Structure

Physi-Chem Properties

Molecular Weight:  236.18
Volume:  269.111
LogP:  2.258
LogD:  2.556
LogS:  -2.587
# Rotatable Bonds:  1
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.687
Synthetic Accessibility Score:  4.602
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.824
MDCK Permeability:  7.94536026660353e-06
Pgp-inhibitor:  0.785
Pgp-substrate:  0.013
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.98
30% Bioavailability (F30%):  0.638

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.311
Plasma Protein Binding (PPB):  58.424869537353516%
Volume Distribution (VD):  1.347
Pgp-substrate:  45.02472686767578%

ADMET: Metabolism

CYP1A2-inhibitor:  0.036
CYP1A2-substrate:  0.111
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.095
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.261
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.688
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.253

ADMET: Excretion

Clearance (CL):  6.642
Half-life (T1/2):  0.339

ADMET: Toxicity

hERG Blockers:  0.058
Human Hepatotoxicity (H-HT):  0.538
Drug-inuced Liver Injury (DILI):  0.037
AMES Toxicity:  0.065
Rat Oral Acute Toxicity:  0.744
Maximum Recommended Daily Dose:  0.991
Skin Sensitization:  0.13
Carcinogencity:  0.905
Eye Corrosion:  0.042
Eye Irritation:  0.875
Respiratory Toxicity:  0.875

Download Data

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

  Natural Product: NPC24443

Natural Product ID:  NPC24443
Common Name*:   Sinugibberodiol
IUPAC Name:   (1S,5R,9R)-2,6-dimethylidene-9-prop-1-en-2-ylcyclodecane-1,5-diol
Synonyms:   Sinugibberodiol
Standard InCHIKey:  LFGFKWGAGHTKPW-KFWWJZLASA-N
Standard InCHI:  InChI=1S/C15H24O2/c1-10(2)13-7-5-11(3)14(16)8-6-12(4)15(17)9-13/h13-17H,1,3-9H2,2H3/t13-,14-,15+/m1/s1
SMILES:  O[C@H]1C[C@@H](CCC(=C)[C@@H](CCC1=C)O)C(=C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL227267
PubChem CID:   20055947
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002456] Germacrane 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
NPO26031 Acacia auriculiformis Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(80)80226-3]
NPO26536 Garcinia humilis Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[15844964]
NPO11310 Baorangia pseudocalopus Species Boletaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26268 Salvia aethiopis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26536 Garcinia humilis Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26431 Aplophyllum sieversii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25745 Grindelia arenicola Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26454 Acacia oswaldii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26136 Abuta racemosa Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26658 Commiphora dalzielii Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26981 Thunbergia laurifolia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26783 Jurinea eriobasis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26379 Metrosideros umbellata Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26031 Acacia auriculiformis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8746 Melaleuca triumphalis 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
NPT65 Cell Line HepG2 Homo sapiens IC50 > 20.0 ug.mL-1 PMID[490313]
NPT1475 Cell Line WI-38 VA13 Homo sapiens IC50 > 20.0 ug.mL-1 PMID[490313]
NPT1374 Cell Line WI-38 Homo sapiens IC50 > 20.0 ug.mL-1 PMID[490313]
NPT1840 Cell Line MDR Activity = 113.0 % PMID[490313]
NPT1840 Cell Line MDR Activity = 137.0 % PMID[490313]
NPT1840 Cell Line MDR Activity = 160.0 % PMID[490313]
NPT1840 Cell Line MDR Activity = 100.0 % PMID[490313]
NPT1840 Cell Line MDR Activity = 120.0 % PMID[490313]
NPT1840 Cell Line MDR Activity = 116.0 % PMID[490313]

