Structure

Physi-Chem Properties

Molecular Weight:  231.2
Volume:  277.187
LogP:  4.404
LogD:  4.171
LogS:  -5.18
# Rotatable Bonds:  3
TPSA:  23.79
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.636
Synthetic Accessibility Score:  3.473
Fsp3:  0.688
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:  -4.406
MDCK Permeability:  2.6445881303516217e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.955
Plasma Protein Binding (PPB):  93.64695739746094%
Volume Distribution (VD):  0.87
Pgp-substrate:  5.167686462402344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.271
CYP1A2-substrate:  0.92
CYP2C19-inhibitor:  0.5
CYP2C19-substrate:  0.849
CYP2C9-inhibitor:  0.374
CYP2C9-substrate:  0.923
CYP2D6-inhibitor:  0.566
CYP2D6-substrate:  0.507
CYP3A4-inhibitor:  0.386
CYP3A4-substrate:  0.506

ADMET: Excretion

Clearance (CL):  4.296
Half-life (T1/2):  0.146

ADMET: Toxicity

hERG Blockers:  0.039
Human Hepatotoxicity (H-HT):  0.878
Drug-inuced Liver Injury (DILI):  0.403
AMES Toxicity:  0.213
Rat Oral Acute Toxicity:  0.964
Maximum Recommended Daily Dose:  0.835
Skin Sensitization:  0.317
Carcinogencity:  0.706
Eye Corrosion:  0.912
Eye Irritation:  0.81
Respiratory Toxicity:  0.983

Download Data

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

  Natural Product: NPC476679

Natural Product ID:  NPC476679
Common Name*:   3-isocyanotheonellin
IUPAC Name:   1-methyl-4-[(2Z,4E)-6-methylhepta-2,4-dien-2-yl]cyclohexane-1-carbonitrile
Synonyms:   3-Isocyanotheonellin
Standard InCHIKey:  CJKGYZTWQDYRJY-JEZZUBLBSA-N
Standard InCHI:  InChI=1S/C16H25N/c1-13(2)6-5-7-14(3)15-8-10-16(4,12-17)11-9-15/h5-7,13,15H,8-11H2,1-4H3/b6-5+,14-7-
SMILES:  CC(C)/C=C/C=C(/C)\C1CCC(CC1)(C)C#N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL460822
PubChem CID:   12039095
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO19990 Axinyssa isabela Species Halichondriidae Eukaryota n.a. Isla Isabel (Gulf of California, Mexico) n.a. PMID[19007287]
NPO19990 Axinyssa isabela Species Halichondriidae 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
NPT82 Cell Line MDA-MB-231 Homo sapiens GI50 = 27000 nM PMID[19007287]
NPT81 Cell Line A549 Homo sapiens GI50 = 36400 nM PMID[19007287]
NPT139 Cell Line HT-29 Homo sapiens GI50 = 33400 nM PMID[19007287]

