote Similarity NPC218918
0.6 Remote Similarity NPC469969
0.5952 Remote Similarity NPC108195
0.5952 Remote Similarity NPC267514
0.5952 Remote Similarity NPC145755
0.5946 Remote Similarity NPC38497
0.5938 Remote Similarity NPC19070
0.5938 Remote Similarity NPC51067
0.5938 Remote Similarity NPC225191
0.5938 Remote Similarity NPC10183
0.5938 Remote Similarity NPC179860
0.5909 Remote Similarity NPC124851
0.5909 Remote Similarity NPC91495
0.5897 Remote Similarity NPC277382
0.5897 Remote Similarity NPC29091
0.5897 Remote Similarity NPC33761
0.5897 Remote Similarity NPC103213
0.5897 Remote Similarity NPC182840
0.5897 Remote Similarity NPC171978
0.5897 Remote Similarity NPC255042
0.5882 Remote Similarity NPC16561
0.5862 Remote Similarity NPC96619
0.5854 Remote Similarity NPC67920
0.5854 Remote Similarity NPC287397
0.5854 Remote Similarity NPC88079
0.5854 Remote Similarity NPC209279
0.5854 Remote Similarity NPC194586
0.5854 Remote Similarity NPC51758
0.5854 Remote Similarity NPC149668
0.5854 Remote Similarity NPC180871
0.5854 Remote Similarity NPC68889
0.5854 Remote Similarity NPC67761
0.5854 Remote Similarity NPC298710
0.5854 Remote Similarity NPC206906
0.5854 Remote Similarity NPC108494
0.5854 Remote Similarity NPC304151
0.5854 Remote Similarity NPC177470
0.5854 Remote Similarity NPC208936
0.5814 Remote Similarity NPC239754
0.5814 Remote Similarity NPC140501
0.5814 Remote Similarity NPC276825
0.5814 Remote Similarity NPC117572
0.5814 Remote Similarity NPC269074
0.5814 Remote Similarity NPC160628
0.5814 Remote Similarity NPC49088
0.5789 Remote Similarity NPC279300
0.5789 Remote Similarity NPC201753
0.5778 Remote Similarity NPC98284
0.5778 Remote Similarity NPC17810
0.575 Remote Similarity NPC12319
0.575 Remote Similarity NPC56917
0.575 Remote Similarity NPC18205
0.575 Remote Similarity NPC323278
0.5714 Remote Similarity NPC216921
0.5714 Remote Similarity NPC252978
0.5682 Remote Similarity NPC308331
0.5682 Remote Similarity NPC180575
0.5682 Remote Similarity NPC19834
0.5682 Remote Similarity NPC55063
0.5676 Remote Similarity NPC58957
0.5652 Remote Similarity NPC474642
0.5652 Remote Similarity NPC249670
0.5652 Remote Similarity NPC59051
0.5652 Remote Similarity NPC473913
0.5652 Remote Similarity NPC474460
0.561 Remote Similarity NPC188596

  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 NPC138325 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
0.6757 Remote Similarity NPD5783 Phase 3
0.6216 Remote Similarity NPD319 Phase 1
0.619 Remote Similarity NPD39 Approved
0.6098 Remote Similarity NPD5326 Phase 3
0.6 Remote Similarity NPD8834 Discontinued
0.5952 Remote Similarity NPD6097 Approved
0.5952 Remote Similarity NPD6096 Approved
0.5909 Remote Similarity NPD5343 Approved
0.5814 Remote Similarity NPD4265 Approved
0.5814 Remote Similarity NPD3174 Discontinued
0.5814 Remote Similarity NPD4222 Approved
0.5778 Remote Similarity NPD8262 Approved
0.575 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