☑ 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 NPC24443 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
0.8333 Intermediate Similarity NPC473508
0.8077 Intermediate Similarity NPC87439
0.7937 Intermediate Similarity NPC311736
0.7903 Intermediate Similarity NPC300593
0.7869 Intermediate Similarity NPC225342
0.7833 Intermediate Similarity NPC122239
0.7812 Intermediate Similarity NPC163290
0.7778 Intermediate Similarity NPC61503
0.7759 Intermediate Similarity NPC84824
0.7759 Intermediate Similarity NPC67508
0.7705 Intermediate Similarity NPC99487
0.7692 Intermediate Similarity NPC266578
0.7692 Intermediate Similarity NPC245795
0.7679 Intermediate Similarity NPC251335
0.7667 Intermediate Similarity NPC155025
0.7576 Intermediate Similarity NPC234511
0.7538 Intermediate Similarity NPC73603
0.7538 Intermediate Similarity NPC259299
0.7538 Intermediate Similarity NPC82337
0.75 Intermediate Similarity NPC300442
0.75 Intermediate Similarity NPC308844
0.75 Intermediate Similarity NPC471200
0.7463 Intermediate Similarity NPC283316
0.746 Intermediate Similarity NPC50435
0.7424 Intermediate Similarity NPC305698
0.7419 Intermediate Similarity NPC240506
0.7419 Intermediate Similarity NPC66020
0.7391 Intermediate Similarity NPC190859
0.7385 Intermediate Similarity NPC267027
0.7377 Intermediate Similarity NPC475830
0.7377 Intermediate Similarity NPC226848
0.7353 Intermediate Similarity NPC469343
0.7344 Intermediate Similarity NPC309300
0.7344 Intermediate Similarity NPC68656
0.7288 Intermediate Similarity NPC286752
0.7273 Intermediate Similarity NPC477791
0.7273 Intermediate Similarity NPC253303
0.7273 Intermediate Similarity NPC269077
0.7258 Intermediate Similarity NPC475931
0.7231 Intermediate Similarity NPC258595
0.7231 Intermediate Similarity NPC250836
0.7193 Intermediate Similarity NPC131623
0.7188 Intermediate Similarity NPC474155
0.7188 Intermediate Similarity NPC473759
0.7183 Intermediate Similarity NPC170148
0.7167 Intermediate Similarity NPC148163
0.7167 Intermediate Similarity NPC227135
0.7167 Intermediate Similarity NPC130209
0.7167 Intermediate Similarity NPC148216
0.7164 Intermediate Similarity NPC276616
0.7164 Intermediate Similarity NPC167527
0.7143 Intermediate Similarity NPC306727
0.7121 Intermediate Similarity NPC476406
0.7121 Intermediate Similarity NPC326310
0.7121 Intermediate Similarity NPC475897
0.7121 Intermediate Similarity NPC202017
0.7077 Intermediate Similarity NPC101128
0.7077 Intermediate Similarity NPC144650
0.7077 Intermediate Similarity NPC219940
0.7077 Intermediate Similarity NPC96793
0.7077 Intermediate Similarity NPC323424
0.7059 Intermediate Similarity NPC74722
0.7059 Intermediate Similarity NPC217570
0.7059 Intermediate Similarity NPC471560
0.7059 Intermediate Similarity NPC90115
0.7059 Intermediate Similarity NPC304690
0.7059 Intermediate Similarity NPC239373
0.7059 Intermediate Similarity NPC329989
0.7059 Intermediate Similarity NPC9942
0.7042 Intermediate Similarity NPC23231
0.7042 Intermediate Similarity NPC60818
0.7031 Intermediate Similarity NPC68679
0.7031 Intermediate Similarity NPC321867
0.7031 Intermediate Similarity NPC207007
0.7015 Intermediate Similarity NPC136813
0.7015 Intermediate Similarity NPC74885
0.7015 Intermediate Similarity NPC308522
0.7 Intermediate Similarity NPC143576
0.6984 Remote Similarity NPC52431
0.6984 Remote Similarity NPC310228
0.697 Remote Similarity NPC86856
0.697 Remote Similarity NPC282619
0.697 Remote Similarity NPC11555
0.697 Remote Similarity NPC2728
0.697 Remote Similarity NPC172613
0.697 Remote Similarity NPC208198
0.697 Remote Similarity NPC19569
0.697 Remote Similarity NPC60837
0.6957 Remote Similarity NPC254845
0.6957 Remote Similarity NPC470041
0.6957 Remote Similarity NPC34834
0.6957 Remote Similarity NPC133873
