Structure

Physi-Chem Properties

Molecular Weight:  222.16
Volume:  239.975
LogP:  3.128
LogD:  2.917
LogS:  -4.163
# Rotatable Bonds:  0
TPSA:  29.6
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.59
Synthetic Accessibility Score:  4.45
Fsp3:  0.929
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.706
MDCK Permeability:  3.088356970692985e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.317

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.701
Plasma Protein Binding (PPB):  87.32877349853516%
Volume Distribution (VD):  1.495
Pgp-substrate:  13.32246208190918%

ADMET: Metabolism

CYP1A2-inhibitor:  0.043
CYP1A2-substrate:  0.542
CYP2C19-inhibitor:  0.071
CYP2C19-substrate:  0.911
CYP2C9-inhibitor:  0.147
CYP2C9-substrate:  0.651
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.807
CYP3A4-inhibitor:  0.026
CYP3A4-substrate:  0.311

ADMET: Excretion

Clearance (CL):  6.899
Half-life (T1/2):  0.736

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.333
Drug-inuced Liver Injury (DILI):  0.335
AMES Toxicity:  0.037
Rat Oral Acute Toxicity:  0.323
Maximum Recommended Daily Dose:  0.531
Skin Sensitization:  0.472
Carcinogencity:  0.08
Eye Corrosion:  0.48
Eye Irritation:  0.777
Respiratory Toxicity:  0.321

Download Data

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

  Natural Product: NPC253204

Natural Product ID:  NPC253204
Common Name*:   Kobusone
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  UETZJEZFLKASPR-UZWIWUQPSA-N
Standard InCHI:  InChI=1S/C14H22O2/c1-13(2)8-9-10(13)6-7-14(3)12(16-14)5-4-11(9)15/h9-10,12H,4-8H2,1-3H3/t9-,10+,12+,14+/m0/s1
SMILES:  O=C1CC[C@H]2O[C@@]2(CC[C@@H]2[C@@H]1CC2(C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3039087
PubChem CID:   6710676
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones

*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
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[27128895]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota Resinous Wood n.a. n.a. PMID[29227647]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12265 Aquilaria agallochum Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12265 Aquilaria agallochum Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12265 Aquilaria agallochum Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14558 Aquilaria sinensis Species Thymelaeaceae 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
NPT34 Cell Line BV-2 Mus musculus IC50 > 81000.0 nM PMID[496916]
NPT73 Individual Protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 64.48 % PMID[496915]
NPT72 Individual Protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 84.64 % PMID[496915]

