Structure

Physi-Chem Properties

Molecular Weight:  204.19
Volume:  251.53
LogP:  5.783
LogD:  4.883
LogS:  -5.437
# Rotatable Bonds:  4
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.572
Synthetic Accessibility Score:  4.144
Fsp3:  0.6
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:  -4.592
MDCK Permeability:  1.6129028153955005e-05
Pgp-inhibitor:  0.279
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.095
30% Bioavailability (F30%):  0.022

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.22
Plasma Protein Binding (PPB):  97.20002746582031%
Volume Distribution (VD):  5.317
Pgp-substrate:  2.80586314201355%

ADMET: Metabolism

CYP1A2-inhibitor:  0.875
CYP1A2-substrate:  0.494
CYP2C19-inhibitor:  0.517
CYP2C19-substrate:  0.873
CYP2C9-inhibitor:  0.466
CYP2C9-substrate:  0.701
CYP2D6-inhibitor:  0.072
CYP2D6-substrate:  0.544
CYP3A4-inhibitor:  0.625
CYP3A4-substrate:  0.43

ADMET: Excretion

Clearance (CL):  14.085
Half-life (T1/2):  0.217

ADMET: Toxicity

hERG Blockers:  0.185
Human Hepatotoxicity (H-HT):  0.804
Drug-inuced Liver Injury (DILI):  0.344
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.045
Maximum Recommended Daily Dose:  0.734
Skin Sensitization:  0.966
Carcinogencity:  0.753
Eye Corrosion:  0.269
Eye Irritation:  0.871
Respiratory Toxicity:  0.938

Download Data

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

  Natural Product: NPC177470

Natural Product ID:  NPC177470
Common Name*:   Beta-Sesquiphellandrene
IUPAC Name:   (3S)-3-[(2R)-6-methylhept-5-en-2-yl]-6-methylidenecyclohexene
Synonyms:   Beta-Sesquiphellandrene
Standard InCHIKey:  PHWISBHSBNDZDX-CABCVRRESA-N
Standard InCHI:  InChI=1S/C15H24/c1-12(2)6-5-7-14(4)15-10-8-13(3)9-11-15/h6,8,10,14-15H,3,5,7,9,11H2,1-2,4H3/t14-,15+/m1/s1
SMILES:  C[C@@H]([C@@H]1CCC(=C)C=C1)CCC=C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL469718
PubChem CID:   11106487
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
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[18177011]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[19271742]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO27265 Hopea parviflora Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27554 Doryanthes palmeri Species Doryanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27265 Hopea parviflora Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27836 Gymnodinium microadriaticum Species Gymnodiniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5306 Infundibulicybe catinus Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27355 Pseudokeronopsis rubra Species Pseudokeronopsidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27073 Poranthera corymbosa Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27447 Yucca aloifolia Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27519 Alternaria chrysanthemi Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6164 Lasiosiphon eriocephalus Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27227 Matricaria occidentalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27533 Senecio bergii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27708 Mythimna separata Species 0ctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27304 Stevia sanguinea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27409 Scabiosa atropurpurea Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27155 Aconitum nasutum Species Ranunculaceae 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
NPT2517 Organism Human rhinovirus 1B Human rhinovirus 1B ED50 = 0.9 ug PMID[468686]
NPT2517 Organism Human rhinovirus 1B Human rhinovirus 1B IC50 = 440.0 nM PMID[468686]

