Structure

Physi-Chem Properties

Molecular Weight:  220.18
Volume:  254.401
LogP:  4.505
LogD:  4.233
LogS:  -5.692
# Rotatable Bonds:  0
TPSA:  12.53
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.439
Synthetic Accessibility Score:  4.564
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:  -4.576
MDCK Permeability:  2.746272184595e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.016
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.32
Plasma Protein Binding (PPB):  95.54048156738281%
Volume Distribution (VD):  1.445
Pgp-substrate:  2.3310205936431885%

ADMET: Metabolism

CYP1A2-inhibitor:  0.148
CYP1A2-substrate:  0.416
CYP2C19-inhibitor:  0.387
CYP2C19-substrate:  0.801
CYP2C9-inhibitor:  0.209
CYP2C9-substrate:  0.716
CYP2D6-inhibitor:  0.256
CYP2D6-substrate:  0.808
CYP3A4-inhibitor:  0.188
CYP3A4-substrate:  0.233

ADMET: Excretion

Clearance (CL):  3.882
Half-life (T1/2):  0.435

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.467
Drug-inuced Liver Injury (DILI):  0.05
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.835
Skin Sensitization:  0.946
Carcinogencity:  0.043
Eye Corrosion:  0.959
Eye Irritation:  0.979
Respiratory Toxicity:  0.047

Download Data

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

  Natural Product: NPC165755

Natural Product ID:  NPC165755
Common Name*:   Alpha-Humulene Epoxide
IUPAC Name:   (1R,4E,7E,11R)-3,3,7,11-tetramethyl-12-oxabicyclo[9.1.0]dodeca-4,7-diene
Synonyms:   Alpha-Humulene Epoxide
Standard InCHIKey:  RKQDKXOBRXTSFS-UOAUIWSESA-N
Standard InCHI:  InChI=1S/C15H24O/c1-12-7-5-9-14(2,3)11-13-15(4,16-13)10-6-8-12/h5,8-9,13H,6-7,10-11H2,1-4H3/b9-5+,12-8+/t13-,15-/m1/s1
SMILES:  C/C/1=CCC[C@]2(C)[C@@H](CC(C)(C)/C=C/C1)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL509909
PubChem CID:   14038843
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000159] Epoxides

*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
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[1402962]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Flower Buds n.a. n.a. PMID[26977531]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[8904847]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3987 Syzygium aromaticum Species Myrtaceae 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
NPT32 Organism Mus musculus Mus musculus Activity = 1.54 micromol/min PMID[516643]
NPT32 Organism Mus musculus Mus musculus Activity = 0.81 micromol/min PMID[516643]
NPT32 Organism Mus musculus Mus musculus Activity = 0.77 micromol/min PMID[516643]
NPT32 Organism Mus musculus Mus musculus Ratio = 2.08 n.a. PMID[516643]
NPT32 Organism Mus musculus Mus musculus Ratio = 3.24 n.a. PMID[516643]
NPT32 Organism Mus musculus Mus musculus Ratio = 1.24 n.a. PMID[516643]