☑ 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 NPC253204 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
0.7746 Intermediate Similarity NPC474419
0.7463 Intermediate Similarity NPC157518
0.7162 Intermediate Similarity NPC226242
0.7119 Intermediate Similarity NPC13105
0.7083 Intermediate Similarity NPC40327
0.6974 Remote Similarity NPC475725
0.6923 Remote Similarity NPC101285
0.6923 Remote Similarity NPC7491
0.6923 Remote Similarity NPC65786
0.6923 Remote Similarity NPC27853
0.6923 Remote Similarity NPC13789
0.6849 Remote Similarity NPC470243
0.6835 Remote Similarity NPC145963
0.6774 Remote Similarity NPC314084
0.6757 Remote Similarity NPC474123
0.6757 Remote Similarity NPC92909
0.6757 Remote Similarity NPC107783
0.6714 Remote Similarity NPC215987
0.6714 Remote Similarity NPC306805
0.6667 Remote Similarity NPC469608
0.6667 Remote Similarity NPC167049
0.6667 Remote Similarity NPC469691
0.6667 Remote Similarity NPC275243
0.6623 Remote Similarity NPC143250
0.662 Remote Similarity NPC473899
0.6618 Remote Similarity NPC478126
0.6618 Remote Similarity NPC40206
0.6615 Remote Similarity NPC300189
0.6613 Remote Similarity NPC305182
0.6579 Remote Similarity NPC475861
0.6579 Remote Similarity NPC179922
0.6579 Remote Similarity NPC469678
0.6579 Remote Similarity NPC475771
0.6579 Remote Similarity NPC469669
0.6543 Remote Similarity NPC472847
0.6543 Remote Similarity NPC227170
0.6538 Remote Similarity NPC207186
0.6538 Remote Similarity NPC474056
0.6528 Remote Similarity NPC329466
0.6528 Remote Similarity NPC472984
0.6528 Remote Similarity NPC328304
0.6522 Remote Similarity NPC306750
0.65 Remote Similarity NPC478262
0.6494 Remote Similarity NPC471046
0.6479 Remote Similarity NPC476330
0.6463 Remote Similarity NPC475796
0.6463 Remote Similarity NPC475689
0.6462 Remote Similarity NPC319589
0.6456 Remote Similarity NPC80999
0.6447 Remote Similarity NPC215030
0.6438 Remote Similarity NPC474954
0.64 Remote Similarity NPC96322
0.6364 Remote Similarity NPC179858
0.6351 Remote Similarity NPC477449
0.6351 Remote Similarity NPC477448
0.6341 Remote Similarity NPC473629
0.6329 Remote Similarity NPC470014
0.6316 Remote Similarity NPC474755
0.6316 Remote Similarity NPC470237
0.6316 Remote Similarity NPC109510
0.631 Remote Similarity NPC475729
0.631 Remote Similarity NPC474215
0.6308 Remote Similarity NPC161473
0.6301 Remote Similarity NPC161612
0.6301 Remote Similarity NPC33583
0.6282 Remote Similarity NPC474527
0.6282 Remote Similarity NPC471726
0.625 Remote Similarity NPC474331
0.625 Remote Similarity NPC622
0.625 Remote Similarity NPC276647
0.6234 Remote Similarity NPC477867
0.6234 Remote Similarity NPC55508
0.6203 Remote Similarity NPC474404
0.6197 Remote Similarity NPC50435
0.6197 Remote Similarity NPC235788
0.6184 Remote Similarity NPC478227
0.6173 Remote Similarity NPC290508
0.6173 Remote Similarity NPC134227
0.6173 Remote Similarity NPC293418
0.6173 Remote Similarity NPC125366
0.6173 Remote Similarity NPC73052
0.6173 Remote Similarity NPC304795
0.6167 Remote Similarity NPC171783
0.6164 Remote Similarity NPC84562
0.6163 Remote Similarity NPC226491
0.6163 Remote Similarity NPC477614
0.6154 Remote Similarity NPC125767
0.6154 Remote Similarity NPC21220
0.6143 Remote Similarity NPC472021
0.6133 Remote Similarity NPC261398
0.6133 Remote Similarity NPC295788
0.6133 Remote Similarity NPC98711
0.6133 Remote Similarity NPC178541
0.6129 Remote Similarity NPC326957
0.6125 Remote Similarity NPC321180
0.6118 Remote Similarity NPC469676
0.6111 Remote Similarity NPC128608
0.6104 Remote Similarity NPC248567
0.6104 Remote Similarity NPC475230
0.6098 Remote Similarity NPC207188
0.6081 Remote Similarity NPC469868
0.6081 Remote Similarity NPC286842
0.6076 Remote Similarity NPC472487
0.6076 Remote Similarity NPC472486
0.6034 Remote Similarity NPC141634
0.6026 Remote Similarity NPC133922
0.6024 Remote Similarity NPC475936
0.6024 Remote Similarity NPC271163
0.6 Remote Similarity NPC18397
0.6 Remote Similarity NPC274261
0.6 Remote Similarity NPC108014
0.6 Remote Similarity NPC291724
0.6 Remote Similarity NPC469924
0.6 Remote Similarity NPC307865
0.6 Remote Similarity NPC119838
0.6 Remote Similarity NPC472019
0.6 Remote Similarity NPC226602
0.6 Remote Similarity NPC472020
