Structure

Physi-Chem Properties

Molecular Weight:  204.19
Volume:  245.61
LogP:  5.001
LogD:  4.462
LogS:  -5.542
# Rotatable Bonds:  1
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.548
Synthetic Accessibility Score:  4.395
Fsp3:  0.733
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:  -4.466
MDCK Permeability:  1.6103795132949017e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.976
30% Bioavailability (F30%):  0.969

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.556
Plasma Protein Binding (PPB):  93.58982849121094%
Volume Distribution (VD):  4.367
Pgp-substrate:  4.982833385467529%

ADMET: Metabolism

CYP1A2-inhibitor:  0.732
CYP1A2-substrate:  0.854
CYP2C19-inhibitor:  0.25
CYP2C19-substrate:  0.905
CYP2C9-inhibitor:  0.391
CYP2C9-substrate:  0.276
CYP2D6-inhibitor:  0.101
CYP2D6-substrate:  0.888
CYP3A4-inhibitor:  0.898
CYP3A4-substrate:  0.48

ADMET: Excretion

Clearance (CL):  12.816
Half-life (T1/2):  0.053

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.186
Drug-inuced Liver Injury (DILI):  0.583
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.125
Maximum Recommended Daily Dose:  0.546
Skin Sensitization:  0.04
Carcinogencity:  0.533
Eye Corrosion:  0.094
Eye Irritation:  0.71
Respiratory Toxicity:  0.487

Download Data

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

  Natural Product: NPC473912

Natural Product ID:  NPC473912
Common Name*:   (3Ar,7S)-1,4-Dimethyl-7-Prop-1-En-2-Yl-1,2,3,3A,4,5,6,7-Octahydroazulene
IUPAC Name:   (3aR,7S)-1,4-dimethyl-7-prop-1-en-2-yl-1,2,3,3a,4,5,6,7-octahydroazulene
Synonyms:  
Standard InCHIKey:  DUYRYUZIBGFLDD-CLRIEMFWSA-N
Standard InCHI:  InChI=1S/C15H24/c1-10(2)13-7-5-11(3)14-8-6-12(4)15(14)9-13/h9,11-14H,1,5-8H2,2-4H3/t11?,12?,13-,14+/m0/s1
SMILES:  CC1CC[C@H]2C1=C[C@H](CCC2C)C(=C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL455046
PubChem CID:   44566864
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
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[19199790]
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[8759172]

☑ 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
NPT91 Cell Line KB Homo sapiens IC50 > 20.0 ug.mL-1 PMID[494354]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 10.0 ug.mL-1 PMID[494354]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 8.46 ug.mL-1 PMID[494354]
NPT2 Others Unspecified Ratio IC50 > 2.3 n.a. PMID[494354]