☑ 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 NPC165755 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
0.8596 High Similarity NPC228574
0.8596 High Similarity NPC294304
0.8519 High Similarity NPC223604
0.8136 Intermediate Similarity NPC283247
0.8 Intermediate Similarity NPC140233
0.8 Intermediate Similarity NPC287744
0.7931 Intermediate Similarity NPC83838
0.7931 Intermediate Similarity NPC143810
0.7797 Intermediate Similarity NPC127824
0.7586 Intermediate Similarity NPC13789
0.7586 Intermediate Similarity NPC101285
0.7586 Intermediate Similarity NPC7491
0.7586 Intermediate Similarity NPC65786
0.7586 Intermediate Similarity NPC27853
0.7206 Intermediate Similarity NPC227814
0.7206 Intermediate Similarity NPC144995
0.7188 Intermediate Similarity NPC327815
0.7119 Intermediate Similarity NPC210316
0.7097 Intermediate Similarity NPC475251
0.7077 Intermediate Similarity NPC259299
0.7059 Intermediate Similarity NPC107783
0.7059 Intermediate Similarity NPC329763
0.7059 Intermediate Similarity NPC92909
0.6984 Remote Similarity NPC217940
0.697 Remote Similarity NPC276290
0.697 Remote Similarity NPC305698
0.6957 Remote Similarity NPC469691
0.6957 Remote Similarity NPC167049
0.6949 Remote Similarity NPC227135
0.6935 Remote Similarity NPC469694
0.6866 Remote Similarity NPC477448
0.6866 Remote Similarity NPC329656
0.6866 Remote Similarity NPC477449
0.6866 Remote Similarity NPC261398
0.6866 Remote Similarity NPC239373
0.6866 Remote Similarity NPC304690
0.6866 Remote Similarity NPC74722
0.6866 Remote Similarity NPC329989
0.6866 Remote Similarity NPC269841
0.6857 Remote Similarity NPC469669
0.6857 Remote Similarity NPC469678
0.6857 Remote Similarity NPC475771
0.6833 Remote Similarity NPC48891
0.6818 Remote Similarity NPC474477
0.6806 Remote Similarity NPC474005
0.6786 Remote Similarity NPC62755
0.6769 Remote Similarity NPC61503
0.6765 Remote Similarity NPC475310
0.6765 Remote Similarity NPC129630
0.6761 Remote Similarity NPC226242
0.6761 Remote Similarity NPC268111
0.6731 Remote Similarity NPC188596
0.6724 Remote Similarity NPC35519
0.6724 Remote Similarity NPC306195
0.6724 Remote Similarity NPC294358
0.6724 Remote Similarity NPC179169
0.6724 Remote Similarity NPC35756
0.6724 Remote Similarity NPC40417
0.6724 Remote Similarity NPC181255
0.6724 Remote Similarity NPC157781
0.6719 Remote Similarity NPC474155
0.6719 Remote Similarity NPC473759
0.6712 Remote Similarity NPC136033
0.6667 Remote Similarity NPC186109
0.6667 Remote Similarity NPC289388
0.6667 Remote Similarity NPC281590
0.6667 Remote Similarity NPC477084
0.6667 Remote Similarity NPC471081
0.6667 Remote Similarity NPC471454
0.6667 Remote Similarity NPC218525
0.6667 Remote Similarity NPC329773
0.6667 Remote Similarity NPC250977
0.6667 Remote Similarity NPC323153
0.662 Remote Similarity NPC113639
0.6618 Remote Similarity NPC22301
0.6615 Remote Similarity NPC300593
0.6615 Remote Similarity NPC309300
0.6615 Remote Similarity NPC225415
0.6615 Remote Similarity NPC290367
0.6615 Remote Similarity NPC469723
0.6613 Remote Similarity NPC10017
0.6613 Remote Similarity NPC181872
0.6575 Remote Similarity NPC207186
0.6575 Remote Similarity NPC474056
0.6571 Remote Similarity NPC476709
0.6567 Remote Similarity NPC161612
0.6567 Remote Similarity NPC33583
0.6567 Remote Similarity NPC45782
0.6562 Remote Similarity NPC225342
0.6557 Remote Similarity NPC249645
0.6557 Remote Similarity NPC55412
0.6557 Remote Similarity NPC252860
0.6557 Remote Similarity NPC141699
0.6552 Remote Similarity NPC244452
0.6552 Remote Similarity NPC214584
0.6552 Remote Similarity NPC26906
0.6545 Remote Similarity NPC165651
0.6545 Remote Similarity NPC210560
0.6545 Remote Similarity NPC24824
0.6522 Remote Similarity NPC469660
0.6515 Remote Similarity NPC19569
0.6515 Remote Similarity NPC238352
0.6515 Remote Similarity NPC308844
0.6515 Remote Similarity NPC477009
0.6508 Remote Similarity NPC122239
0.6508 Remote Similarity NPC475931
0.6508 Remote Similarity NPC5698
0.6491 Remote Similarity NPC234597
0.6481 Remote Similarity NPC86538
0.6479 Remote Similarity NPC190859
0.6479 Remote Similarity NPC104644
0.6479 Remote Similarity NPC471525
0.6462 Remote Similarity NPC50435
0.6452 Remote Similarity NPC165808
0.6452 Remote Similarity NPC52012
0.6452 Remote Similarity NPC281986
0.6452 Remote Similarity NPC321568
0.6452 Remote Similarity NPC22019
0.6452 Remote Similarity NPC208749
0.6447 Remote Similarity NPC145963
0.6441 Remote Similarity NPC170167
0.6441 Remote Similarity NPC177112
0.6441 Remote Similarity NPC68014
0.6441 Remote Similarity NPC71506
0.6418 Remote Similarity NPC267027
0.6406 Remote Similarity NPC252809
0.6406 Remote Similarity NPC240506
0.6406 Remote Similarity NPC135648
0.6406 Remote Similarity NPC19241
0.6406 Remote Similarity NPC258788
0.6393 Remote Similarity NPC232247
0.6393 Remote Similarity NPC251666
0.6393 Remote Similarity NPC298299
0.6389 Remote Similarity NPC475861
0.6389 Remote Similarity NPC93213
0.6379 Remote Similarity NPC142103
0.6379 Remote Similarity NPC26960
0.6379 Remote Similarity NPC182102
0.6377 Remote Similarity NPC471560
0.6377 Remote Similarity NPC16964
0.6364 Remote Similarity NPC248411
0.6364 Remote Similarity NPC226066
0.6364 Remote Similarity NPC96793
0.6364 Remote Similarity NPC34883
0.6364 Remote Similarity NPC110241
0.6364 Remote Similarity NPC323424
0.6349 Remote Similarity NPC155025
0.6349 Remote Similarity NPC475830
0.6338 Remote Similarity NPC470237
0.6338 Remote Similarity NPC16349
0.6338 Remote Similarity NPC222244
0.6333 Remote Similarity NPC69898
0.6333 Remote Similarity NPC295777
0.6324 Remote Similarity NPC136813
0.6324 Remote Similarity NPC477791
0.6324 Remote Similarity NPC472266
0.6324 Remote Similarity NPC114651
0.6324 Remote Similarity NPC96962
0.6308 Remote Similarity NPC68679
0.6308 Remote Similarity NPC260573
0.6308 Remote Similarity NPC274704
0.6308 Remote Similarity NPC64971
0.6308 Remote Similarity NPC207007
0.6308 Remote Similarity NPC321867
0.6308 Remote Similarity NPC210346
0.6301 Remote Similarity NPC301525
0.6301 Remote Similarity NPC271070
0.6301 Remote Similarity NPC170148
0.6301 Remote Similarity NPC476607
0.6296 Remote Similarity NPC180871
0.6296 Remote Similarity NPC194586
0.6296 Remote Similarity NPC108494
0.6296 Remote Similarity NPC68889
0.6296 Remote Similarity NPC51758
0.6296 Remote Similarity NPC88079
0.6296 Remote Similarity NPC67761
0.6296 Remote Similarity NPC209279
0.629 Remote Similarity NPC473865
0.629 Remote Similarity NPC274396
0.629 Remote Similarity NPC96663
0.629 Remote Similarity NPC474643
0.629 Remote Similarity NPC39068
0.6286 Remote Similarity NPC49422
0.6286 Remote Similarity NPC9161
0.6286 Remote Similarity NPC145498
0.6282 Remote Similarity NPC186155
0.6282 Remote Similarity NPC78673
0.6282 Remote Similarity NPC160517
0.6271 Remote Similarity NPC474495
0.6271 Remote Similarity NPC473672
0.6269 Remote Similarity NPC471200
0.6267 Remote Similarity NPC325869
0.6267 Remote Similarity NPC233295
0.6267 Remote Similarity NPC471537
0.625 Remote Similarity NPC296337
0.625 Remote Similarity NPC278202
0.625 Remote Similarity NPC87439
0.625 Remote Similarity NPC473866
0.6234 Remote Similarity NPC259858
0.6232 Remote Similarity NPC167527

