Structure

Physi-Chem Properties

Molecular Weight:  168.12
Volume:  185.267
LogP:  2.201
LogD:  1.4
LogS:  -1.084
# 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:  4.45
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:  -4.297
MDCK Permeability:  2.8703027055598795e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.04
30% Bioavailability (F30%):  0.567

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.898
Plasma Protein Binding (PPB):  47.65885925292969%
Volume Distribution (VD):  1.015
Pgp-substrate:  50.725894927978516%

ADMET: Metabolism

CYP1A2-inhibitor:  0.061
CYP1A2-substrate:  0.801
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.85
CYP2C9-inhibitor:  0.022
CYP2C9-substrate:  0.389
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.676
CYP3A4-inhibitor:  0.23
CYP3A4-substrate:  0.284

ADMET: Excretion

Clearance (CL):  9.453
Half-life (T1/2):  0.551

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.501
Drug-inuced Liver Injury (DILI):  0.031
AMES Toxicity:  0.615
Rat Oral Acute Toxicity:  0.857
Maximum Recommended Daily Dose:  0.525
Skin Sensitization:  0.369
Carcinogencity:  0.928
Eye Corrosion:  0.937
Eye Irritation:  0.908
Respiratory Toxicity:  0.969

Download Data

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

  Natural Product: NPC294358

Natural Product ID:  NPC294358
Common Name*:   (-)-(1S,4S)-P-Mentha-2,8-Dien-1-Hydroperoxide
IUPAC Name:   (3S,6S)-3-hydroperoxy-3-methyl-6-prop-1-en-2-ylcyclohexene
Synonyms:  
Standard InCHIKey:  LCOVCELWSKTKHX-NXEZZACHSA-N
Standard InCHI:  InChI=1S/C10H16O2/c1-8(2)9-4-6-10(3,12-11)7-5-9/h4,6,9,11H,1,5,7H2,2-3H3/t9-,10-/m1/s1
SMILES:  OO[C@@]1(C)CC[C@@H](C=C1)C(=C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL467825
PubChem CID:   10329704
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 MLC = 0.8 uM PMID[487607]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Activity = 0.13 % PMID[487607]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Activity = 12.0 n.a. PMID[487607]