☑ 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 NPC473912 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
0.8409 Intermediate Similarity NPC49088
0.8222 Intermediate Similarity NPC323445
0.7727 Intermediate Similarity NPC177470
0.766 Intermediate Similarity NPC178644
0.7619 Intermediate Similarity NPC229262
0.7619 Intermediate Similarity NPC297643
0.7619 Intermediate Similarity NPC139717
0.7561 Intermediate Similarity NPC92224
0.7556 Intermediate Similarity NPC109813
0.7556 Intermediate Similarity NPC90506
0.7556 Intermediate Similarity NPC60556
0.7556 Intermediate Similarity NPC90803
0.7556 Intermediate Similarity NPC23145
0.7556 Intermediate Similarity NPC86538
0.75 Intermediate Similarity NPC473614
0.75 Intermediate Similarity NPC218918
0.75 Intermediate Similarity NPC144023
0.75 Intermediate Similarity NPC120926
0.7391 Intermediate Similarity NPC202189
0.7391 Intermediate Similarity NPC248411
0.7381 Intermediate Similarity NPC34764
0.7381 Intermediate Similarity NPC190810
0.7381 Intermediate Similarity NPC76145
0.7358 Intermediate Similarity NPC278550
0.7347 Intermediate Similarity NPC200129
0.7273 Intermediate Similarity NPC246165
0.7273 Intermediate Similarity NPC183670
0.7234 Intermediate Similarity NPC229403
0.7234 Intermediate Similarity NPC296337
0.7234 Intermediate Similarity NPC86683
0.7222 Intermediate Similarity NPC472830
0.7209 Intermediate Similarity NPC239039
0.7209 Intermediate Similarity NPC266298
0.7174 Intermediate Similarity NPC166362
0.7174 Intermediate Similarity NPC141777
0.7174 Intermediate Similarity NPC474118
0.7174 Intermediate Similarity NPC51762
0.7174 Intermediate Similarity NPC227670
0.7143 Intermediate Similarity NPC282119
0.7091 Intermediate Similarity NPC143834
0.7091 Intermediate Similarity NPC469321
0.7 Intermediate Similarity NPC206088
0.6939 Remote Similarity NPC124851
0.6875 Remote Similarity NPC114239
0.6875 Remote Similarity NPC13991
0.6875 Remote Similarity NPC241784
0.6829 Remote Similarity NPC213749
0.6818 Remote Similarity NPC45727
0.6818 Remote Similarity NPC48638
0.68 Remote Similarity NPC22765
0.68 Remote Similarity NPC17518
0.6727 Remote Similarity NPC55004
0.6727 Remote Similarity NPC49575
0.6727 Remote Similarity NPC267626
0.6667 Remote Similarity NPC470893
0.6667 Remote Similarity NPC123194
0.6607 Remote Similarity NPC469769
0.6607 Remote Similarity NPC30215
0.6596 Remote Similarity NPC190232
0.6596 Remote Similarity NPC105246
0.6585 Remote Similarity NPC3649
0.6585 Remote Similarity NPC471327
0.6585 Remote Similarity NPC100879
0.6552 Remote Similarity NPC274704
0.6538 Remote Similarity NPC27438
0.6538 Remote Similarity NPC471681
0.6522 Remote Similarity NPC227632
0.6522 Remote Similarity NPC62086
0.6522 Remote Similarity NPC78551
0.65 Remote Similarity NPC469326
0.65 Remote Similarity NPC261782
0.65 Remote Similarity NPC205618
0.65 Remote Similarity NPC183422
0.65 Remote Similarity NPC187619
0.6491 Remote Similarity NPC5698
0.6491 Remote Similarity NPC309825
0.6471 Remote Similarity NPC106990
0.6458 Remote Similarity NPC192529
0.6429 Remote Similarity NPC230823
0.6429 Remote Similarity NPC193695
0.6415 Remote Similarity NPC179169
0.6415 Remote Similarity NPC157781
0.6415 Remote Similarity NPC306195
0.6415 Remote Similarity NPC35519
0.6415 Remote Similarity NPC473728
0.6415 Remote Similarity NPC181255
0.6383 Remote Similarity NPC103290
0.6379 Remote Similarity NPC25853
0.6379 Remote Similarity NPC47840
0.6379 Remote Similarity NPC135648
0.6379 Remote Similarity NPC323153
0.6379 Remote Similarity NPC252809
0.6379 Remote Similarity NPC234264
0.6346 Remote Similarity NPC26960
0.6346 Remote Similarity NPC329773
0.6346 Remote Similarity NPC182102
0.6316 Remote Similarity NPC266295
0.6316 Remote Similarity NPC94991
0.6296 Remote Similarity NPC192962
0.629 Remote Similarity NPC136813
0.6271 Remote Similarity NPC213152
