Structure

Physi-Chem Properties

Molecular Weight:  222.2
Volume:  257.037
LogP:  4.504
LogD:  4.192
LogS:  -4.446
# Rotatable Bonds:  1
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.669
Synthetic Accessibility Score:  4.066
Fsp3:  0.867
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:  -4.532
MDCK Permeability:  1.2475936273403931e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.884
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.481
Plasma Protein Binding (PPB):  64.58061218261719%
Volume Distribution (VD):  0.888
Pgp-substrate:  30.17466926574707%

ADMET: Metabolism

CYP1A2-inhibitor:  0.423
CYP1A2-substrate:  0.581
CYP2C19-inhibitor:  0.137
CYP2C19-substrate:  0.632
CYP2C9-inhibitor:  0.295
CYP2C9-substrate:  0.626
CYP2D6-inhibitor:  0.06
CYP2D6-substrate:  0.746
CYP3A4-inhibitor:  0.153
CYP3A4-substrate:  0.237

ADMET: Excretion

Clearance (CL):  8.448
Half-life (T1/2):  0.172

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.284
Drug-inuced Liver Injury (DILI):  0.078
AMES Toxicity:  0.012
Rat Oral Acute Toxicity:  0.045
Maximum Recommended Daily Dose:  0.562
Skin Sensitization:  0.752
Carcinogencity:  0.248
Eye Corrosion:  0.471
Eye Irritation:  0.834
Respiratory Toxicity:  0.781

Download Data

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

  Natural Product: NPC286752

Natural Product ID:  NPC286752
Common Name*:   14-Hydroxy-4,5-Dihydro-Beta-Caryophyllene
IUPAC Name:   [(1R,4S,9S)-11,11-dimethyl-8-methylidene-4-bicyclo[7.2.0]undecanyl]methanol
Synonyms:  
Standard InCHIKey:  QPKKKWDNDWSIRV-BFHYXJOUSA-N
Standard InCHI:  InChI=1S/C15H26O/c1-11-5-4-6-12(10-16)7-8-14-13(11)9-15(14,2)3/h12-14,16H,1,4-10H2,2-3H3/t12-,13+,14+/m0/s1
SMILES:  C=C1CCC[C@@H](CC[C@@H]2[C@@H]1CC2(C)C)CO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL501643
PubChem CID:   10036514
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
NPO32980 betula litwinowii Species Betulaceae Eukaryota n.a. n.a. n.a. PMID[10924162]

☑ 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
NPT2647 Organism Drechslera Drechslera Inhibition = 75.0 % PMID[520668]
NPT314 Organism Bacillus cereus Bacillus cereus MIC = 125.0 ug.mL-1 PMID[520668]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 250.0 ug.mL-1 PMID[520668]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 250.0 ug.mL-1 PMID[520668]
NPT2600 Organism Fusarium solani Fusarium solani Inhibition = 59.0 % PMID[520668]
NPT6242 Organism Ceratobasidium cereale Ceratobasidium cereale Inhibition = 100.0 % PMID[520668]
NPT6315 Organism Lecanicillium muscarium Lecanicillium muscarium Inhibition = 100.0 % PMID[520668]
NPT554 Organism Candida glabrata Candida glabrata MIC = 125.0 ug.mL-1 PMID[520668]
NPT729 Organism Micrococcus luteus Micrococcus luteus MIC = 250.0 ug.mL-1 PMID[520668]
NPT19 Organism Escherichia coli Escherichia coli MIC = 250.0 ug.mL-1 PMID[520668]