  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 NPC165755 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
0.7302 Intermediate Similarity NPD2685 Clinical (unspecified phase)
0.6786 Remote Similarity NPD9410 Clinical (unspecified phase)
0.6557 Remote Similarity NPD4219 Approved
0.6364 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6308 Remote Similarity NPD368 Approved
0.6286 Remote Similarity NPD7144 Approved
0.6286 Remote Similarity NPD7143 Approved
0.6197 Remote Similarity NPD7152 Approved
0.6197 Remote Similarity NPD7150 Approved
0.6197 Remote Similarity NPD7151 Approved
0.6143 Remote Similarity NPD6923 Approved
0.6143 Remote Similarity NPD6922 Approved
0.6027 Remote Similarity NPD6926 Approved
0.6027 Remote Similarity NPD6924 Approved
0.6 Remote Similarity NPD6932 Approved
0.5946 Remote Similarity NPD8264 Approved
0.5946 Remote Similarity NPD8039 Approved
0.5932 Remote Similarity NPD8262 Approved
0.5921 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5909 Remote Similarity NPD1145 Discontinued
0.589 Remote Similarity NPD4732 Discontinued
0.5873 Remote Similarity NPD342 Phase 1
0.5867 Remote Similarity NPD6933 Approved
0.5823 Remote Similarity NPD5209 Approved
0.5769 Remote Similarity NPD7514 Phase 3
0.5769 Remote Similarity NPD7332 Phase 2
0.575 Remote Similarity NPD6695 Phase 3
0.5733 Remote Similarity NPD7339 Approved
0.5733 Remote Similarity NPD6942 Approved
0.5714 Remote Similarity NPD7145 Approved
0.5714 Remote Similarity NPD1799 Clinical (unspecified phase)
0.5696 Remote Similarity NPD6902 Approved
0.5679 Remote Similarity NPD7338 Clinical (unspecified phase)
0.566 Remote Similarity NPD319 Phase 1
0.5658 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5641 Remote Similarity NPD7645 Phase 2
0.5641 Remote Similarity NPD6683 Phase 2
0.561 Remote Similarity NPD1733 Clinical (unspecified phase)
0.56 Remote Similarity NPD4784 Approved
0.56 Remote Similarity NPD4785 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