☑ 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 NPC177470 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
0.9744 High Similarity NPC144023
0.9487 High Similarity NPC183670
0.8974 High Similarity NPC239039
0.8974 High Similarity NPC48638
0.8974 High Similarity NPC45727
0.878 High Similarity NPC120926
0.878 High Similarity NPC218918
0.85 High Similarity NPC139717
0.85 High Similarity NPC229262
0.85 High Similarity NPC297643
0.8462 Intermediate Similarity NPC282119
0.825 Intermediate Similarity NPC34764
0.825 Intermediate Similarity NPC76145
0.825 Intermediate Similarity NPC190810
0.8182 Intermediate Similarity NPC248411
0.8182 Intermediate Similarity NPC202189
0.8049 Intermediate Similarity NPC266298
0.8 Intermediate Similarity NPC296337
0.8 Intermediate Similarity NPC86683
0.7872 Intermediate Similarity NPC17810
0.7727 Intermediate Similarity NPC473912
0.7692 Intermediate Similarity NPC213749
0.766 Intermediate Similarity NPC124851
0.7647 Intermediate Similarity NPC470893
0.7609 Intermediate Similarity NPC241784
0.7609 Intermediate Similarity NPC13991
0.7609 Intermediate Similarity NPC114239
0.7561 Intermediate Similarity NPC92224
0.7556 Intermediate Similarity NPC60556
0.7556 Intermediate Similarity NPC109813
0.7556 Intermediate Similarity NPC86538
0.75 Intermediate Similarity NPC17518
0.7447 Intermediate Similarity NPC323445
0.7436 Intermediate Similarity NPC206088
0.7436 Intermediate Similarity NPC3649
0.7333 Intermediate Similarity NPC105246
0.7333 Intermediate Similarity NPC190232
0.7255 Intermediate Similarity NPC476679
0.7234 Intermediate Similarity NPC49088
0.7222 Intermediate Similarity NPC469769
0.7179 Intermediate Similarity NPC60288
0.7174 Intermediate Similarity NPC192529
0.7143 Intermediate Similarity NPC22765
0.7059 Intermediate Similarity NPC35519
0.7059 Intermediate Similarity NPC181255
0.7059 Intermediate Similarity NPC306195
0.7059 Intermediate Similarity NPC473728
0.7059 Intermediate Similarity NPC179169
0.7059 Intermediate Similarity NPC157781
0.7 Intermediate Similarity NPC200129
0.6939 Remote Similarity NPC178644
0.6923 Remote Similarity NPC138113
0.6923 Remote Similarity NPC69898
0.6923 Remote Similarity NPC295777
0.6889 Remote Similarity NPC78551
0.6889 Remote Similarity NPC227632
0.6889 Remote Similarity NPC62086
0.6863 Remote Similarity NPC26906
0.6863 Remote Similarity NPC214584
0.6852 Remote Similarity NPC55412
0.6852 Remote Similarity NPC249645
0.6842 Remote Similarity NPC469728
0.6786 Remote Similarity NPC475716
0.6739 Remote Similarity NPC103290
0.6735 Remote Similarity NPC159420
0.6731 Remote Similarity NPC40417
0.6731 Remote Similarity NPC71506
0.6731 Remote Similarity NPC294358
0.6731 Remote Similarity NPC177112
0.6727 Remote Similarity NPC321568
0.6727 Remote Similarity NPC208749
0.6727 Remote Similarity NPC22019
0.6727 Remote Similarity NPC281986
0.6667 Remote Similarity NPC176621
0.6667 Remote Similarity NPC64176
0.6667 Remote Similarity NPC173592
0.6667 Remote Similarity NPC288991
0.6667 Remote Similarity NPC469770
0.6667 Remote Similarity NPC305759
0.6667 Remote Similarity NPC262789
0.6667 Remote Similarity NPC99088
0.6604 Remote Similarity NPC14002
0.6604 Remote Similarity NPC268564
0.6596 Remote Similarity NPC193180
0.6585 Remote Similarity NPC151719
0.6585 Remote Similarity NPC66577
0.6585 Remote Similarity NPC100879
0.6585 Remote Similarity NPC471327
0.6538 Remote Similarity NPC244038
0.6538 Remote Similarity NPC27438
0.6522 Remote Similarity NPC246165
0.6481 Remote Similarity NPC5626
0.6471 Remote Similarity NPC106990
0.6441 Remote Similarity NPC474086
0.6429 Remote Similarity NPC474528
0.6429 Remote Similarity NPC470369
0.6429 Remote Similarity NPC470370
0.6429 Remote Similarity NPC475696
0.6429 Remote Similarity NPC474415
0.6415 Remote Similarity NPC208638
0.6415 Remote Similarity NPC68014
0.6383 Remote Similarity NPC473614
0.6364 Remote Similarity NPC123194
0.6346 Remote Similarity NPC182102
0.6346 Remote Similarity NPC26960
0.6346 Remote Similarity NPC32351
0.6346 Remote Similarity NPC329773
0.6316 Remote Similarity NPC60772
0.6296 Remote Similarity NPC23117
0.6296 Remote Similarity NPC37644
0.6275 Remote Similarity NPC91962
0.6271 Remote Similarity NPC317177
0.6271 Remote Similarity NPC317025
0.6271 Remote Similarity NPC329416
0.6271 Remote Similarity NPC135924
0.6271 Remote Similarity NPC225342
0.6271 Remote Similarity NPC326645
0.625 Remote Similarity NPC4881
0.625 Remote Similarity NPC141699
0.623 Remote Similarity NPC155172
0.623 Remote Similarity NPC268039
0.623 Remote Similarity NPC32312
0.623 Remote Similarity NPC198023
0.6207 Remote Similarity NPC474454
0.6207 Remote Similarity NPC474420
0.6207 Remote Similarity NPC474455
0.6207 Remote Similarity NPC276764
0.6207 Remote Similarity NPC472304
0.6207 Remote Similarity NPC143834
0.6182 Remote Similarity NPC63396
0.6182 Remote Similarity NPC202850
0.6167 Remote Similarity NPC202118
0.6167 Remote Similarity NPC197238
0.6167 Remote Similarity NPC174956
0.6154 Remote Similarity NPC266539
0.6154 Remote Similarity NPC287191
0.6154 Remote Similarity NPC266144
0.6154 Remote Similarity NPC31891
0.614 Remote Similarity NPC115385
0.614 Remote Similarity NPC474457
0.614 Remote Similarity NPC165808
0.614 Remote Similarity NPC11130
0.6136 Remote Similarity NPC182392
0.6129 Remote Similarity NPC149680
0.6129 Remote Similarity NPC255781
0.6122 Remote Similarity NPC51762
0.6122 Remote Similarity NPC474118
0.6122 Remote Similarity NPC90803
0.6122 Remote Similarity NPC23145
0.6122 Remote Similarity NPC166362
0.6122 Remote Similarity NPC90506
0.6122 Remote Similarity NPC141777
0.6122 Remote Similarity NPC227670
0.6102 Remote Similarity NPC311809
0.6102 Remote Similarity NPC127582
0.6102 Remote Similarity NPC135648
0.6098 Remote Similarity NPC34671
0.6098 Remote Similarity NPC123965
0.6098 Remote Similarity NPC115959
0.6066 Remote Similarity NPC476559
0.6066 Remote Similarity NPC150162
0.6066 Remote Similarity NPC4638
0.6066 Remote Similarity NPC88566
0.6066 Remote Similarity NPC45756
0.6066 Remote Similarity NPC226066
0.6066 Remote Similarity NPC469662
0.6066 Remote Similarity NPC473959
0.6042 Remote Similarity NPC188596
0.6038 Remote Similarity NPC163984
0.6038 Remote Similarity NPC176819
0.6038 Remote Similarity NPC58970
0.6034 Remote Similarity NPC311852
0.6032 Remote Similarity NPC193770
0.6 Remote Similarity NPC45283
0.6 Remote Similarity NPC210849
0.6 Remote Similarity NPC213152
0.6 Remote Similarity NPC79576
0.6 Remote Similarity NPC194208
0.6 Remote Similarity NPC165755
0.6 Remote Similarity NPC282694
0.5968 Remote Similarity NPC251118
0.5965 Remote Similarity NPC274396
0.5965 Remote Similarity NPC469967
0.5965 Remote Similarity NPC473733
0.5938 Remote Similarity NPC310992
0.5938 Remote Similarity NPC216460
0.5938 Remote Similarity NPC32055
0.5932 Remote Similarity NPC309825
0.5909 Remote Similarity NPC62779
0.5909 Remote Similarity NPC181204
0.5909 Remote Similarity NPC470078
0.5902 Remote Similarity NPC165695
0.5902 Remote Similarity NPC145715
0.5902 Remote Similarity NPC29680
0.5902 Remote Similarity NPC288253
0.5902 Remote Similarity NPC283247
0.5897 Remote Similarity NPC38513
0.5897 Remote Similarity NPC88325
0.5893 Remote Similarity NPC168518
0.5893 Remote Similarity NPC105780