☑ 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 NPC286752 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
0.84 Intermediate Similarity NPC87439
0.807 Intermediate Similarity NPC101285
0.807 Intermediate Similarity NPC27853
0.807 Intermediate Similarity NPC65786
0.807 Intermediate Similarity NPC13789
0.807 Intermediate Similarity NPC7491
0.8065 Intermediate Similarity NPC161612
0.8065 Intermediate Similarity NPC33583
0.8 Intermediate Similarity NPC474155
0.8 Intermediate Similarity NPC473759
0.7705 Intermediate Similarity NPC50435
0.7627 Intermediate Similarity NPC10017
0.7619 Intermediate Similarity NPC473929
0.7619 Intermediate Similarity NPC475897
0.7581 Intermediate Similarity NPC107540
0.7541 Intermediate Similarity NPC147524
0.75 Intermediate Similarity NPC171225
0.7463 Intermediate Similarity NPC329763
0.7419 Intermediate Similarity NPC211291
0.7419 Intermediate Similarity NPC133368
0.7414 Intermediate Similarity NPC67508
0.7414 Intermediate Similarity NPC84824
0.7377 Intermediate Similarity NPC40206
0.7302 Intermediate Similarity NPC144650
0.7302 Intermediate Similarity NPC68656
0.7302 Intermediate Similarity NPC219940
0.7302 Intermediate Similarity NPC101128
0.7302 Intermediate Similarity NPC225415
0.7302 Intermediate Similarity NPC309300
0.7288 Intermediate Similarity NPC264779
0.7288 Intermediate Similarity NPC39068
0.7288 Intermediate Similarity NPC24443
0.7273 Intermediate Similarity NPC474248
0.7258 Intermediate Similarity NPC15152
0.7188 Intermediate Similarity NPC61503
0.7188 Intermediate Similarity NPC282619
0.7188 Intermediate Similarity NPC208198
0.7188 Intermediate Similarity NPC27243
0.7188 Intermediate Similarity NPC60837
0.7188 Intermediate Similarity NPC477009
0.7188 Intermediate Similarity NPC2728
0.7188 Intermediate Similarity NPC238352
0.7188 Intermediate Similarity NPC172613
0.7188 Intermediate Similarity NPC11555
0.7188 Intermediate Similarity NPC300442
0.7188 Intermediate Similarity NPC258595
0.7188 Intermediate Similarity NPC476737
0.7077 Intermediate Similarity NPC162309
0.7077 Intermediate Similarity NPC476406
0.7077 Intermediate Similarity NPC149680
0.7049 Intermediate Similarity NPC475830
0.7049 Intermediate Similarity NPC189290
0.7049 Intermediate Similarity NPC474769
0.7037 Intermediate Similarity NPC165651
0.7037 Intermediate Similarity NPC24824
0.7037 Intermediate Similarity NPC210560
0.7031 Intermediate Similarity NPC290367
0.6984 Remote Similarity NPC225342
0.697 Remote Similarity NPC269077
0.697 Remote Similarity NPC68703
0.697 Remote Similarity NPC308522
0.697 Remote Similarity NPC139207
0.697 Remote Similarity NPC74885
0.697 Remote Similarity NPC136813
0.697 Remote Similarity NPC197805
0.697 Remote Similarity NPC477791
0.697 Remote Similarity NPC69649
0.697 Remote Similarity NPC185874
0.697 Remote Similarity NPC253303
0.6964 Remote Similarity NPC62755
0.6935 Remote Similarity NPC184049
0.6935 Remote Similarity NPC99480
0.6935 Remote Similarity NPC5698
0.6923 Remote Similarity NPC19569
0.6866 Remote Similarity NPC96484
0.6866 Remote Similarity NPC244790
0.6866 Remote Similarity NPC167527
0.6866 Remote Similarity NPC160209
0.6866 Remote Similarity NPC276616
0.6866 Remote Similarity NPC245795
0.6866 Remote Similarity NPC216460
0.6866 Remote Similarity NPC208999
0.6833 Remote Similarity NPC148216
0.6833 Remote Similarity NPC130209
0.6833 Remote Similarity NPC148163
0.6825 Remote Similarity NPC66020
0.6825 Remote Similarity NPC323153
0.6825 Remote Similarity NPC135648
0.6825 Remote Similarity NPC162109
0.6818 Remote Similarity NPC286669
0.6818 Remote Similarity NPC476039
0.6818 Remote Similarity NPC222366
0.6806 Remote Similarity NPC211279
0.68 Remote Similarity NPC177022
0.6786 Remote Similarity NPC100445
0.678 Remote Similarity NPC161473
0.6769 Remote Similarity NPC323424
0.6769 Remote Similarity NPC300593
0.6769 Remote Similarity NPC96793
0.6765 Remote Similarity NPC471560
0.6765 Remote Similarity NPC9942
0.6724 Remote Similarity NPC251335
0.6721 Remote Similarity NPC179024
0.6719 Remote Similarity NPC41160
0.6719 Remote Similarity NPC475251
0.6716 Remote Similarity NPC114651
0.6712 Remote Similarity NPC475980
0.6712 Remote Similarity NPC321180
0.6667 Remote Similarity NPC133873
0.6667 Remote Similarity NPC163678
0.6667 Remote Similarity NPC45296
0.6667 Remote Similarity NPC53209
0.6667 Remote Similarity NPC283316
0.6667 Remote Similarity NPC145498
0.6667 Remote Similarity NPC92801
0.6667 Remote Similarity NPC91369
0.6667 Remote Similarity NPC122239
0.6667 Remote Similarity NPC15162
0.6667 Remote Similarity NPC310643
0.6667 Remote Similarity NPC472472
0.6667 Remote Similarity NPC471200
0.6667 Remote Similarity NPC34834
0.6618 Remote Similarity NPC470040
0.6618 Remote Similarity NPC471238
0.6618 Remote Similarity NPC32055
0.6615 Remote Similarity NPC279200
0.6615 Remote Similarity NPC473508
0.6613 Remote Similarity NPC278550
0.661 Remote Similarity NPC306195
0.661 Remote Similarity NPC35519
0.661 Remote Similarity NPC157781
0.661 Remote Similarity NPC181255
0.661 Remote Similarity NPC179169
0.66 Remote Similarity NPC61665
0.6571 Remote Similarity NPC164045
0.6571 Remote Similarity NPC242001
0.6571 Remote Similarity NPC164022
0.6571 Remote Similarity NPC301226
0.6571 Remote Similarity NPC40327
0.6571 Remote Similarity NPC477792
0.6571 Remote Similarity NPC111234
0.6571 Remote Similarity NPC471662
0.6571 Remote Similarity NPC167706
0.6567 Remote Similarity NPC202017
0.6567 Remote Similarity NPC267027
0.6567 Remote Similarity NPC272125
0.6562 Remote Similarity NPC240506
0.6562 Remote Similarity NPC99487
0.6562 Remote Similarity NPC252809
0.6552 Remote Similarity NPC131623
0.6552 Remote Similarity NPC142103
0.6552 Remote Similarity NPC329773
0.6538 Remote Similarity NPC221022
0.6522 Remote Similarity NPC90115
0.6522 Remote Similarity NPC473893
0.6522 Remote Similarity NPC217570
0.6515 Remote Similarity NPC110241
0.6508 Remote Similarity NPC155025
0.65 Remote Similarity NPC192962
0.6479 Remote Similarity NPC474743
0.6479 Remote Similarity NPC471799
0.6479 Remote Similarity NPC182717
0.6479 Remote Similarity NPC474140
0.6479 Remote Similarity NPC14352
0.6479 Remote Similarity NPC68443
0.6479 Remote Similarity NPC310608
0.6479 Remote Similarity NPC472506
0.6479 Remote Similarity NPC195489
0.6479 Remote Similarity NPC211009
0.6479 Remote Similarity NPC234527
0.6479 Remote Similarity NPC95165
0.6479 Remote Similarity NPC476609
0.6471 Remote Similarity NPC472255
0.6471 Remote Similarity NPC472253
0.6462 Remote Similarity NPC274704
0.6462 Remote Similarity NPC210346
0.6452 Remote Similarity NPC274396
0.6452 Remote Similarity NPC48891
0.6441 Remote Similarity NPC26906
0.6441 Remote Similarity NPC214584
0.6418 Remote Similarity NPC64123
0.6415 Remote Similarity NPC227632
0.6415 Remote Similarity NPC62086
0.6415 Remote Similarity NPC78551
0.6406 Remote Similarity NPC475931
0.6406 Remote Similarity NPC310228
0.6406 Remote Similarity NPC52431
0.6389 Remote Similarity NPC62657
0.6389 Remote Similarity NPC196358
0.6389 Remote Similarity NPC5046
0.6389 Remote Similarity NPC476366
0.6389 Remote Similarity NPC100334
0.6389 Remote Similarity NPC469534
0.6389 Remote Similarity NPC78527
0.6389 Remote Similarity NPC308440
0.6389 Remote Similarity NPC472503
0.6389 Remote Similarity NPC25511
0.6389 Remote Similarity NPC27395
0.6389 Remote Similarity NPC91858
0.6389 Remote Similarity NPC49168