☑ 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 NPC294358 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
1.0 High Similarity NPC40417
0.8269 Intermediate Similarity NPC26906
0.8269 Intermediate Similarity NPC214584
0.8148 Intermediate Similarity NPC105780
0.8148 Intermediate Similarity NPC168518
0.8113 Intermediate Similarity NPC157781
0.8113 Intermediate Similarity NPC306195
0.8113 Intermediate Similarity NPC181255
0.8113 Intermediate Similarity NPC35519
0.8113 Intermediate Similarity NPC179169
0.7931 Intermediate Similarity NPC66020
0.7797 Intermediate Similarity NPC207007
0.7797 Intermediate Similarity NPC321867
0.7797 Intermediate Similarity NPC68679
0.7778 Intermediate Similarity NPC71506
0.7778 Intermediate Similarity NPC177112
0.7778 Intermediate Similarity NPC68014
0.7736 Intermediate Similarity NPC329773
0.7667 Intermediate Similarity NPC174956
0.7627 Intermediate Similarity NPC240506
0.7581 Intermediate Similarity NPC267027
0.7544 Intermediate Similarity NPC141699
0.7458 Intermediate Similarity NPC475931
0.7414 Intermediate Similarity NPC165808
0.7377 Intermediate Similarity NPC81615
0.7368 Intermediate Similarity NPC130209
0.7368 Intermediate Similarity NPC148163
0.7368 Intermediate Similarity NPC148216
0.7368 Intermediate Similarity NPC227135
0.7368 Intermediate Similarity NPC251666
0.7368 Intermediate Similarity NPC232247
0.7288 Intermediate Similarity NPC155025
0.7288 Intermediate Similarity NPC181872
0.7258 Intermediate Similarity NPC300593
0.7255 Intermediate Similarity NPC15162
0.7241 Intermediate Similarity NPC48891
0.72 Intermediate Similarity NPC188596
0.7188 Intermediate Similarity NPC73603
0.7167 Intermediate Similarity NPC122239
0.7143 Intermediate Similarity NPC208638
0.7143 Intermediate Similarity NPC308844
0.7059 Intermediate Similarity NPC209279
0.7059 Intermediate Similarity NPC194586
0.7059 Intermediate Similarity NPC67761
0.7059 Intermediate Similarity NPC68889
0.7059 Intermediate Similarity NPC51758
0.7059 Intermediate Similarity NPC180871
0.7059 Intermediate Similarity NPC88079
0.7059 Intermediate Similarity NPC108494
0.7049 Intermediate Similarity NPC99487
0.7049 Intermediate Similarity NPC135648
0.7037 Intermediate Similarity NPC100445
0.7031 Intermediate Similarity NPC326310
0.7031 Intermediate Similarity NPC279434
0.7 Intermediate Similarity NPC226848
0.6981 Remote Similarity NPC24824
0.6981 Remote Similarity NPC165651
0.6981 Remote Similarity NPC210560
0.697 Remote Similarity NPC471560
0.697 Remote Similarity NPC473893
0.6964 Remote Similarity NPC251335
0.6964 Remote Similarity NPC244038
0.6949 Remote Similarity NPC274396
0.6935 Remote Similarity NPC282694
0.6935 Remote Similarity NPC469728
0.6935 Remote Similarity NPC194208
0.6935 Remote Similarity NPC210346
0.6935 Remote Similarity NPC79576
0.6935 Remote Similarity NPC475251
0.6923 Remote Similarity NPC82337
0.6912 Remote Similarity NPC259049
0.6885 Remote Similarity NPC83838
0.6885 Remote Similarity NPC143810
0.6875 Remote Similarity NPC471200
0.6863 Remote Similarity NPC144023
0.6833 Remote Similarity NPC278550
0.6825 Remote Similarity NPC473508
0.6818 Remote Similarity NPC117804
0.6786 Remote Similarity NPC182102
0.6786 Remote Similarity NPC131623
0.6786 Remote Similarity NPC26960
0.6786 Remote Similarity NPC474460
0.678 Remote Similarity NPC223604
0.678 Remote Similarity NPC218525
0.678 Remote Similarity NPC281590
0.6774 Remote Similarity NPC176621
0.6774 Remote Similarity NPC19241
0.6774 Remote Similarity NPC323153
0.6774 Remote Similarity NPC469694
0.6774 Remote Similarity NPC127824
0.6769 Remote Similarity NPC230107
0.6769 Remote Similarity NPC202017
0.6765 Remote Similarity NPC126061
0.6765 Remote Similarity NPC23954
0.6735 Remote Similarity NPC34764
0.6735 Remote Similarity NPC76145
0.6735 Remote Similarity NPC190810
0.6731 Remote Similarity NPC177470
0.6724 Remote Similarity NPC165755
0.6719 Remote Similarity NPC96793
0.6719 Remote Similarity NPC323424
0.6719 Remote Similarity NPC107540
0.6716 Remote Similarity NPC474900
0.6667 Remote Similarity NPC55412
0.6667 Remote Similarity NPC259299
0.6667 Remote Similarity NPC130665
0.6667 Remote Similarity NPC249645
0.6667 Remote Similarity NPC225342
0.6667 Remote Similarity NPC220939
0.6667 Remote Similarity NPC39068
0.6667 Remote Similarity NPC265485
0.6667 Remote Similarity NPC63111
0.6667 Remote Similarity NPC179024
0.6667 Remote Similarity NPC136813
0.6667 Remote Similarity NPC278895
0.6667 Remote Similarity NPC183670
0.6667 Remote Similarity NPC114651
0.6618 Remote Similarity NPC472017
0.6618 Remote Similarity NPC34834
0.6613 Remote Similarity NPC5698
0.6613 Remote Similarity NPC469321
0.6607 Remote Similarity NPC234597
0.6604 Remote Similarity NPC269862
0.66 Remote Similarity NPC229262
0.66 Remote Similarity NPC239039
0.66 Remote Similarity NPC297643
0.66 Remote Similarity NPC139717
0.6567 Remote Similarity NPC224532
0.6567 Remote Similarity NPC272961
0.6567 Remote Similarity NPC96484
0.6567 Remote Similarity NPC471238
0.6567 Remote Similarity NPC305698
0.6562 Remote Similarity NPC474155
0.6562 Remote Similarity NPC474480
0.6562 Remote Similarity NPC473759
0.6557 Remote Similarity NPC52012
0.6552 Remote Similarity NPC35756
0.6528 Remote Similarity NPC475025
0.6528 Remote Similarity NPC475027
0.6522 Remote Similarity NPC471272
0.6522 Remote Similarity NPC471660
0.6522 Remote Similarity NPC95863
0.6515 Remote Similarity NPC327815
0.6515 Remote Similarity NPC197089
0.6515 Remote Similarity NPC311736
0.6508 Remote Similarity NPC252809
0.65 Remote Similarity NPC329686
0.65 Remote Similarity NPC298299
0.6491 Remote Similarity NPC289388
0.6491 Remote Similarity NPC32351
0.6479 Remote Similarity NPC199445
0.6479 Remote Similarity NPC69383
0.6479 Remote Similarity NPC133580
0.6479 Remote Similarity NPC171148
0.6479 Remote Similarity NPC313179
0.6471 Remote Similarity NPC239373
0.6471 Remote Similarity NPC469914
0.6471 Remote Similarity NPC136473
0.6471 Remote Similarity NPC329989
0.6471 Remote Similarity NPC304690
0.6471 Remote Similarity NPC74722
0.6471 Remote Similarity NPC265574
0.6471 Remote Similarity NPC474248
0.6471 Remote Similarity NPC107130
0.6462 Remote Similarity NPC110241
0.6462 Remote Similarity NPC150162
0.6462 Remote Similarity NPC290367
0.6441 Remote Similarity NPC474496
0.6441 Remote Similarity NPC14002
0.6441 Remote Similarity NPC268564
0.6441 Remote Similarity NPC192962
0.6438 Remote Similarity NPC121200
0.6429 Remote Similarity NPC474543
0.6429 Remote Similarity NPC238425
0.6429 Remote Similarity NPC472018
0.6429 Remote Similarity NPC186042
0.6429 Remote Similarity NPC91962
0.6418 Remote Similarity NPC163290
0.6418 Remote Similarity NPC69649
0.6418 Remote Similarity NPC477791
0.6418 Remote Similarity NPC171225
0.6418 Remote Similarity NPC474477
0.6418 Remote Similarity NPC68703
0.6406 Remote Similarity NPC317177
0.6406 Remote Similarity NPC41160
0.6406 Remote Similarity NPC329416
0.6406 Remote Similarity NPC317025
0.6406 Remote Similarity NPC326645
0.64 Remote Similarity NPC47761
0.6393 Remote Similarity NPC473865
0.6393 Remote Similarity NPC474643
0.6389 Remote Similarity NPC474447
0.6389 Remote Similarity NPC472305
0.6389 Remote Similarity NPC151622
0.6389 Remote Similarity NPC253190
0.6389 Remote Similarity NPC265588
0.6389 Remote Similarity NPC474231
0.6389 Remote Similarity NPC7629
0.6379 Remote Similarity NPC148056
0.6379 Remote Similarity NPC474495