  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 NPC177470 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
0.825 Intermediate Similarity NPD319 Phase 1
0.7872 Intermediate Similarity NPD8262 Approved
0.7333 Intermediate Similarity NPD1799 Clinical (unspecified phase)
0.6852 Remote Similarity NPD4219 Approved
0.6271 Remote Similarity NPD4192 Approved
0.6271 Remote Similarity NPD4194 Approved
0.6271 Remote Similarity NPD4191 Approved
0.6271 Remote Similarity NPD4193 Approved
0.6066 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5789 Remote Similarity NPD342 Phase 1
0.5763 Remote Similarity NPD287 Approved
0.5758 Remote Similarity NPD7144 Approved
0.5758 Remote Similarity NPD7143 Approved
0.5738 Remote Similarity NPD368 Approved
0.5735 Remote Similarity NPD4687 Approved
0.5735 Remote Similarity NPD4058 Approved
0.5672 Remote Similarity NPD5276 Approved
0.5672 Remote Similarity NPD7150 Approved
0.5672 Remote Similarity NPD7151 Approved
0.5672 Remote Similarity NPD7152 Approved
0.5652 Remote Similarity NPD8264 Approved
0.5606 Remote Similarity NPD6923 Approved
0.5606 Remote Similarity NPD1673 Approved
0.5606 Remote Similarity NPD6922 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