0.6271 Remote Similarity NPC63111
0.6271 Remote Similarity NPC475795
0.625 Remote Similarity NPC193180
0.625 Remote Similarity NPC20603
0.625 Remote Similarity NPC274396
0.6226 Remote Similarity NPC214584
0.6226 Remote Similarity NPC26906
0.6207 Remote Similarity NPC259261
0.619 Remote Similarity NPC66577
0.619 Remote Similarity NPC151719
0.619 Remote Similarity NPC167527
0.6182 Remote Similarity NPC63396
0.6182 Remote Similarity NPC202850
0.6167 Remote Similarity NPC124112
0.6167 Remote Similarity NPC474086
0.6167 Remote Similarity NPC165695
0.6167 Remote Similarity NPC474480
0.6167 Remote Similarity NPC279200
0.6154 Remote Similarity NPC17810
0.6111 Remote Similarity NPC177112
0.6111 Remote Similarity NPC68014
0.6111 Remote Similarity NPC71506
0.6098 Remote Similarity NPC138113
0.6098 Remote Similarity NPC123965
0.6098 Remote Similarity NPC115959
0.6094 Remote Similarity NPC162867
0.6094 Remote Similarity NPC61702
0.6094 Remote Similarity NPC144647
0.6071 Remote Similarity NPC469770
0.6066 Remote Similarity NPC475704
0.6066 Remote Similarity NPC140233
0.6066 Remote Similarity NPC287744
0.6066 Remote Similarity NPC473902
0.6066 Remote Similarity NPC309300
0.6042 Remote Similarity NPC188596
0.6034 Remote Similarity NPC10017
0.6034 Remote Similarity NPC475830
0.6 Remote Similarity NPC268564
0.6 Remote Similarity NPC474141
0.6 Remote Similarity NPC471781
0.6 Remote Similarity NPC210346
0.6 Remote Similarity NPC127944
0.6 Remote Similarity NPC476679
0.5968 Remote Similarity NPC477009
0.5968 Remote Similarity NPC238352
0.5952 Remote Similarity NPC60288
0.5926 Remote Similarity NPC244038
0.5909 Remote Similarity NPC41886
0.5902 Remote Similarity NPC211291
0.5902 Remote Similarity NPC133368
0.5893 Remote Similarity NPC95581
0.5882 Remote Similarity NPC210560
0.5882 Remote Similarity NPC24824
0.5882 Remote Similarity NPC165651
0.5873 Remote Similarity NPC92327
0.5873 Remote Similarity NPC176171
0.5873 Remote Similarity NPC162309
0.5873 Remote Similarity NPC272125
0.5873 Remote Similarity NPC135650
0.5862 Remote Similarity NPC470369
0.5862 Remote Similarity NPC475696
0.5862 Remote Similarity NPC474415
0.5862 Remote Similarity NPC470370
0.5862 Remote Similarity NPC474457
0.5862 Remote Similarity NPC11130
0.5862 Remote Similarity NPC474528
0.5846 Remote Similarity NPC297358
0.5821 Remote Similarity NPC469320
0.5821 Remote Similarity NPC300940
0.5818 Remote Similarity NPC40417
0.5818 Remote Similarity NPC294358
0.5806 Remote Similarity NPC212210
0.5789 Remote Similarity NPC275472
0.5789 Remote Similarity NPC223604
0.5789 Remote Similarity NPC218525
0.5781 Remote Similarity NPC472255
0.5781 Remote Similarity NPC176107
0.5781 Remote Similarity NPC472253
0.5778 Remote Similarity NPC182392
0.5769 Remote Similarity NPC195246
0.5769 Remote Similarity NPC22098
0.5769 Remote Similarity NPC8610
0.5769 Remote Similarity NPC276009
0.5769 Remote Similarity NPC262558
0.5763 Remote Similarity NPC60772
0.575 Remote Similarity NPC266539
0.575 Remote Similarity NPC266144
0.575 Remote Similarity NPC31891
0.575 Remote Similarity NPC287191
0.5741 Remote Similarity NPC32351
0.5738 Remote Similarity NPC219621
0.5714 Remote Similarity NPC165755
0.5714 Remote Similarity NPC14002
0.5714 Remote Similarity NPC19569
0.5714 Remote Similarity NPC45283
0.5714 Remote Similarity NPC34671
0.5714 Remote Similarity NPC296311
0.5714 Remote Similarity NPC23117
0.5692 Remote Similarity NPC22760

  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 NPC473912 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
0.7381 Intermediate Similarity NPD319 Phase 1
0.6596 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6154 Remote Similarity NPD8262 Approved
0.5846 Remote Similarity NPD1673 Approved
0.5606 Remote Similarity NPD6923 Approved
0.5606 Remote Similarity NPD6922 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