  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 NPC294358 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
0.7797 Intermediate Similarity NPD368 Approved
0.7368 Intermediate Similarity NPD342 Phase 1
0.6735 Remote Similarity NPD319 Phase 1
0.6667 Remote Similarity NPD4219 Approved
0.6515 Remote Similarity NPD7331 Phase 2
0.6479 Remote Similarity NPD8264 Approved
0.6406 Remote Similarity NPD4193 Approved
0.6406 Remote Similarity NPD4191 Approved
0.6406 Remote Similarity NPD4194 Approved
0.6406 Remote Similarity NPD4192 Approved
0.6364 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6216 Remote Similarity NPD7322 Clinical (unspecified phase)
0.6197 Remote Similarity NPD4732 Discontinued
0.6119 Remote Similarity NPD7341 Phase 2
0.6111 Remote Similarity NPD4785 Approved
0.6111 Remote Similarity NPD4784 Approved
0.6071 Remote Similarity NPD4265 Approved
0.6056 Remote Similarity NPD4243 Approved
0.6053 Remote Similarity NPD7514 Phase 3
0.6053 Remote Similarity NPD7332 Phase 2
0.597 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5921 Remote Similarity NPD4195 Approved
0.5915 Remote Similarity NPD7143 Approved
0.5915 Remote Similarity NPD7144 Approved
0.589 Remote Similarity NPD6924 Approved
0.589 Remote Similarity NPD6926 Approved
0.5867 Remote Similarity NPD6932 Approved
0.5833 Remote Similarity NPD7151 Approved
0.5833 Remote Similarity NPD7152 Approved
0.5833 Remote Similarity NPD7150 Approved
0.5811 Remote Similarity NPD4190 Phase 3
0.5811 Remote Similarity NPD8039 Approved
0.5811 Remote Similarity NPD5275 Approved
0.5802 Remote Similarity NPD4623 Approved
0.5802 Remote Similarity NPD4519 Discontinued
0.5789 Remote Similarity NPD7145 Approved
0.5775 Remote Similarity NPD15 Approved
0.5775 Remote Similarity NPD6923 Approved
0.5775 Remote Similarity NPD791 Approved
0.5775 Remote Similarity NPD6922 Approved
0.5769 Remote Similarity NPD6902 Approved
0.5763 Remote Similarity NPD9410 Clinical (unspecified phase)
0.5763 Remote Similarity NPD8262 Approved
0.5758 Remote Similarity NPD1145 Discontinued
0.5733 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5733 Remote Similarity NPD6933 Approved
0.5692 Remote Similarity NPD287 Approved
0.5658 Remote Similarity NPD5776 Phase 2
0.5658 Remote Similarity NPD6925 Approved
0.5641 Remote Similarity NPD6931 Approved
0.5641 Remote Similarity NPD4821 Approved
0.5641 Remote Similarity NPD4820 Approved
0.5641 Remote Similarity NPD4822 Approved
0.5641 Remote Similarity NPD6930 Phase 2
0.5641 Remote Similarity NPD4819 Approved
0.56 Remote Similarity NPD6942 Approved
0.56 Remote Similarity NPD7339 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