0.6944 Remote Similarity NPC236228
0.6944 Remote Similarity NPC329626
0.6944 Remote Similarity NPC256720
0.6944 Remote Similarity NPC253190
0.6944 Remote Similarity NPC126969
0.6923 Remote Similarity NPC83200
0.6912 Remote Similarity NPC224532
0.6912 Remote Similarity NPC96484
0.6912 Remote Similarity NPC471238
0.6885 Remote Similarity NPC251666
0.6885 Remote Similarity NPC232247
0.6866 Remote Similarity NPC272125
0.6857 Remote Similarity NPC477792
0.6857 Remote Similarity NPC23954
0.6857 Remote Similarity NPC471662
0.6852 Remote Similarity NPC249801
0.6852 Remote Similarity NPC46248
0.6849 Remote Similarity NPC476703
0.6849 Remote Similarity NPC31037
0.6842 Remote Similarity NPC100445
0.6833 Remote Similarity NPC474496
0.6825 Remote Similarity NPC181872
0.6818 Remote Similarity NPC225415
0.6818 Remote Similarity NPC110241
0.6812 Remote Similarity NPC16964
0.6812 Remote Similarity NPC474248
0.6806 Remote Similarity NPC32832
0.6786 Remote Similarity NPC165651
0.6786 Remote Similarity NPC210560
0.6786 Remote Similarity NPC24824
0.678 Remote Similarity NPC473672
0.678 Remote Similarity NPC474495
0.6774 Remote Similarity NPC48891
0.6769 Remote Similarity NPC475251
0.6769 Remote Similarity NPC63111
0.6765 Remote Similarity NPC161612
0.6765 Remote Similarity NPC68703
0.6765 Remote Similarity NPC472253
0.6765 Remote Similarity NPC114651
0.6765 Remote Similarity NPC69649
0.6765 Remote Similarity NPC476650
0.6765 Remote Similarity NPC139207
0.6765 Remote Similarity NPC185874
0.6765 Remote Similarity NPC33583
0.6765 Remote Similarity NPC472255
0.6761 Remote Similarity NPC220939
0.6761 Remote Similarity NPC234527
0.6761 Remote Similarity NPC329763
0.6761 Remote Similarity NPC476709
0.6761 Remote Similarity NPC95165
0.6761 Remote Similarity NPC14352
0.6761 Remote Similarity NPC472506
0.6761 Remote Similarity NPC476609
0.6761 Remote Similarity NPC275098
0.6761 Remote Similarity NPC477085
0.6761 Remote Similarity NPC265485
0.6757 Remote Similarity NPC475
0.6757 Remote Similarity NPC472502
0.6757 Remote Similarity NPC475980
0.6757 Remote Similarity NPC472499
0.6757 Remote Similarity NPC472500
0.6727 Remote Similarity NPC15162
0.6716 Remote Similarity NPC238352
0.6716 Remote Similarity NPC474304
0.6716 Remote Similarity NPC474329
0.6716 Remote Similarity NPC287339
0.6716 Remote Similarity NPC477009
0.6714 Remote Similarity NPC4299
0.6714 Remote Similarity NPC471781
0.6712 Remote Similarity NPC268111
0.6667 Remote Similarity NPC86971
0.6667 Remote Similarity NPC279200
0.6667 Remote Similarity NPC211291
0.6667 Remote Similarity NPC133368
0.6667 Remote Similarity NPC308440
0.6667 Remote Similarity NPC244790
0.6667 Remote Similarity NPC52012
0.6667 Remote Similarity NPC472503
0.6667 Remote Similarity NPC476316
0.6667 Remote Similarity NPC24504
0.6622 Remote Similarity NPC84360
0.662 Remote Similarity NPC471272
0.662 Remote Similarity NPC477087
0.662 Remote Similarity NPC471268
0.662 Remote Similarity NPC477086
0.662 Remote Similarity NPC164045
0.662 Remote Similarity NPC41886
0.662 Remote Similarity NPC471271
0.662 Remote Similarity NPC472254
0.6618 Remote Similarity NPC469328
0.6618 Remote Similarity NPC473929
0.6618 Remote Similarity NPC162309
0.6615 Remote Similarity NPC471081
0.6613 Remote Similarity NPC281590
0.6613 Remote Similarity NPC329686
0.661 Remote Similarity NPC182102
0.661 Remote Similarity NPC142103
0.661 Remote Similarity NPC26960
0.6579 Remote Similarity NPC324772
0.6579 Remote Similarity NPC47149
0.6579 Remote Similarity NPC96362
0.6575 Remote Similarity NPC476605
0.6575 Remote Similarity NPC185536
0.6575 Remote Similarity NPC144075
0.6575 Remote Similarity NPC313185
0.6571 Remote Similarity NPC473893
0.6571 Remote Similarity NPC101622
0.6567 Remote Similarity NPC290367