☑ 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 NPC476679 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
0.8571 High Similarity NPC475716
0.8448 Intermediate Similarity NPC474086
0.8214 Intermediate Similarity NPC474457
0.8214 Intermediate Similarity NPC474415
0.8214 Intermediate Similarity NPC474528
0.8214 Intermediate Similarity NPC475696
0.7931 Intermediate Similarity NPC474455
0.7931 Intermediate Similarity NPC474454
0.7931 Intermediate Similarity NPC474420
0.7593 Intermediate Similarity NPC476681
0.7547 Intermediate Similarity NPC124851
0.75 Intermediate Similarity NPC474416
0.7255 Intermediate Similarity NPC177470
0.7091 Intermediate Similarity NPC17810
0.7091 Intermediate Similarity NPC17518
0.7091 Intermediate Similarity NPC22765
0.7059 Intermediate Similarity NPC144023
0.6981 Remote Similarity NPC248411
0.6923 Remote Similarity NPC190232
0.6923 Remote Similarity NPC105246
0.6885 Remote Similarity NPC469769
0.6863 Remote Similarity NPC183670
0.6852 Remote Similarity NPC296337
0.6852 Remote Similarity NPC86683
0.6825 Remote Similarity NPC219621
0.68 Remote Similarity NPC229262
0.68 Remote Similarity NPC139717
0.68 Remote Similarity NPC297643
0.68 Remote Similarity NPC239039
0.68 Remote Similarity NPC266298
0.6735 Remote Similarity NPC282119
0.6731 Remote Similarity NPC120926
0.6731 Remote Similarity NPC218918
0.6727 Remote Similarity NPC323445
0.6667 Remote Similarity NPC176621
0.6667 Remote Similarity NPC470893
0.66 Remote Similarity NPC76145
0.66 Remote Similarity NPC34764
0.66 Remote Similarity NPC190810
0.6562 Remote Similarity NPC469728
0.6545 Remote Similarity NPC13991
0.6545 Remote Similarity NPC49088
0.6545 Remote Similarity NPC114239
0.6545 Remote Similarity NPC241784
0.6508 Remote Similarity NPC472827
0.6481 Remote Similarity NPC86538
0.6481 Remote Similarity NPC192529
0.6481 Remote Similarity NPC109813
0.6481 Remote Similarity NPC60556
0.6471 Remote Similarity NPC48638
0.6471 Remote Similarity NPC45727
0.6406 Remote Similarity NPC311809
0.6406 Remote Similarity NPC317778
0.64 Remote Similarity NPC92224
0.6393 Remote Similarity NPC469770
0.6364 Remote Similarity NPC202189
0.6349 Remote Similarity NPC472830
0.6296 Remote Similarity NPC193180
0.629 Remote Similarity NPC55412
0.629 Remote Similarity NPC249645
0.6226 Remote Similarity NPC62086
0.6226 Remote Similarity NPC227632
0.6226 Remote Similarity NPC78551
0.619 Remote Similarity NPC321568
0.619 Remote Similarity NPC281986
0.619 Remote Similarity NPC470370
0.619 Remote Similarity NPC22019
0.619 Remote Similarity NPC470369
0.619 Remote Similarity NPC208749
0.6176 Remote Similarity NPC37792
0.6176 Remote Similarity NPC474456
0.6129 Remote Similarity NPC123194
0.6119 Remote Similarity NPC473959
0.6111 Remote Similarity NPC103290
0.6102 Remote Similarity NPC200129
0.6094 Remote Similarity NPC60772
0.6066 Remote Similarity NPC295777
0.6066 Remote Similarity NPC69898
0.6034 Remote Similarity NPC178644
0.6032 Remote Similarity NPC4881
0.6029 Remote Similarity NPC268039
0.6 Remote Similarity NPC473912
0.597 Remote Similarity NPC145715
0.597 Remote Similarity NPC283247
0.5968 Remote Similarity NPC476683
0.5946 Remote Similarity NPC125828
0.5942 Remote Similarity NPC149680
0.5938 Remote Similarity NPC115385
0.5938 Remote Similarity NPC11130
0.5932 Remote Similarity NPC106990
0.5918 Remote Similarity NPC66577
0.5918 Remote Similarity NPC206088
0.5915 Remote Similarity NPC476431
0.5915 Remote Similarity NPC184919
0.5915 Remote Similarity NPC138409
0.5902 Remote Similarity NPC473728
0.5882 Remote Similarity NPC50266
0.5882 Remote Similarity NPC469662
0.5882 Remote Similarity NPC476559
0.5867 Remote Similarity NPC110264
0.5862 Remote Similarity NPC159420
0.5857 Remote Similarity NPC193770
0.5821 Remote Similarity NPC317177
0.5821 Remote Similarity NPC317025
0.5821 Remote Similarity NPC326645
0.5821 Remote Similarity NPC329416
0.5821 Remote Similarity NPC60565
0.58 Remote Similarity NPC13217
0.58 Remote Similarity NPC213749
0.5781 Remote Similarity NPC318036
0.5775 Remote Similarity NPC216460
0.5775 Remote Similarity NPC32055
0.5775 Remote Similarity NPC310992
0.5758 Remote Similarity NPC28755
0.5758 Remote Similarity NPC152211
0.5753 Remote Similarity NPC470078
0.5753 Remote Similarity NPC21773
0.5753 Remote Similarity NPC265789
0.5735 Remote Similarity NPC202118
0.5735 Remote Similarity NPC197238
0.5714 Remote Similarity NPC250977
0.5714 Remote Similarity NPC286669
0.5714 Remote Similarity NPC5626
0.5714 Remote Similarity NPC178527
0.5714 Remote Similarity NPC279434
0.5714 Remote Similarity NPC476039
0.5714 Remote Similarity NPC176171
0.5714 Remote Similarity NPC92327
0.5714 Remote Similarity NPC60288
0.5714 Remote Similarity NPC222366
0.5694 Remote Similarity NPC200936
0.5692 Remote Similarity NPC173815
0.5686 Remote Similarity NPC305759
0.5686 Remote Similarity NPC173592
0.5686 Remote Similarity NPC99088
0.5679 Remote Similarity NPC477289
0.5652 Remote Similarity NPC226066
0.5652 Remote Similarity NPC4638
0.5645 Remote Similarity NPC179169
0.5645 Remote Similarity NPC157781
0.5645 Remote Similarity NPC181255
0.5645 Remote Similarity NPC306195
0.5645 Remote Similarity NPC35519
0.5645 Remote Similarity NPC208638
0.5636 Remote Similarity NPC246165
0.5634 Remote Similarity NPC176107
0.5634 Remote Similarity NPC197805
0.5625 Remote Similarity NPC200258
0.5616 Remote Similarity NPC49422
0.5616 Remote Similarity NPC9161
0.5606 Remote Similarity NPC27610
0.5606 Remote Similarity NPC231129
0.5606 Remote Similarity NPC324944
0.5606 Remote Similarity NPC56905
0.56 Remote Similarity NPC471327
0.56 Remote Similarity NPC329866
0.56 Remote Similarity NPC3649
0.56 Remote Similarity NPC476904
0.56 Remote Similarity NPC474797
0.56 Remote Similarity NPC151719
0.56 Remote Similarity NPC474796

  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 NPC476679 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
0.7091 Intermediate Similarity NPD8262 Approved
0.6923 Remote Similarity NPD1799 Clinical (unspecified phase)
0.66 Remote Similarity NPD319 Phase 1
0.629 Remote Similarity NPD4219 Approved
0.6029 Remote Similarity NPD173 Clinical (unspecified phase)
0.6 Remote Similarity NPD2205 Approved
0.6 Remote Similarity NPD2208 Approved
0.5833 Remote Similarity NPD6938 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6939 Phase 2
0.5821 Remote Similarity NPD4193 Approved
0.5821 Remote Similarity NPD4194 Approved
0.5821 Remote Similarity NPD4192 Approved
0.5821 Remote Similarity NPD4191 Approved
0.5783 Remote Similarity NPD5675 Discontinued
0.5696 Remote Similarity NPD8028 Phase 2
0.5652 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5616 Remote Similarity NPD7144 Approved
0.5616 Remote Similarity NPD7143 Approved
0.56 Remote Similarity NPD4687 Approved
0.56 Remote Similarity NPD4058 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