Structure

Physi-Chem Properties

Molecular Weight:  168.12
Volume:  185.267
LogP:  2.35
LogD:  1.931
LogS:  -1.915
# Rotatable Bonds:  2
TPSA:  29.46
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.39
Synthetic Accessibility Score:  4.154
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.44
MDCK Permeability:  1.1285994332865812e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.015
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.917
30% Bioavailability (F30%):  0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.971
Plasma Protein Binding (PPB):  54.22364807128906%
Volume Distribution (VD):  1.207
Pgp-substrate:  47.619850158691406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.112
CYP1A2-substrate:  0.327
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.558
CYP2C9-inhibitor:  0.02
CYP2C9-substrate:  0.889
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.876
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.231

ADMET: Excretion

Clearance (CL):  8.022
Half-life (T1/2):  0.532

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.834
Drug-inuced Liver Injury (DILI):  0.3
AMES Toxicity:  0.893
Rat Oral Acute Toxicity:  0.2
Maximum Recommended Daily Dose:  0.931
Skin Sensitization:  0.431
Carcinogencity:  0.93
Eye Corrosion:  0.936
Eye Irritation:  0.978
Respiratory Toxicity:  0.928

Download Data

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

  Natural Product: NPC251335

Natural Product ID:  NPC251335
Common Name*:   (-)-(2R,4S)-P-Mentha-1(7),8-Dien-2-Hydroperoxide
IUPAC Name:   (2R,4S)-2-hydroperoxy-1-methylidene-4-prop-1-en-2-ylcyclohexane
Synonyms:  
Standard InCHIKey:  CSOZFPOODGAASP-VHSXEESVSA-N
Standard InCHI:  InChI=1S/C10H16O2/c1-7(2)9-5-4-8(3)10(6-9)12-11/h9-11H,1,3-6H2,2H3/t9-,10+/m0/s1
SMILES:  C=C(C)[C@H]1CCC(=C)[C@@H](C1)OO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL448266
PubChem CID:   10103548
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001401] Menthane monoterpenoids

*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
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[11975490]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[18679750]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]

☑ 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
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Activity = 63.0 % PMID[556218]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi MLC = 1.6 uM PMID[556218]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Activity = 4.4 % PMID[556218]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Activity = 18.6 n.a. PMID[556218]