  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 NPC286752 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
0.6833 Remote Similarity NPD342 Phase 1
0.6389 Remote Similarity NPD6924 Approved
0.6389 Remote Similarity NPD6926 Approved
0.6316 Remote Similarity NPD384 Approved
0.6316 Remote Similarity NPD385 Approved
0.6301 Remote Similarity NPD7339 Approved
0.6301 Remote Similarity NPD6942 Approved
0.6286 Remote Similarity NPD6922 Approved
0.6286 Remote Similarity NPD6923 Approved
0.6216 Remote Similarity NPD6933 Approved
0.6216 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6212 Remote Similarity NPD368 Approved
0.6197 Remote Similarity NPD7144 Approved
0.6197 Remote Similarity NPD7143 Approved
0.6111 Remote Similarity NPD7151 Approved
0.6111 Remote Similarity NPD7152 Approved
0.6111 Remote Similarity NPD7150 Approved
0.5974 Remote Similarity NPD6929 Approved
0.5974 Remote Similarity NPD7645 Phase 2
0.5938 Remote Similarity NPD4219 Approved
0.5897 Remote Similarity NPD6931 Approved
0.5897 Remote Similarity NPD7525 Registered
0.5897 Remote Similarity NPD7509 Discontinued
0.5897 Remote Similarity NPD6930 Phase 2
0.589 Remote Similarity NPD4243 Approved
0.5867 Remote Similarity NPD8264 Approved
0.5821 Remote Similarity NPD1145 Discontinued
0.575 Remote Similarity NPD3667 Approved
0.5733 Remote Similarity NPD4784 Approved
0.5733 Remote Similarity NPD4785 Approved
0.5714 Remote Similarity NPD6925 Approved
0.5714 Remote Similarity NPD5776 Phase 2
0.5714 Remote Similarity NPD6932 Approved
0.5679 Remote Similarity NPD4788 Approved
0.5679 Remote Similarity NPD6695 Phase 3
0.5658 Remote Similarity NPD4190 Phase 3
0.5658 Remote Similarity NPD5275 Approved
0.5641 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5641 Remote Similarity NPD7145 Approved
0.5625 Remote Similarity NPD857 Phase 3
0.5614 Remote Similarity NPD1799 Clinical (unspecified phase)
0.561 Remote Similarity NPD3133 Approved
0.561 Remote Similarity NPD3665 Phase 1
0.561 Remote Similarity NPD3666 Approved
0.561 Remote Similarity NPD4786 Approved
0.561 Remote Similarity NPD7338 Clinical (unspecified phase)

  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