Structure

Physi-Chem Properties

Molecular Weight:  492.09
Volume:  445.387
LogP:  1.076
LogD:  0.129
LogS:  -1.283
# Rotatable Bonds:  3
TPSA:  245.67
# H-Bond Aceptor:  13
# H-Bond Donor:  10
# Rings:  4
# Heavy Atoms:  13

MedChem Properties

QED Drug-Likeness Score:  0.131
Synthetic Accessibility Score:  4.564
Fsp3:  0.273
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  3
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.525
MDCK Permeability:  2.637944135130965e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.045
Human Intestinal Absorption (HIA):  0.926
20% Bioavailability (F20%):  0.548
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.005
Plasma Protein Binding (PPB):  93.97776794433594%
Volume Distribution (VD):  0.703
Pgp-substrate:  13.259263038635254%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.028
CYP2C19-inhibitor:  0.008
CYP2C19-substrate:  0.038
CYP2C9-inhibitor:  0.04
CYP2C9-substrate:  0.036
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.074
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.001

ADMET: Excretion

Clearance (CL):  1.631
Half-life (T1/2):  0.946

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.19
Drug-inuced Liver Injury (DILI):  0.993
AMES Toxicity:  0.308
Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.004
Skin Sensitization:  0.799
Carcinogencity:  0.021
Eye Corrosion:  0.003
Eye Irritation:  0.438
Respiratory Toxicity:  0.066

Download Data

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

  Natural Product: NPC106990

Natural Product ID:  NPC106990
Common Name*:   (1Z,4Z)-7Alphah-11-Aminogermacra-1(10),4-Diene
IUPAC Name:   2-[(1R,3Z,7Z)-4,8-dimethylcyclodeca-3,7-dien-1-yl]propan-2-amine
Synonyms:  
Standard InCHIKey:  FMELZXAKSAUHLF-IDYIYGFPSA-N
Standard InCHI:  InChI=1S/C15H27N/c1-12-6-5-7-13(2)9-11-14(10-8-12)15(3,4)16/h6,9,14H,5,7-8,10-11,16H2,1-4H3/b12-6-,13-9-/t14-/m1/s1
SMILES:  C/C/1=C/CC/C(=CC[C@@H](CC1)C(C)(C)N)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL452646
PubChem CID:   11276079
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002456] Germacrane 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
NPO33261 axinyssa n. sp. Species Halichondriidae Eukaryota n.a. Thai n.a. PMID[15043445]

☑ 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
NPT20 Organism Candida albicans Candida albicans IZ = 27.0 mm PMID[489229]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 23.0 mm PMID[489229]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 22.0 mm PMID[489229]

☑ 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 NPC106990 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
0.7292 Intermediate Similarity NPC120926
0.7292 Intermediate Similarity NPC218918
0.7 Intermediate Similarity NPC86538
0.6897 Remote Similarity NPC470369
0.6897 Remote Similarity NPC470370
0.66 Remote Similarity NPC144023
0.6596 Remote Similarity NPC92224
0.6557 Remote Similarity NPC317778
0.6557 Remote Similarity NPC311809
0.65 Remote Similarity NPC472830
0.6471 Remote Similarity NPC177470
0.6471 Remote Similarity NPC473912
0.6458 Remote Similarity NPC76145
0.6458 Remote Similarity NPC34764
0.6458 Remote Similarity NPC190810
0.6444 Remote Similarity NPC100879
0.64 Remote Similarity NPC183670
0.6349 Remote Similarity NPC145715
0.6346 Remote Similarity NPC109813
0.6346 Remote Similarity NPC60556
0.6327 Remote Similarity NPC239039
0.6327 Remote Similarity NPC139717
0.6327 Remote Similarity NPC229262
0.6327 Remote Similarity NPC297643
0.6327 Remote Similarity NPC266298
0.625 Remote Similarity NPC473959
0.625 Remote Similarity NPC282119
0.6226 Remote Similarity NPC248411
0.6226 Remote Similarity NPC202189
0.619 Remote Similarity NPC219621
0.614 Remote Similarity NPC27438
0.6111 Remote Similarity NPC86683
0.6111 Remote Similarity NPC296337
0.6111 Remote Similarity NPC114239
0.6111 Remote Similarity NPC13991
0.6111 Remote Similarity NPC49088
0.6111 Remote Similarity NPC241784
0.6094 Remote Similarity NPC472544
0.6087 Remote Similarity NPC206088
0.6034 Remote Similarity NPC68014
0.6 Remote Similarity NPC45727
0.6 Remote Similarity NPC323445
0.6 Remote Similarity NPC48638
0.5957 Remote Similarity NPC213749
0.5932 Remote Similarity NPC476679
0.5902 Remote Similarity NPC4881
0.5902 Remote Similarity NPC318036
0.5893 Remote Similarity NPC124851
0.5873 Remote Similarity NPC472827
0.5833 Remote Similarity NPC63396
0.5833 Remote Similarity NPC202850
0.5821 Remote Similarity NPC37792
0.5806 Remote Similarity NPC474528
0.5806 Remote Similarity NPC173815
0.5806 Remote Similarity NPC474415
0.5806 Remote Similarity NPC475696
0.5806 Remote Similarity NPC474457
0.5797 Remote Similarity NPC184919
0.5797 Remote Similarity NPC138409
0.5789 Remote Similarity NPC17518
0.5789 Remote Similarity NPC22765
0.5745 Remote Similarity NPC471327
0.5745 Remote Similarity NPC3649
0.5714 Remote Similarity NPC324944
0.5714 Remote Similarity NPC231129
0.569 Remote Similarity NPC329773
0.5634 Remote Similarity NPC476329
0.5625 Remote Similarity NPC152211
0.5625 Remote Similarity NPC28755
0.5625 Remote Similarity NPC474420
0.5625 Remote Similarity NPC82919
0.5625 Remote Similarity NPC13217
0.5625 Remote Similarity NPC474455
0.5625 Remote Similarity NPC474454
0.5625 Remote Similarity NPC475716
0.5614 Remote Similarity NPC178644

  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 NPC106990 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
0.6458 Remote Similarity NPD319 Phase 1
0.6226 Remote Similarity NPD9675 Approved
0.6226 Remote Similarity NPD9674 Approved
0.5857 Remote Similarity NPD5365 Phase 2
0.5686 Remote Similarity NPD635 Phase 3
0.5686 Remote Similarity NPD636 Phase 3
0.5634 Remote Similarity NPD292 Approved
0.5634 Remote Similarity NPD294 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