☑ 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 NPC251335 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
0.8148 Intermediate Similarity NPC67508
0.8148 Intermediate Similarity NPC84824
0.7719 Intermediate Similarity NPC240206
0.7679 Intermediate Similarity NPC210316
0.7679 Intermediate Similarity NPC24443
0.7451 Intermediate Similarity NPC87439
0.7377 Intermediate Similarity NPC68656
0.7377 Intermediate Similarity NPC219940
0.7377 Intermediate Similarity NPC144650
0.7377 Intermediate Similarity NPC101128
0.7258 Intermediate Similarity NPC172613
0.7258 Intermediate Similarity NPC60837
0.7258 Intermediate Similarity NPC2728
0.7258 Intermediate Similarity NPC11555
0.7258 Intermediate Similarity NPC208198
0.7258 Intermediate Similarity NPC300442
0.7258 Intermediate Similarity NPC282619
0.7258 Intermediate Similarity NPC258595
0.7188 Intermediate Similarity NPC276616
0.7188 Intermediate Similarity NPC266578
0.7188 Intermediate Similarity NPC245795
0.717 Intermediate Similarity NPC100445
0.7167 Intermediate Similarity NPC240506
0.7143 Intermediate Similarity NPC475897
0.7097 Intermediate Similarity NPC225415
0.7077 Intermediate Similarity NPC9942
0.7077 Intermediate Similarity NPC234511
0.7031 Intermediate Similarity NPC139207
0.7031 Intermediate Similarity NPC269077
0.7031 Intermediate Similarity NPC253303
0.7031 Intermediate Similarity NPC185874
0.7 Intermediate Similarity NPC122239
0.697 Remote Similarity NPC283316
0.6964 Remote Similarity NPC40417
0.6964 Remote Similarity NPC294358
0.6923 Remote Similarity NPC244790
0.6923 Remote Similarity NPC96484
0.6923 Remote Similarity NPC471238
0.6909 Remote Similarity NPC142103
0.6897 Remote Similarity NPC130209
0.6897 Remote Similarity NPC148216
0.6897 Remote Similarity NPC148163
0.6885 Remote Similarity NPC66020
0.6875 Remote Similarity NPC473929
0.6875 Remote Similarity NPC476406
0.6875 Remote Similarity NPC202017
0.6875 Remote Similarity NPC267027
0.6875 Remote Similarity NPC326310
0.6866 Remote Similarity NPC477792
0.6866 Remote Similarity NPC23954
0.6833 Remote Similarity NPC189290
0.6833 Remote Similarity NPC475830
0.6833 Remote Similarity NPC226848
0.6833 Remote Similarity NPC474769
0.6825 Remote Similarity NPC96793
0.6825 Remote Similarity NPC300593
0.6825 Remote Similarity NPC323424
0.678 Remote Similarity NPC264779
0.678 Remote Similarity NPC39068
0.6774 Remote Similarity NPC225342
0.6769 Remote Similarity NPC476650
0.6769 Remote Similarity NPC74885
0.6769 Remote Similarity NPC308522
0.6765 Remote Similarity NPC220939
0.6765 Remote Similarity NPC265485
0.6765 Remote Similarity NPC259049
0.6724 Remote Similarity NPC286752
0.6719 Remote Similarity NPC471200
0.6716 Remote Similarity NPC92801
0.6716 Remote Similarity NPC34834
0.6667 Remote Similarity NPC7491
0.6667 Remote Similarity NPC101285
0.6667 Remote Similarity NPC83200
0.6667 Remote Similarity NPC306727
0.6667 Remote Similarity NPC27853
0.6667 Remote Similarity NPC65786
0.6667 Remote Similarity NPC81615
0.6667 Remote Similarity NPC84030
0.6667 Remote Similarity NPC223468
0.6667 Remote Similarity NPC176309
0.6667 Remote Similarity NPC287550
0.6667 Remote Similarity NPC147343
0.6667 Remote Similarity NPC198540
0.6667 Remote Similarity NPC13789
0.6667 Remote Similarity NPC473508
0.6667 Remote Similarity NPC50435
0.6618 Remote Similarity NPC471268
0.6618 Remote Similarity NPC164022
0.6618 Remote Similarity NPC471271
0.6618 Remote Similarity NPC242992
0.6618 Remote Similarity NPC242001
0.6618 Remote Similarity NPC469343
0.6618 Remote Similarity NPC471272
0.6618 Remote Similarity NPC167706
0.6613 Remote Similarity NPC162109
0.6613 Remote Similarity NPC99487
0.661 Remote Similarity NPC251666
0.661 Remote Similarity NPC223604
0.661 Remote Similarity NPC232247
0.6607 Remote Similarity NPC131623
0.6571 Remote Similarity NPC185536
0.6571 Remote Similarity NPC144075
0.6571 Remote Similarity NPC133580
0.6567 Remote Similarity NPC474248
0.6567 Remote Similarity NPC471560
0.6562 Remote Similarity NPC309300
0.6557 Remote Similarity NPC155025
0.6522 Remote Similarity NPC95165
0.6522 Remote Similarity NPC68443
0.6522 Remote Similarity NPC476609
0.6522 Remote Similarity NPC472506
0.6522 Remote Similarity NPC211009
0.6515 Remote Similarity NPC68703
0.6515 Remote Similarity NPC477791
0.6515 Remote Similarity NPC69649
0.6515 Remote Similarity NPC474477
0.6515 Remote Similarity NPC82337
0.6515 Remote Similarity NPC73603
0.6508 Remote Similarity NPC194208
0.6508 Remote Similarity NPC321867
0.6508 Remote Similarity NPC41160
0.6508 Remote Similarity NPC68679
0.6508 Remote Similarity NPC207007
0.6508 Remote Similarity NPC147524
0.6508 Remote Similarity NPC475251
0.6508 Remote Similarity NPC282694
0.6508 Remote Similarity NPC79576
0.65 Remote Similarity NPC48891
0.6481 Remote Similarity NPC24824
0.6481 Remote Similarity NPC165651
0.6481 Remote Similarity NPC210560
0.6479 Remote Similarity NPC265588
0.6479 Remote Similarity NPC38141
0.6479 Remote Similarity NPC253190
0.6471 Remote Similarity NPC45296
0.6471 Remote Similarity NPC145498
0.6462 Remote Similarity NPC287339
0.6462 Remote Similarity NPC86856
0.6462 Remote Similarity NPC308844
0.6462 Remote Similarity NPC61503
0.6452 Remote Similarity NPC475931
0.6429 Remote Similarity NPC476366
0.6429 Remote Similarity NPC476736
0.6429 Remote Similarity NPC201048
0.6429 Remote Similarity NPC469593
0.6429 Remote Similarity NPC243342
0.6429 Remote Similarity NPC469534
0.6429 Remote Similarity NPC477138
0.6429 Remote Similarity NPC91858
0.6429 Remote Similarity NPC199316
0.6429 Remote Similarity NPC102313
0.6429 Remote Similarity NPC71152
0.6429 Remote Similarity NPC469533
0.6429 Remote Similarity NPC308440
0.6429 Remote Similarity NPC472503
0.6418 Remote Similarity NPC167527
0.6418 Remote Similarity NPC208999
0.6415 Remote Similarity NPC144891
0.6415 Remote Similarity NPC15162
0.6406 Remote Similarity NPC474155
0.6406 Remote Similarity NPC473759
0.6406 Remote Similarity NPC174956
0.6389 Remote Similarity NPC470711
0.6389 Remote Similarity NPC212241
0.6389 Remote Similarity NPC31037
0.6389 Remote Similarity NPC119355
0.6389 Remote Similarity NPC91594
0.6389 Remote Similarity NPC138502
0.6389 Remote Similarity NPC331618
0.6389 Remote Similarity NPC470758
0.6389 Remote Similarity NPC307336
0.6389 Remote Similarity NPC248830
0.6389 Remote Similarity NPC257191
0.6389 Remote Similarity NPC260301
0.6379 Remote Similarity NPC157781
0.6379 Remote Similarity NPC35519
0.6379 Remote Similarity NPC181255
0.6379 Remote Similarity NPC306195
0.6379 Remote Similarity NPC179169
0.6377 Remote Similarity NPC111234
0.6377 Remote Similarity NPC301226
0.6377 Remote Similarity NPC164045
0.6364 Remote Similarity NPC311736
0.6364 Remote Similarity NPC469328
0.6364 Remote Similarity NPC272125
0.6338 Remote Similarity NPC240235
0.6338 Remote Similarity NPC70982
0.6338 Remote Similarity NPC178383
0.6338 Remote Similarity NPC32832
0.6338 Remote Similarity NPC104387
0.6338 Remote Similarity NPC212879
0.6338 Remote Similarity NPC231256
0.6338 Remote Similarity NPC66566
0.6338 Remote Similarity NPC230704
0.6338 Remote Similarity NPC477923
0.6338 Remote Similarity NPC291503
0.6338 Remote Similarity NPC3403
0.6338 Remote Similarity NPC476605
0.6333 Remote Similarity NPC227135
0.6324 Remote Similarity NPC329989