  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 NPC24443 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
0.7167 Intermediate Similarity NPD342 Phase 1
0.7031 Intermediate Similarity NPD368 Approved
0.6667 Remote Similarity NPD6929 Approved
0.6579 Remote Similarity NPD6931 Approved
0.6579 Remote Similarity NPD6930 Phase 2
0.64 Remote Similarity NPD6925 Approved
0.64 Remote Similarity NPD5776 Phase 2
0.6379 Remote Similarity NPD384 Approved
0.6379 Remote Similarity NPD385 Approved
0.6329 Remote Similarity NPD6695 Phase 3
0.6316 Remote Similarity NPD7145 Approved
0.625 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6216 Remote Similarity NPD6926 Approved
0.6216 Remote Similarity NPD6924 Approved
0.6207 Remote Similarity NPD388 Approved
0.6207 Remote Similarity NPD386 Approved
0.6173 Remote Similarity NPD6893 Approved
0.6154 Remote Similarity NPD7514 Phase 3
0.6154 Remote Similarity NPD7332 Phase 2
0.6133 Remote Similarity NPD8264 Approved
0.6119 Remote Similarity NPD1145 Discontinued
0.6081 Remote Similarity NPD4732 Discontinued
0.6076 Remote Similarity NPD6898 Phase 1
0.6076 Remote Similarity NPD6902 Approved
0.6053 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6053 Remote Similarity NPD6933 Approved
0.6024 Remote Similarity NPD7524 Approved
0.6024 Remote Similarity NPD7750 Discontinued
0.6024 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5974 Remote Similarity NPD6932 Approved
0.5965 Remote Similarity NPD1462 Approved
0.5932 Remote Similarity NPD4265 Approved
0.5921 Remote Similarity NPD6942 Approved
0.5921 Remote Similarity NPD7339 Approved
0.5897 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5893 Remote Similarity NPD1460 Approved
0.589 Remote Similarity NPD6923 Approved
0.589 Remote Similarity NPD6922 Approved
0.5823 Remote Similarity NPD7645 Phase 2
0.5823 Remote Similarity NPD6683 Phase 2
0.5811 Remote Similarity NPD7143 Approved
0.5811 Remote Similarity NPD7144 Approved
0.5758 Remote Similarity NPD4219 Approved
0.575 Remote Similarity NPD4819 Approved
0.575 Remote Similarity NPD7509 Discontinued
0.575 Remote Similarity NPD4821 Approved
0.575 Remote Similarity NPD4820 Approved
0.575 Remote Similarity NPD4822 Approved
0.575 Remote Similarity NPD7525 Registered
0.5747 Remote Similarity NPD7087 Discontinued
0.5733 Remote Similarity NPD7150 Approved
0.5733 Remote Similarity NPD7151 Approved
0.5733 Remote Similarity NPD7152 Approved
0.5732 Remote Similarity NPD5332 Approved
0.5732 Remote Similarity NPD5331 Approved
0.5732 Remote Similarity NPD7154 Phase 3
0.5732 Remote Similarity NPD5362 Discontinued
0.5696 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5696 Remote Similarity NPD4271 Approved
0.5696 Remote Similarity NPD4268 Approved
0.5682 Remote Similarity NPD5778 Approved
0.5682 Remote Similarity NPD5779 Approved
0.5679 Remote Similarity NPD4790 Discontinued
0.5645 Remote Similarity NPD9410 Clinical (unspecified phase)
0.5634 Remote Similarity NPD371 Approved
0.5632 Remote Similarity NPD7838 Discovery
0.561 Remote Similarity NPD3667 Approved
0.561 Remote Similarity NPD4270 Approved
0.561 Remote Similarity NPD4269 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