0.6 Remote Similarity NPC211279
0.5974 Remote Similarity NPC311102
0.5974 Remote Similarity NPC197701
0.5974 Remote Similarity NPC89310
0.5968 Remote Similarity NPC63182
0.5968 Remote Similarity NPC145045
0.5968 Remote Similarity NPC105329
0.5968 Remote Similarity NPC282440
0.5968 Remote Similarity NPC52700
0.5955 Remote Similarity NPC474699
0.5952 Remote Similarity NPC475842
0.5952 Remote Similarity NPC54468
0.5952 Remote Similarity NPC53867
0.5952 Remote Similarity NPC108045
0.5952 Remote Similarity NPC475622
0.5949 Remote Similarity NPC72444
0.5949 Remote Similarity NPC35871
0.5949 Remote Similarity NPC471491
0.5949 Remote Similarity NPC68565
0.5949 Remote Similarity NPC159789
0.5926 Remote Similarity NPC474341
0.5921 Remote Similarity NPC5714
0.5921 Remote Similarity NPC475062
0.5921 Remote Similarity NPC327728
0.5921 Remote Similarity NPC6120
0.5921 Remote Similarity NPC296522
0.5921 Remote Similarity NPC324607
0.5921 Remote Similarity NPC131892
0.5921 Remote Similarity NPC144511
0.5921 Remote Similarity NPC321732
0.5921 Remote Similarity NPC213178
0.5915 Remote Similarity NPC475412
0.5915 Remote Similarity NPC66145
0.5909 Remote Similarity NPC174765
0.5904 Remote Similarity NPC77311
0.5904 Remote Similarity NPC329490
0.5904 Remote Similarity NPC254123
0.5904 Remote Similarity NPC50658
0.5904 Remote Similarity NPC328639
0.5897 Remote Similarity NPC473775
0.5897 Remote Similarity NPC475232
0.5897 Remote Similarity NPC473699
0.5897 Remote Similarity NPC51249
0.5897 Remote Similarity NPC474100
0.5897 Remote Similarity NPC329763
0.5897 Remote Similarity NPC475260
0.5889 Remote Similarity NPC475488
0.5882 Remote Similarity NPC9060
0.5882 Remote Similarity NPC291310
0.5882 Remote Similarity NPC477434
0.5882 Remote Similarity NPC181871
0.5875 Remote Similarity NPC92489
0.5875 Remote Similarity NPC271070
0.5873 Remote Similarity NPC249754
0.5873 Remote Similarity NPC83187
0.5873 Remote Similarity NPC98246
0.5873 Remote Similarity NPC285814
0.5867 Remote Similarity NPC41542
0.5854 Remote Similarity NPC472310
0.5854 Remote Similarity NPC469690
0.5854 Remote Similarity NPC245029
0.5854 Remote Similarity NPC469620
0.5854 Remote Similarity NPC476177
0.5854 Remote Similarity NPC31302
0.5854 Remote Similarity NPC73013
0.5844 Remote Similarity NPC475310
0.5833 Remote Similarity NPC123880
0.5833 Remote Similarity NPC475807
0.5833 Remote Similarity NPC212340
0.5833 Remote Similarity NPC469922
0.5833 Remote Similarity NPC469923
0.5833 Remote Similarity NPC10659
0.5833 Remote Similarity NPC471159
0.5833 Remote Similarity NPC317066
0.5824 Remote Similarity NPC470423
0.5824 Remote Similarity NPC477495
0.5823 Remote Similarity NPC469643
0.5823 Remote Similarity NPC317212
0.5823 Remote Similarity NPC469641
0.5823 Remote Similarity NPC159325
0.5823 Remote Similarity NPC168511
0.5814 Remote Similarity NPC478245

  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 NPC253204 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
0.6184 Remote Similarity NPD5777 Approved
0.6027 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6 Remote Similarity NPD387 Clinical (unspecified phase)
0.6 Remote Similarity NPD229 Approved
0.597 Remote Similarity NPD615 Clinical (unspecified phase)
0.597 Remote Similarity NPD3729 Clinical (unspecified phase)
0.5949 Remote Similarity NPD3702 Approved
0.5949 Remote Similarity NPD3703 Phase 2
0.5921 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5921 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5921 Remote Similarity NPD3698 Phase 2
0.5844 Remote Similarity NPD4244 Approved
0.5844 Remote Similarity NPD4245 Approved
0.5806 Remote Similarity NPD2699 Approved
0.5775 Remote Similarity NPD3198 Approved
0.5769 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5769 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5714 Remote Similarity NPD634 Phase 3
0.5676 Remote Similarity NPD7909 Approved
0.5641 Remote Similarity NPD4789 Approved
0.5625 Remote Similarity NPD345 Approved
0.5625 Remote Similarity NPD343 Approved
0.5625 Remote Similarity NPD344 Approved
0.56 Remote Similarity NPD9496 Clinical (unspecified phase)
0.56 Remote Similarity NPD7341 Phase 2

  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