  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 NPC251335 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
0.7037 Intermediate Similarity NPD9410 Clinical (unspecified phase)
0.6897 Remote Similarity NPD342 Phase 1
0.6885 Remote Similarity NPD1145 Discontinued
0.6667 Remote Similarity NPD384 Approved
0.6667 Remote Similarity NPD385 Approved
0.6508 Remote Similarity NPD368 Approved
0.6226 Remote Similarity NPD1462 Approved
0.6197 Remote Similarity NPD6924 Approved
0.6197 Remote Similarity NPD6926 Approved
0.6154 Remote Similarity NPD1460 Approved
0.6027 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6027 Remote Similarity NPD6933 Approved
0.6 Remote Similarity NPD7645 Phase 2
0.6 Remote Similarity NPD6929 Approved
0.5921 Remote Similarity NPD7509 Discontinued
0.5921 Remote Similarity NPD6930 Phase 2
0.5921 Remote Similarity NPD6931 Approved
0.5921 Remote Similarity NPD7525 Registered
0.5893 Remote Similarity NPD386 Approved
0.5893 Remote Similarity NPD388 Approved
0.589 Remote Similarity NPD6942 Approved
0.589 Remote Similarity NPD7339 Approved
0.589 Remote Similarity NPD8264 Approved
0.5857 Remote Similarity NPD6922 Approved
0.5857 Remote Similarity NPD6923 Approved
0.5775 Remote Similarity NPD7144 Approved
0.5775 Remote Similarity NPD7143 Approved
0.5735 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5733 Remote Similarity NPD6925 Approved
0.5733 Remote Similarity NPD5776 Phase 2
0.5696 Remote Similarity NPD6695 Phase 3
0.5694 Remote Similarity NPD7150 Approved
0.5694 Remote Similarity NPD7152 Approved
0.5694 Remote Similarity NPD7151 Approved
0.5658 Remote Similarity NPD7145 Approved
0.5658 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5625 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5616 Remote Similarity NPD4732 Discontinued

  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